EP1789798A2 - Markers for autoimmune disease detection - Google Patents

Abstract

The present invention provides genes and their expression patterns, wherein the expression patterns are associated with autoimmune diseases, particularly with systemic lupus erythematosus (SLE) and Wegener's granulomatosus, ANCA+ vasculitis (WG). The invention provides a group of 1645 genes and a number of sub-groups of the 1645 genes the expression patterns of which are useful in methods of identifying autoimmune diseases, differential diagnosis of autoimmune disease, particularly SLE, and classification of diseases, such as SLE and WG into disease sub-groups that are related to the disease activity. The invention also provides methods for differentiating SLE from other autoimmune diseases. The invention further provides a method for predicting SLE flare-ups by analyzing the expression pattern of a group of genes. The invention provides a fast, accurate, and inexpensive method of continuously monitoring SLE patients throughout their lives for prediction of flare-ups. The invention also provides a fast, accurate and inexpensive way to detect medication induced lupus.

Description

MARKERS FOR AUTOIMMUNE DISEASE DETECTION

CROSS-REFERENCE TO RELATED APPLICATIONS

[001] The present application claims the benefit, under 35 U.S.C. 119(e) of the U.S. provisional application No. 60/601,109, filed August 13, 2004, the content of which is herein incorporated by reference in its entirety.

FIELD OF THE INVENTION

[002] The present invention relates to newly identified gene sets and their expression patterns and uses of the expression patterns in screening for and classifying autoimmune diseases.

BACKGROUND OF THE INVENTION

[003] Identification of various autoimmune diseases is difficult because of the variability in the phenotype within any particular disease, as they are currently classified. This hampers both selection of therapeutic intervention from existing therapies shown to be effective in treating specific autoimmune diseases, as well as development and testing of new therapies. Therefore, it would be important to find more accurate ways to screen for and classify autoimmune diseases.

[004] For example, systemic lupus erythematosus (SLE), is known as a chronic, inflammatory autoimmune disease characterized by dysregulation of the immune system resulting in the production of antinuclear antibodies, the generation of circulating immune complexes, and the activation of the complement system. The immune complexes build up in the tissues and joints causing inflammation, and degradation to both joints and tissues.

[005] The body's immune system normally makes proteins called antibodies to protect the body against viruses, bacteria and other foreign materials (collectively referred to as antigens). In an autoimmune disorder, such as SLE, the immune system loses its ability to tell the difference between foreign or non-self antigens and its own cells and tissues. The immune system then makes antibodies directed against itself. These antibodies, called "auto-antibodies," react with the "self autoantigens" to form immune complexes, which build up in the tissues, causing inflammation, injury to tissues, and pain.

[006] While the word "systemic" in SLE correctly suggests that the disease affects the entire body and most organ systems, the disease involves inflammation and consequent injury to the joints, skin, kidney, brain, the membranes in body cavities, lung, heart, and/or gastrointestinal tract. An individual with SLE often experiences unpredictable acute episodes or "flares" and equally unexpected remissions. The pathologic hallmark of the disease is recurrent, widespread, and diverse vascular lesions resembling a rash or changes on the surface of the skin.

[007] French dermatologist Laurent Theodore Biett first described SLE in 1828. Early studies were simply descriptions of the disease, with emphasis on the skin rashes typically present in those afflicted with the disease as well as other easily visible symptoms. Forty- five years later a dermatologist named Kaposi noted that some patients with lupus erythematosus (LE) skin lesions showed signs of affected internal organs. In the 1890s, Sir William Osier, a Canadian physician, observed that SLE could affect internal organs without the occurrence of skin changes. In 1948, Dr. Malcolm Hargraves of the Mayo Clinic isolated and described the particular morphology of the LE cell. This cell was found in the blood of patients with SLE. Hargraves' discovery has enabled physicians to identify many more cases of SLE by using a simple blood test. The test is only positive, however, in about half of SLE patients and is no longer used routinely. Since 1954, the various unusual antibodies found to be associated with SLE have been used to study the disease. The above difficulty in identifying the disease, and those afflicted with it, has led to an effort to use the presence of these antibodies as a tool to diagnose the disease. However, the presence of these antibodies may be the result of factors other than SLE, and to date no single autoantibody has been found to be universal to all individuals with SLE.

[008] U.S. Patent No. 6,177,254 to Rattner et al. discloses a nucleolus protein, named ASE-I, that has been found to be a reliable serum marker for SLE in 22% of patients. The screening can be done using an ELISA assay, western blot techniques, or by binding the antigen to microspheres and identifying reactive sera by flow cytometry. ASE-I has a molecular weight of about 55kDa and localizes to the nucleolus organizer regions of the chromosome during cell division.

[009] U.S. Patent No. 6,280,941 to Tsao et al. discloses a genetic testing method for diagnosing SLE. The method is related to amplifying nucleic acids from human tissue samples and analyzing for a variant allele of a gene encoding poly(ADP- ribosyl)transferase expression (PARP), which is diagnostic of SLE or indicates a genetic predisposition for developing SLE. Also disclosed are useful oligonucleotide primers, primer sets and genetic testing kits for detecting a genetic predisposition for developing SLE.

[0010] U.S. Patent Application Publication No. 2004/0033498 to Behrens et al. discloses methods and materials involved in diagnosing SLE, diagnosing severe SLE, and assessing a mammal's susceptibility to develop severe SLE. The application provides nucleic acid arrays that can be used to diagnose SLE but only in comparison with healthy individuals. Behrens does not distinguish or diagnose SLE specifically in comparison with other autoimmune diseases because such patient populations were not examined. The application discloses a set of genes that are differentially expressed between SLE patients and healthy individuals. Further, the application discloses a set of fourteen genes that mark a predisposition to develop severe SLE or SLE-AIP (SLE accompanied by the activation of an interferon pathway). This application also provides data from gene expression analysis of only isolated from peripheral blood mononuclear cells. The sample material of only one cell type may critically skew the expression level analysis.

[0011] The above markers, however, suffer from false positive result because of the inability of the markers to distinguish SLE from other autoimmune diseases, such as Wegener's Granulomatosus, and Rheumatoid Arthritis. Therefore, there remains a need for a method to detect autoimmune diseases, such as SLE without the drawbacks of the prior art.

SUMMARY OF THE INVENTION

[0012] We have now discovered a series of gene sets that can be useful in screening for and classifying autoimmune diseases. The expression signatures or expression profiles of these genes can be used in diagnosis and/or prognosis of autoimmune diseases and can further be used in identifying whether the individual has systemic lupus erythematosus (SLE), Wegeners granulomatosis anti-neutrophilic autoantibody (ANCA+) vasculitis (WG), and differentiating these deseases from rheumatoid arthritis and healthy controls as well as from each other. Accordingly, the invention also provides methods for screening patients for SLE and WG. In one embodiment, the invention provides a method for differential diagnosis of SLE from other autoimmune diseases. The method can also be used to determine the severety of the disease.

[0013] Additionally, the invention provides methods of classifying SLE and WG based on specific gene expression signatures or expression profiles using the discovered genes. For example, traditionally the disease activity of WG and SLE has been measured either by the Birmingham Vasculitis Activity Score (BVAS) (Luqmani RA, Bacon, PA, Moots RJ, Janssen BA, Pall A, Emery P, Savage C, Adu, D. Birmingham Vasculitis Activity Score (BVAS) in systemic necrotizing vasculitis, QJM 1994;87(ll):671-8) for WG patients or SLE Disease Activity Index (SLEDAI) (Bombardier C, Gladman DD, Urowitz MB, Caron D, Chang CH. Derivation of the SLEDAI, A disease activity index for lupus patients, The Committee on Prognosis Studies in SLE. Arthritis Rheum. 1992.;35(6):630-40) and the BILAG (BILAG, British Isles Lupus Assessment Group, scoring system has been in use over three decades and has been refined to improve its sensitivity., in 1998, it was computerised by ADS-Limathon Ltd as the BLIPS program, British Lupus Integrated Prospective System) for SLE patients. We have now discovered that classes of different disease activity in both WG and SLE can be differentiated using gene expression profiles from the subsets of 1645 genes provided by the present invention.

[0014] The present invention is based upon the discovery that expression of a defined set of genes is changed in biological samples from patients affected with different autoimmune diseases as compared to non-autoimmune diseases and even other autoimmune disease, such as SLE, WG, and RA and that detection of the expression profile of these genes provides a tool to screen for, diagnose, and also classify the disease activity of these autoimmune diseases. [0015] We identified 1645 genes that were found to be differentially expressed in autoimmune diseases as compared to non-autoimmune disease samples. The group of 1645 genes is set forth in Table 6. The probe ID numbers in column 1 are from the June 2005 annotated Affymetrix Ul 33 +2 Gene Set. The "scores" presented in columns 4-7 refer to a difference from an "average score" (centroid score) of all the measured samples in the four phenotype group (all-sample score), including healthy, SLE, RA, and WG samples, that was set to 0. The difference towards positive from 0 score indicates that the expression of the corresponding gene is increased in the group when compared to the all- sample "average". The difference towards negative from 0 score indicates that the expression of the corresponding gene is decreased when compared to all-sample "average." Accordingly, a gene that gives a well varied score for all the four groups is indicative of a gene useful in differentiating these four phenotypes based on the gene's expression profile.

[0016] Columns 8 and 9 in Table 6, represent scores differentiating SLE samples from average of all other samples (non-SLE samples). Accordingly, a difference in the score between SLE and "other 3" of about 0.1 or greater, alternatively about 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0 or even greater, is indicative of that gene being a good marker in differentiating between SLE and non-SLE samples. Accordingly a skilled artisan can easily select a smaller gene set for diagnostic and/or screening purposes.

[0017] Columns 10 and 11 in Table 6, represent scores differentiating SLE samples from WG samples. Accordingly, a difference in the score between SLE and WG samples of about 0.1 or greater, alternatively about 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0 or even greater, is indicative of that gene being a good marker in differentiating between SLE and WG samples.

[0018] Columns 12 and 13 in Table 6, represent scores differentiating WG (col 13) form the "other 3" (healthy, SLA and RA average, col 12) samples. Accordingly, a difference in the score between WG and "other 3" of about 0.1 or greater, alternatively about 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0 or even greater, is indicative of that gene being a good marker in differentiating between WG and "other 3" samples.

[0019] The disease-specific gene expression signatures of the present invention provide substantially improved diagnostic power as compared to other methods that have been used in an attempt to diagnose autoimmune diseases such as SLE and WG.

[0020] The invention also provides a gene transcript groups the expression of which can differentiate between SLE and other autoimmune diseases such as rheumatoid arthritis (RA) and WG. Accordingly, we have identified a master gene set and several gene sub-sets that allow creation of diagnostic tools, such as diagnostic kits, diagnostic bead sets and diagnostic nucleic acid arrays, for autoimmune diseases.

[0021] Although sometimes it may be preferable to analyze expression of the entire set of genes provided in the signatures of the present invention to provide a diagnosis, one does not have to analyze all of the identified genes simultaneously or at all in diagnosis/prognosis but one can also use a subset of the genes.

[0022] In one embodiment, a cut-off score difference between the expression of gene in one group (such as SLE, see e.g. col 8, Table 6) and another group (such as the average or centroid score measured in a sample group consisting of healthy, WG and RA samples, see e.g. col. 9, Table 6) of about 0.1 or over, 0.2 or over, 0.3 or over, 0.4 or over, 0.5 or over, 0.6 or over, 0.7 or over, 0.8 or over, 0.9 or over, 1.0 or over, 1.1 or over, 1.2 or over, 1.3 or over, 1.4 or over, 1.5 or over, 1.6 or over, 1.7 or over, 1.8 or over, 1.9 or over, 2.0 or over as presented in Table 6 can be used to select a smalle sub-group of genes that can differentiate between samples from individuals with an autoimmune disease phenotype and samples between individuals with non-autoimmune disease phenotypes (normal, or control or healthy samples).

[0023] When the centroid was moved towards greater discrimination, smaller subgroups of useful genes were identified as described herein.

[0024] Transcription profile of fewer than 1645, preferably fewer than about 279, alternatively fewer than about 279-200, alternatively fewer than about 200-150, alternatively fewer than about 150-125, alternatively fewer than about 125-100, alternatively fewer than about 100-90, alternatively fewer than about 90-80, alternatively fewer than about 80-70, alternatively fewer than about 70-60, alternatively fewer than about 60-50, alternatively fewer than about 50-40, alternatively fewer than about 40-30, alternatively fewer than about 30-25, alternatively fewer than about 25-20, alternatively fewer than about 20-15, alternatively fewer than about 15-10, alternatively fewer than about 10-6, alternatively fewer than about 5 genes selected from the 1645 genes are used in diagnostic applications. In some embodiments, even analysis of expression of individual genes selected from the group of 1645 genes can be used in the diagnosis of the autoimmune diseases, particularly differentiating individuals with SLE, WG, RA and individuals with no autoimmune disease. In other embodiments, it may be preferable to analyze a larger gene set. In some embodiments, it may be preferable to analyze the expression of fewer genes. So, for example, if a two or more genes are selected from the interferon gene family or interferon inducible genes, also included can be, for example, genes that are not inducible by interferon. Such genes can be readily identified from the list of 1645 genesin Table 6 by a skilled artisan based on the score values provided in Table 6 and explained in more detail above.

[0025] Table 6 provides the set of 1645 genes and the corresponding scores the difference of which from the centroid value 0 indicate how useful they are in the diagnosis of any particular condition. Expression of any of these genes, any combination of these genes or all of these genes can be used in diagnostic methods according to this invention. Typically, in a diagnostic kit or array or bead set, one also uses also at least one, or more housekeeping genes as internal controls. The bigger the score difference between compared groups (comparison of one phenotype agains average seen in all samples in columns 4-7, columns 8-9, comparison between SLE samples and the average seen in WG, RA and healthy samples, columns 10-11 comparison between SLE samples and WG samples, and columns 12-13 cmparison between WG and combined samples from SLE, RA and healthy individuals) , the more power the expression analysis of that particular marker gene provides. [0026] The genes the expression of which has at least 0.1 , 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.O., 3.0, 4.0, 5.0-fold or greater, such as 6, 7, 8, 9, 0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 fold or more difference between each compared group (such as SLE versus WG, or SLE versus non- SLE) at p-value < 0.01 were considered differentially expressed. In one embodiment, if a cross comparison of all sample sets is performed the genes are considered differentially expressed between the groups if the fold-change difference is > 1.8 and the p-value, as determined by a Welch's t-test, is <0.01.

[0027] Table 7 provides the set or group of 279 genes the expression profile of which can differentiate between all four analyzed phenotypes: SLE, WG, RA and healthy individuals. Accordingly, one can select 1, 2, 3, 4, 5, 6, 7, 8, 9, 10-20, 20-30, 30-40, 40- 50, 50-100, 100-200, or up to 279 genes from this group to diagnose and /or screen for an individual for an autoimmune disease. The genes can also be used to correctly classify the autoimmune disease in an individual as WG, SLE or RA based on the expression differences of thr genes from the all-sample average (0) as shown, for example, in Table 6, columns 4-7.

[0028] Table 1 provides 147 genes that are differentially expressed in SLE and non- SLE samples. The expression of these genes in SLE is increased as compared to non- SLE samples (including healthy individuals, individuals affected with RA and individuals affected with WG). Accordingly, one can select 1, 2, 3, 4, 5, 6, 7, 8, 9, 10-20, 20-30, 30- 40, 40-50, 50-100 or up to 147 genes from this group to diagnose an individual as having an autoimmune disease, as well as correctly classifying the autoimmune disease to WG, SLE or RA.

[0029] Table 4 provides 105 genes from which one can select 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10-20, 20-30, 30-40, 40-50, 50-100 or up to 105 that can be used as an alternative powerful set of genes the expression of these genes in SLE is increased as compared to non-SLE samples.

[0030] Table 8 provides 28 genes from which one can select to measure the expression of 1, 2, 3, 4, 5, 6, 7, ,8 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or all 28, the expression changes of which can be used to differentiate SLE from other autoimmune samples as well as from normal samples.

[0031] We have also shown that the differential expression of the identified sets of genes provides a picture of disease activity. For example, the classification scores at Table 6 that are positive in individuals with a particular phenotype and negative in others, are upregulated in that phenotype relative to other sample groups. Similarly, the classification scores at Table 6 that are negative in individuals with a particular phenotype positive in others, are downregulated in that phenotype relative to other sample groups. Accordingly, one can readily select sub-groups from Table 6 based on the scores. The bigger the difference in the score, the better the expression change of that gene differentiates that phenotype from the other phenotypes.

[0032] Therefore, the same gene set can also be used in monitoring disease activity, for example in response to treatment methods, such as pharmaceuticals and other therapies, including dietary interventions, herbal therapies, acupuncture, and mind-body relaxation techniques, such as meditation or hypnosis to control the autoimmune diseases. Monitoring the gene expression profiles provided by the present invention also provides a way to assess effectiveness in clinical trials of new therapeutic interventions, such as pharmaceuticals to autoimmune diseases, such as SLE and WG. Accordingly, the invention provides methods for these described purposes.

[0033] For example, Tables 1OA and 1OB provide gene sets the expression of which correlates with WG activity. We discovered that the increased expression of the 33 genes in WG samples presented in Table 1OA was all associated with increased BVAS score, i.e. increased WG disease activity. The decreased expression of the 61 genes presented in Table 1OB was also associated with increased BVAS score. Accordingly, measuring the expression of these genes in a patient affected with WG can classify these patients according the disease activity.

[0034] In addition, we discovered that SLE patients can be classified intoat least two different groups based on the analysis of the 1645 genes. Table 13 summarizes the data from 659 gene probes representing 279 genes that were able to classify individuals into SLE patients who also express higher levels of anti-ds-DNA antibodies, and thus have more active SLE disease, and SLE patients who have low levels or no anti-ds-DNA antibodies, and thus have less active disease, and healthy individuals, with no SLE. Expression was measured from whole blood sample.

[0035] Table 15 provides 186 genes (368 probes), a subset of the 279 genes of Table 13, which provides a more powerful set of genes the expression of which is most variable between the two above-mentioned SLE groups (anti-ds-DNA+ and anti-ds-DNA- groups) and can therefore best differentiate the two SLE classes with different disease activity.

[0036] Table 14 provides the results from the expression measurements and their comparisons between healthy and SLE patients. The expression of the 69 genes represented by the 88 probes were able to differentiate SLE patients from healthy controls when expression was measured from whole blood.

[0037] Table 16 provides a sub-group of 53 genes, of the 69 genes of Table 14, the expression profile of which can be used to differentiate individuals into SLE, WG, RA and healthy phenotypes.

[0038] Table 17 provides a sub-set of 211 genes from the 1645 genes, the expression profile of which is corrected by gender (by moving male samples from the controls, to remove the female/male differences because all the SLE patient samples were female). Changes in the xpression profile of any of measured 1, 2, 3, 4, 5, 6, 7, 8, 9, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-200, 200-277, genes of the 277 genes can provide a diagnosis of SLE for a patient having autoimmune disease symptoms or can be used to screen SLE patients from a population.

[0039] The disease-specific gene expression signatures of the present invention provide substantially improved diagnostic power as compared to other methods that have been used in an attempt to diagnose autoimmune diseases such as SLE and WG.

[0040] For example, analysis of the gene group of 279 genes of the 1645 (the 279 group is as described below in Table 7) in a biological sample from an individual, can result in a correct disease classification of the patient in about or over 60%, preferably over 75%, still more preferably over 77%, still more preferably over 78%, more preferably over 79%, more preferably over 80%, more preferably over 81%, more preferably over 82%, more preferably over 83%, more preferably over 84%, more preferably over 85%, more preferably over 86%, more preferably over 87%, still more preferably over 88%, still more preferably over 89%, still more preferably over 90% or even higher into groups of SLE, RA, WG or normal. Also provided are groups of 147 genes, 105 genes, 101 genes, 28 genes, and 6 genes, as described below, all of which are sub-groups of the 1645 gene group and which provide at least similar accuracy in autoimmune disease diagnosis as the one described above. The diagnostic accuracy typically depends on the genetic background of the population that the individual belongs.

[0041] Given the difficulty in diagnosing and classifying autoimmune diseases, for example SLE, which may in some cases take years, the present invention provides a powerful new tool to help in early diagnosis of these autoimmune diseases as well as tools for disease monitoring and monitoring of effects of new therapeutic interventions. Monitoring clinical trials of new autoimmune disease drugs can thus be vastly improved by the expression profiles of the present invention.

[0042] The present invention further provides a gene chip, or gene bead selection for the detection of autoimmune diseases, particularly for the diagnosis if SLE and WG, and classification of SLE and WG based on the disease activity. The chip comprises probes for specifically binding with a selection of 1 to about 1645 sequences selected from Table 6. Preferably the chip or the bead selection has fewer than 1645 genes. For each disease, as described in Table 6, one can select the best probe combination based on the score difference between the specific phenotype and the other phenotypes.

[0043] Accordingly, for example, genes selected from Table 7, represent one preferred group of 279 genes the transcription of which is particularly useful in classification, screening and diagnosis of autoimmune diseases, such as SLE, WG, and RA. Genes selected from Table 1, represent one alternative group of 147 genes the transcription of which is particularly useful in diagnosis of SLE. Genes selected from Table 8, represent another alternative group of 28 genes the transcription of which is particularly useful in diagnosis of SLE. The group of 6 top genes from Table 8, provide another alternative group of genes the transcription of which is useful in diagnosing SLE. Other alternative groups can be created by a skilled artisan based on the scores shown in Table 6: the higher the score in a particular phenotype, the higher its expression in the disease, and the lower the score in a particular phenotype the lower the expression of the gene as compared to a comtrol.

[0044] The control can be, for example, a mean expression of that gene in a group of healthy individuals when comparing SLE to non-SLE samples; mean expression in a group of RA, WG, and healthy individuals when comparing SLE to non-SLE samples; mean expression of the gene in any of the groups RA patients, WG patient or other autoimmune patients, when comparing SLE to non-SLE samples.

[0045] The SLE kidney-disease specific gene group is presented in Figure 4, and includes Intercellular adhesion molecule 2; Interferon induced with helicase C domain 1; Hypothetical protein FLJ38348; Hect domain and RLD 5; Hypothetical protein FLJ20035; Interferon-induced protein with tetratricopeptide repeats 1; Epithelial stromal interaction 1 breast; Zinc finger CCCH type domain containing 1 ; Interferon regulatory factor 7; Viperin; XIAP associated factor-1; Hect domain and RLD 6; Myxovirus influenza virus resistance 2 mouse; Interferon-induced protein 44; Chromosome 1 open reading frame 29; Myxovirus influenza virus resistance 1; Interferon alpha-inducible protein clone IFI- 15K; Interferon alpha-inducible protein clone IFI-6-16; Interferon alpha-inducible protein 27; Bone marrow stromal cell antigen 2; Hypothetical protein LOC 129607; Lectin galactoside-binding, soluble, 3 binding protein; Interferon-induced protein with tetratricopeptide repeats 3; XIAP associated factor-1; Signal transducer and activator of transcription 1, 9IkDa; Interferon-induced protein 44; Major histocompatibility complex, class II; LOC441164; Ring finger protein 135; Ribosomal protein S27a; Similar to 60S ribosomal protein L35; Metallothionein IX; Metallothionein 2 A; Metallothionein IE functional, Metallothionein IF; Serine or cysteine proteinase inhibitor, clade B, member 1; Inhibin, beta A activin A, activin AB alpha polypeptide; Vanin 1 ; Pleckstrin homology domain containing, family A member 1 ; UDP- Gal:betaGlcNAc polypeptide 5; CDNA FLJ32589 fis, clone SPLEN2000443; Interleukin 7 receptor; Chemokine C-X-C motif ligand 1; Lactotransferrin; Secretory leukocyte protease inhibitor; Olfactomedin 4; and Ubiquitin-conjugating enzyme E2, Jl. The public accession ID numbers for all these genes can be found in Table 6.

[0046] The invention also provides a group of genes for analyzing the disease activity in WG. For example, we found that change in the expression of certain of the 1645 genes was in linear correlation with the BVAS score. The score in Table 6 is positive if change is increased expression, and negative, if change is discreased expression as compared to the centroid score, which is zero. Centroid score represents roughly an average of epression in the entire group. For example, in columns 4-7, Table 6, the entire group "average" is determined by measuring expression of the gene in samples from all the analyzed phenotypes, and each individual class of individuals (SLE, WG, RA and healthy) is scored against the average.

[0047] One particular group of genes the expression of which linearly correlate with patient BVAS score consists of Serine hydroxymethyltransferase 2 mitochondrial; Lactate dehydrogenase B; Brix domain containing 1; Pyrophosphatase inorganic; Serine hydroxyltransferase 2 mitochondrial; Killer cell lectin-like receptor subfamily D, member 1; Hypothetical protein FLJ20315; Autism susceptibility candidate 2; Interleukin 7 receptor; LDL receptor adaptor protein; Chromosome 16 open reading frame 3; MEL- Like 2 chicken; T cell receptor alpha chain; T Cell receptor alpha locus; B-CeIl CLL/lymphoma HB zinc finger protein; IL2-inducible I-cell kinase; IDP-ribosylation factor-like 1; Mannosidase, alpha, class 1C, member 1; Bridging Integrator 1; Actin- binding LIM protein 1; Nuclear factor of activated T-cells, calcineuria-dependent 2; V-ets erythroblastosis virus E26 oncogene homolog 1; 3-Oxoacid CoA transferase 1; Ubiquitin conjugating enzyme E2; Hypothetical LOC3B3185; B-cell CLL/lymphoma 6 zinc finger protein 51 ; V-ets erythroblastosis virus E26 oncogene homolog 2; Nuclear factor, interleukin 3 regulated; Nuclear factor erythroid-derived 2, 45kDa; Ring finger protein 24; Similar to GL 15821 -PA; Carbonic anhydrase IV; Solute carrier family 22, member 4; Solute carrier family 11, member 1; Acyl-CoA synthetase, long chain family member 1; Rho GTPase activation protein 26; Leukotriene H4 receptor; Lymphocyte alpha-kinase; Hypothetical protein FLJl 4001; Kelch-like 2, Mayven (Drosophila); and Transcribed locus, moderately similar to XP 375499.1. Accordingly, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and up to all 41 of these genes can be used in determining the disease activity of WG.

[0048] In one preferred embodiment, a group of 33 genes are used in determining the disease activity of WG, wherein the increased expression is indicative of higher BVAS score and therefore higher disease activity, the genes selected from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10-33 of the genes in Table 1OA.

[0049] In another preferred embodiment, a group of 61 genes are used in determining the disease activity of WG, wherein the decreased expression is indicative of higher BVAS score and therefore higher disease activity, the genes selected from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10-61 of the genes in Table 1OB.

[0050] In one embodiment, a combination of genes with increased and decreased expression are used in determining the WG disease activity, the genes selected from the Tables 1OA and 1OB. Any of these genes combination may be used. Preferably at least 5 genes or more are analyzed.

[0051] The present invention further provides methods for distinguishing between SLE and other autoimmune diseases, such as WG, and Rlieumatoid Arthritis. The methods comprise detecting the expression of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and up to about 1645 gene products selected from the group consisting of gene products of Table 6, and correlating the expression pattern with SLE, or the other rheumatic autoimmune diseases. In one preferred embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and up to about 279 of the gene group presented in Table 7 are used. In another preferred embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and up to about 147 of the gene group presented in Table 1 are used. In yet another embodiment, the group of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and up to about 105 gene described in Table 4 are used. In one embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, and up to 46 genes of SLE kidney specific group as described above are used (see, also Figure 4).

[0052] Any of the gene groups or sub-groups of them as described herein and throughout the specification can be used in the methods provided according to the present invention. [0053] The present invention further provides methods for monitoring the treatment of a patient with SLE. The methods comprise administering the treatment, such as a pharmaceutical composition to the patient, obtaining a biological sample from the patient, and measuring the expression in the cells of the sample of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and up to about 1645 gene products selected from the group consisting of gene products as presented in Table 6, Table 7, Table 8, Table 14, Table 15, Table 16, and Table 17, and determining whether the treatment results in partial or complete normalization of the expression profile thereby indicating that the treatment has had a clinical effect on the phenotype. By measuring changes in the individual's expression profile over time, one can obtain prognostic evaluation of the disease and effectiveness of the treatment.

[0054] The present invention further provides methods for screening for an agent capable of modulating the onset or progression of SLE. The methods comprise exposing a cell, for example, a cell isolated from an individual affected with SLE, to the agent, measuring expression of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or up to about 1645 gene products selected from the group consisting of gene products of Tables 6, 7, 8, 1OA, 1OB, 13, 14,

15, 16, and 17, and comparing the expression profile of the same genes to a normal expression profile of the genes, wherein normalization of the expression profile upon exposure to the agent, is indicative of the agent being effective in modulating the onset or progression of SLE.

[0055] The present invention further provides methods for detecting drug induced SLE. The methods comprise taking a biological sample from an individual exposed to a drug, for example a drug that is known to induce SLE in some individuals, or a drug that is suspected of causing SLE in some individuals, and analyzing the expression of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or up to 1645 genes selected from Tables 6, 7, 8, 1OA, 1OB, 13, 14, 15,

16, and 17, wherein expression profile similar to a SLE profile is indicative of drug having induced SLE in the individual. Similarly, if the expression profile is similar to the expression profile in non-SLE samples, it is indicative that the drug has not induced SLE in the individual. The method of the invention can be used to follow-up patients on drug therapies, that have been reported or that are suspected to induce SLE. Such follow-up can include taking several samples from the individual using the drug and determining whether the expression pattern of the genes changes. Also, one can determine a baseline expression pattern from a biological sample taken from the individual before she/he has been exposed to the drug and then determine if the expression pattern changes towards the SLE expression pattern during the continued use of the drug. Subtle changes in the expression pattern may be used as a warning sign and as a guide to discontinue use of the drug to prevent induction of drug induced SLE in the individual.

[0056] The present invention further provides methods for screening for an agent capable of causing SLE. The methods comprise exposing a cell to the agent, measuring the expression of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or up to gene products selected from Tables 6, 7, 8, 1OA, 1OB, 13, 14, 15, 16, and 17, and comparing the expression pattern of the genes to a SLE or non-SLE expression pattern as provided by the scores in Table 6, wherein the expression pattern similar to a non-SLE sample, is indicative of agent that does not likely induce SLE, and wherein expression pattern similar to SLE-sample pattern is indicative of the agent being capable of inducing SLE.

[0057] In one embodiment, the invention provides a method for classifying SLE patients into at least two groups based on the expression level of 279 genes listed in Table 13. We identified three major clusters 1) Healthy control samples, 2) SLE samples with a relatively high IFN-regulated gene signature and 3) SLE samples with a relatively low IFN-regulated gene signature. The group with relatively high IFN-regulated gene signature co-existed with the presence of anti-ds-DNA antibodies, and more active SLE disease. One or more of these genes can therefore now be used to predict SLE flares that are also known to be associated with increased anti-ds-DNA antibodies. Accordingly, the invention also provides a method for predicting SLE flares in SLE patients wherein the expression of one or more of these genes is analyzed and significant increase in the expression is indicative of impending SLE flare.

[0058] The gene products as recited herein can be RNA and/or proteins, preferably the gene products are RNA. When measuring the expression of the genes in cells one can use any of the transcript or protein measurement technique well known to one skilled in the art and are discussed in more detail in the detailed description part. BRIEF DESCRIPTION OF THE DRAWINGS

[0059] Figure IA shows cross-validation plots of the four sample classes. The results from ten fold cross-validation using nearest shrunken centroid classification performed using the PAM software. The overall misclassification error is reported for each of the four classes (healthy, lupus, RA, and ANCA) at increasing rates of centroid shrinkage (threshold values). The number of genes that significantly contribute to sample classification at each threshold value are indicated at the top of the plot. The vertical arrow indicates a centroid shrinkage threshold value of 3.75.

[0060] Figure IB shows cross-validation probabilities of each sample within the four sample classes. The probability of belonging to each class centroid, as determined by nearest shrunken centroid classification applied in the PAM software, is indicated for each of the 153 samples using the top 279 genes (see Legend). A sample was classified to a particular class as determined by the highest probability amongst the four classes. The samples are arranged sequentially by class, as indicated by the header, and each sample-class group is separated by a solid vertical line. A centroid shrinkage threshold of 3.75 identified 279 genes with the following classification rates: healthy 96.4% (27 of 28 samples), SLE 77.8% (56 of 72 samples), RA 23.1% (6 of 26 samples) and ANCA 85.2% (23 of 27 samples).

[0061] Figure 2 shows classification Probabilities of each SLE and "Other" non-SLE sample. The probability of belonging to each class centroid, as determined by nearest shrunken centroid classification applied in the PAM software, is indicated for each of the samples in the reference or test data sets. A sample was classified to a particular class as determined by the highest probability amongst the two classes. The samples are arranged sequentially by class, as indicated by the header, and each sample-class group is separated by a solid vertical line. A centroid shrinkage threshold value of 5.4 selected 28 gene features for sample classification (Table 4). A) Cross-validation probabilities of each SLE and "Other" non-SLE sample within the Reference sample set (n=98). Of the 52 SLE samples, 46 (88.5%) were correctly classified; and of the 46 "other" (healthy + RA + ANCA) samples, 42 (91.3%) were correctly classified. B) Verification probabilities of each SLE and "Other" sample within the independent Test sample set (n=55). Applying the previously identified set of 28 gene features to the independent test set resulted in correctly classifying 16 of 20 (80.0%) and 31 of 35 (88.6%) SLE and "Other" non-SLE samples, respectively.

[0062] Figure 3 shows Immune Cell Biology Gene expression that was determined for the SLE classification gene fragments. Expression intensities were converted to log 10 and normalized to the unit standard deviation using the Avadis software. Hierarchical clustering was performed using the Cluster Algorithms described by Eisen followed by visualization of the output using the program Tree View. Data is presented as a heat map where genes with higher expression are shown in reddarker grey and those with lower expression in lighter grey. Figure 3 A. Expression analysis of the SLE associated genes across numerous immune cell biology samples from healthy donors. The samples in the white box have been magnified in Figure 3B. Figure 3B. A magnified version of the region in 3 A showing expression of the top SLE classification genes in CD4+ T-cells stimulated with either anti-CD3 and anti-CD28 or ICAMl for 72 hours. Also shown are monocytes stimulated with LPS for 8 hours.

[0063] Figure 4 shows expression analysis of kidney biopsies. Kidney biopsy material was processed for RNA and subjected to microsample amplification prior to hybridization to Affymetrix Ul 33 chips. The expression of genes differentially expressed in kidney samples was subjected to hierarchical clustering using Eisen 's method. Graphical representation in gene expression changes are shown with lighter grey corresponding to down-regulated and darker grey to up-regulated expression with the maximum intensity corresponding to a change of 0.16 based upon log 10.

[0064] Figures 5A and 5B show classification for each SLE and healthy control sample. The probability of belonging to each class centroid, as determined by nearest shrunken centroid classification applied in the PAM software, is indicated for each of the samples in the reference or test data sets. A sample was classified to a particular class as determined by the highest probability amongst the two classes. A solid circle indicates the probability of being an SLE sample, while an unfilled circle indicates the probability of being a healthy control sample. The samples are arranged sequentially by class, as indicated by the header, and each sample-class group is separated by a solid vertical line. A centroid shrinkage threshold value of 4.2 selected 88 gene features for sample classification (Table 12). Figure 5 A shows cross-validation probabilities for each SLE and healthy control samples within the Reference sample set (n=80). Of the 51 SLE samples, 47 (92.2%) were correctly classified; and of the 29 healthy control samples, 26 (89.7%) were correctly classified. Figure 5B shows verification probabilities for each SLE and healthy control sample within the Test sample set (n=40). Applying the previously identified set of 88 gene features to the test set resulted in correctly classifying 24 of 25 (96.0%) and 14 of 15 (93.0%) SLE and healthy control samples, respectively.

DETAILED DESCRIPTION OF THE INVENTION

[0065] Many biological functions are accomplished by altering the expression of various genes through transcriptional (e.g., through control of initiation, provision of RNA precursors, RNA processing, etc.) and/or translational control. For example, fundamental biological processes such as cell cycle, cell differentiation and cell death, are often characterized by the variations in the expression levels of groups of genes.

[0066] Changes in the expression levels of particular genes serve as signposts for the presence and progression of various diseases. Monitoring changes in gene expression may also provide certain advantages during drug screening development. Often drugs are screened and prescreened for the ability to interact with a major target without regard to other effects the drugs have on cells. Often such other effects cause toxicity in the whole animal, which prevent the development and use of the potential drug.

[0067] The present invention provides a gene sets that are subsets of 1645 genes that we discovered were differentially expressed in autoimmune disease patients as. The expression signatures or expression profiles of the identified genes are useful in diagnosis of and screening for autoimmune diseases, particularly in diagnosing systemic lupus erythematosus (SLE) and Wegeners granulomatosis anti-neutrophilic autoantibody (ANCA+) vasculitis (WG), and differentiating them from rheumatoid arthritis (RA) and each other. Accordingly, the invention also provides methods for screening for SLE and WG. In one embodiment, the invention provides a method for differential diagnosis of SLE from other autoimmune diseases. Additionally, the invention provides methods of classifying SLE and WG based on specific gene expression signatures or expression profiles using the discovered genes.

[0068] The invention is based upon the discovery that expression of a defined set of genes is changed in biological samples from patients affected with different autoimmune diseases as compared to non-autoimmune diseases and even other autoimmune diseases, such as SLE and WG, and that detection of the expression profile of these genes provides a tool to diagnose and screen for these autoimmune diseases.

[0069] The invention provides a master set of genes consisting of 1645 genes that were found to be differentially expressed in autoimmune diseases as compared to non- autoimmune disease samples. The group of 1645 genes is set forth in Table 6.

[0070] We have also shown that the increased expression of the identified sets of genes provides a picture of a more or less active disease. Therefore, the same gene set can also be used in monitoring disease activity, for example in response to treatment methods, such as pharmaceuticals and other therapies, including dietary interventions, herbal therapies, acupuncture, and mind-body relaxation techniques, such as meditation or hypnosis to control the autoimmune diseases. Monitoring the gene expression profiles provided by the present invention also provides a way to assess effectiveness in clinical trials of new therapeutic interventions to autoimmune diseases, such as SLE and WG. Accordingly, the invention provides methods for these described purposes.

[0071] The invention provides a master set of genes consisting of 1645 genes that were found to be differentially expressed in autoimmune diseases as compared to non- autoimmune disease samples. The group of 1645 genes are set forth in Table 6. Detailes of the scores for healthy donor samples, SLE white blood cell samples, RA samples and WG white blood cell samples are provided in Table 6.

[0072] Specifically, in one embodiment, the present invention provides a diagnostic/prognostic gene expression signature, i.e. a diagnostic/prognostic expression profile of a gene set of 279 or less genes, that is indicative of systemic lupus erythematosus (SLE). The diagnostic gene expression signature or profile consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 10-15, 15-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-110, 110-120, 120-130, 130-140, 140-150, 150-160, 160-170, 170-180, 180- 190, 190-200, 210-220, 220-230, 230-240, 240-250, 250-260, 260-270, 270-279 genes selected from the group of genes set forth in Table 7, wherein altered expression of said genes is indicative of the individual being affected with SLE.

[0073] In another embodiment, the invention provides a group of genes consisting of 147 genes or less selected from the group of genes consisting of genes set forth in Table 1, wherein altered expression of said genes is indicative of the individual being affected with SLE.

[0074] In another embodiment, the invention provides a group of genes consisting of 105 genes or fewer selected from the group consisting of genes set forth in Table 4, wherein altered expression of said genes is indicative of the individual being affected with SLE.

[0075] In another embodiment, the invention provides a gene group consisting of RSAD2/CIG5, Corf29, IFITl, IFIT3, GIP2, LY6E, wherein the expression of one or more of genes is altered in kidney biopsies or cells from urine sediment of SLE patients and thus can be used as a disgnostic gene group for determining SLE related kidney disease. In another embodiment, the invention provides an SLE kidney gene expression profile group as shown in Figure 4, wherein the expression of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 10-15, 15-20, 20-30, 30-40, 40-46 of genes in Figure 4 are analyzed in a kidney biopsy sample or urine sediment cell sample and wherein changed expression in these genes in the biological sample is indicative of SLE kidney disease.

[0076] In one preferred embodiment, the analysis is non-invasive, and involves taking of a urine sample and sedimenting cells present in the urine sample and analyzing expression of the SLE kidney groups of genes in these cells, (see, e.g. Li, B. C. et al., N. Engl. J. Med, 344(13): 947-54).

[0077] In another embodiment, the invention provides a gene group consisting of metallothionein, lactotransferrin, olfactomedin wherein the expression of one or more of these genes is altered in kidney tissue of WG patients and thus can be used as a diagnostic gene group for determining WG related kidney disease. [0078] The reference to "altered expression" or "changed expression" or "differential expression" as used herein and throughout the specification refer to gene expression that is changed, i.e. either increased or decreased in a patient with autoimmune disease, particularly with an active autoimmune disease as compared to a control, that provides a baseline or alternatively "normal" expression level or expression level range for any of the genes that are part of the expression profile of the invention. Gene expression in a disease sample is preferably at least comparable to another disease sample. Accordingly, similar levels of expression will also convey the type of disease classification, i.e., the gene is important to the disease because it is different from a control sample or control sample group, or it is similar to the disease sample, or disease sample group.

[0079] The scores indicated in the Tables, are read as follows: High score indicates higher than control or baseline expression, low score indicates lower than control or baseline expression, and score close to zero indicates normal or baseline average expression.

[0080] The expression levels in each sample are standardized using housekeeping genes, i.e. genes that are involved in basic functions needed for the sustenance of the cell. Housekeeping genes are constitutively expressed (they are always turned "on"). A skilled artisan can readily determine a baseline housekeeping gene, such as beta-actin or GAPDH. Other examples of possible housekeeping genes useful according to the methods of the invention are provided, infra.

[0081] Accordingly, the expression can be compared to, for example, a simultaneously analyzed biological sample from one or more healthy, or non-SLE or non- WG patient of the same type as the sample to be diagnosed. Alternatively, the baseline can be created using a median or average expression of separately analyzed more than one control samples of the same biological origin, i.e. kidney sample for analysis of kidney biopsy and blood leukocyte sample for analysis of blood leukocytes, and whole blood sample for analysis of whole blood. These samples may be an average or median expression level from 2, 3, 4, 5, 6, 7, 8, 9, 10-100 or more individuals who do not have an autoimmune disease, as well as an average or median expression level from individuals with different autoimmune diseases. A control panel can be created with control samples from healthy non-autoimmune disease affected individuals, and/or samples from individuals with known autoimmune disease diagnosis. The control panel may also comprise expression patterns of the genes of the invention that distinguish different disease activity within the autoimmune disease patient group, such as different stages or classes of SLE. Such control panel provides a way to compare the expression level of the gene signature group and assess, which group the unknown sample belongs based on its expression profile of the selected genes. Therefore, for example, if the control is a positive control consisting of one or more samples from individuals affected with SLE, the expression similar to the SLE control is indicative of the individual being affected with SLE. Although it is desirable to include at least negative, and often also positive control sample with the analysis of the unknown sample, the control signatures may also be collected and saved in a computer database, thereby allowing analysis of samples even without simultaneous analysis of a control sample. The housekeeping gene expression is used to standardize the expression pattern.

[0082] In another embodiment, the genes are selected from the group of 28 genes consisting of AI337069; AW189843; NM_006820; NM_001548; NM_001549; NM_005101; NM_002346; AI742057; AA781795; NM_016323; NM_002534; NM_006417; AA633203; NMJ302462; NM_006187; NM_017631; NMJH7414; AA131041; AI075407; BC002548; BE049439; NMJH7523; BE888744; NM_017654; NM_016817; AA142842; NMJH4314; and NMJ) 16816, the expression provides a diagnostic signature profile, wherein altered expression of these 28 genes is indicative of SLE diagnosis.

[0083] Accordingly, the invention also provides methods of diagnosing SLE and WG, comprising analyzing in a biological sample of an individual in need of autoimmune disease diagnosis, the expression of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10-15, 15-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-110, 110-120, 120-130, 130-140, 140- 150, 150-160, 160-170, 170-180, 180-190, 190-200, 200-210, 210-220, 220-230, 230- 240, 240-250, 250-260, 260-270, 270-279, of genes selected from Table 7 or Table 17 wherein altered expression of the genes is indicative of the individual being affected with SLE. [0084] The invention further provides a method of differential diagnosis of SLE from other autoimmune diseases such as rheumatoid arthritis (RA), and WG. The method comprises analyzing the gene expression in an individual in need of autoimmune disease diagnosis, such as an individual in need of differential diagnosis for autoimmune disease, in a biological sample, of genes selected from Table 7, wherein altered expression of said genes as compared to an individual with other types of autoimmune diseases than SLE is indicative of the individual being affected with SLE.

[0085] The invention also provides methods for determining the classification of SLE or WG patients based on expression analysis of a gene set of at least 2, 3, 4, 5, 6, 7, 8, 19, 10 or more genes in a biological sample, such as peripheral lymphocytes or whole blood, or cells isolated from urine sediment or a tissue biopsy, such as kidney biopsy, comprising analysis of expression of genes that are differentially expressed in more severely affected individuals that have belong to different disease sub-group of SLE or WG that indicate different disease activity.

[0086] For example, we showed that the detection of the presence of anti-dsDNA antibodies (DNA) and steroid use was significantly increased in the set of patients belonging to the high IFN-regulated gene group; while the mean age was found to be significantly lower in this group. We also noted increased presence of mucosal ulcers (MUC) in the low IFN-regulated gene group approached significance (p=0.055). For example, multivariate analysis using logistic regression indicated that increased anti- dsDNA antibodies was significantly correlated with the high IFN-regulated gene group (Bayesian information criterion = 3.76). The genes that were found significantly upregulated in biological samples that typically also had increased amounts of anti-ds¬ DNA antibodies, included AA056548; AA083478; AA083478; AA131041; AA142842; AA150460; AA195074; AA233374; AA523958; AA573502; AA577672; AA741307; AA781795; AA976354; AF043337; AF063612; AF093744; AF129536; AF134715; AF208043; AF218365; AF220028; AF220030; AF237916; AF240697; AF240698; AF280094; AF307338; AF312735; AF312735; AF317129; AF323540; AI064690; AI075407; AI143416; AI304317; AI337069; AI421071; AI539443; AI557312; AI559696; AI608902; AI631846; AI651594; AI654857; AI688640; AI709406; AI738416; AI742057; AI798098; AI809206; AI825926; AI857639; AI859280; AI859865; AI862559; AI925506; AI954660; AI967971; AI984040; AK000229; AK002064; AK023661; AK023724; AK023743; AK025064; AK026751; AL045882; ALl 17607; AL121829; AL121994; AL136680; AL136924; AL161961; AU147903; AV706522; AV755522; AW008051; AW014557; AW014593; AW083820; AW151360; AW188198; AW189843; AW275016; AW297731; AW474434; AW575754; AW847318; BC000080; BCOOl 165; BC001356; BC001463; BC002548; BC002666; BC006456; BE049439; BE328243; BE549540; BE645480; BE669858; BE674118; BE676543; BE788439; BE788984; BE886225; BE888744; BE966604; BFl 10588; BF223193; BF446719; BF509371; BF589359; BG035151; BG256677; BG260886; BG271923; BG291961; BG538627; BG545653; D43949; H98105; H99792; L03419; N47725; N53555; NMJ300062; NM__000593; NM_001295; NM_001511; NM_001548; NM_001549; NMJ)01695; NMJ)01827; NMJ)01862; NM_002053; NM_002201; NM_002346; NM_002450; NM_002462; NM_002462; NM_002463; NM_002534; NM_002535; NM_002592; NM_002759; NM_002796; NM _002801; NM_003113; NM_003810; NM_003902; NM_004030; NM_004223; NM_004335; NM_004643; NM_004802; NM _004832; NM_005101; NM_005138; NMJ305274; NM_005306; NM_005531; NM_005532; NM_005567; NM_005771; NM_005915; NMJ305952; NM_005953; NM_006187; NM_006417; NM_006639; NMJW6700; NM_006820; NM_006994; NMJ)07115; NM_007237; NM_012420; NM_014314; NM_014398; NMJH4705; NM_014788; NM_015907; NM_015961; NM_016323; NMJH6381; NM_016410; NM_016816; NM_016817; NM_017414; NM_017523; NM_017631; NM_017654; NM_017912; NM_018381; NM_021105; NMJ321127; NM_021170; NMJ)22147; NM_022168; NMJ)22750; NM_022763; NMJ)22873; NM_023068; NM_024119; NM_030930; U13699; U57059; U65590; U90548; and X16354. The expression of the same set of genes was moderately increased with individuals typically having few or no anti-ds-DNA antibodies in their serum. The expression changes were measured against samples from healthy individuals with no autoimmune disease and normalized using housekeeping gene standards, such as beta-actin.

[0087] The increased expression of the genes listed above is considered indicative of high level if the expression is at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 fold that of a control, such as the expression of moderate or low IFN gene expressing SLE patient samples. Table 18 gives examples of the power of the genes to differentiate between low and high disease activity in SLE.

[0088] The association between the increased expression of the IFN-regulated genes and an increased level of dsDNA binding (as indicated by a Fair assay) is an important one. The detection of α-dsDNA antibodies in blood is highly specific to SLE. The appearance of α-dsDNA antibodies in serum has been shown to occur many years prior to the onset of clinical SLE, indicating the prognostic potential of this test (Swaak & Smeenk, Arm Rheum Dis. 1985 44:245-51; Arbuckle et al, NEJM 2003 349:1526-33). Further, an increase in α-dsDNA antibodies in the sera of SLE patients has been shown to occur prior to, and predictive of, SLE flares (Swaak & Smeenk, Ann Rheum Dis. 1985 44:245-51; Spronk et al., Lupus 1995 4:86-94; ter Borg et al., Arthritis Rheum. 1990 33:634-43; Ho et al., Arthritis Rheum 2001 44:2342-9; Linnik et al., Arthritis Rheum. 2005 52:1129-37). Although changes in α-dsDNA antibody titers is often used as part of clinical assessment of SLE patients, there are some studies indicating no association between α-dsDNA antibodie changes and SLE flare (WaIz et al., J Rheumatol. 1994 21:2239-41; Esdaile et al., Arthritis Rheum. 1996 39:370-8).

[0089] Thus, the increased expression of IFN-regulated genes is significantly correlated with α-dsDNA antibodies in SLE patients. Without wishing to be bound by a theory, we have therefore demonstrated that the expression of these genes as single markers as well as a group are useful, in any combination, as biomarkers for assessing SLE activity as well as predicting SLE flares. Furthermore, only 20 of the 44 patients had a positive α-dsDNA antibody test in the high IFN-regulated gene signature group, while 3 of the 28 were positive in the low IFN-regulated gene signature group. Without wishing to be bound by a theory, we have therefore shown that this particular signature is more useful than the antibody test because it is more sensitive and specific than the α-dsDNA antibody test for assessing SLE disease activity.

[0090] Accordingly, the invention provides a diagnostic/prognostic gene expression signature, or gene set as set forth in Table 13 and Table 15, that is indicative of two different classes of SLE patients: a high IFN-related gene expression group, wherein the patients typically also exhibit increase in anti-ds-DNA antibodies, and a low IFN-related gene expression group, wherein the patients typically exhibit decreased or no anti-ds- DNA antibodies. Patients with higher expression of IFN-related genes either have more active disease or are at risk of developing or about to develop an SLE flare-up, i.e. increase in disease activity and accompanying clinical symptoms, whereas patients with low IFN-related gene expression, exhibit lower disease activity.

[0091] In another embodiment, the invention provides a diagnostic/prognostic gene expression signature, that is indicative of different WG disease activity. Here, the higher increase in the expression of 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, and 33 of the genes corresponds in linear correlation with the higher BVAS WG diseaseactivity score. The gene set comprises the group consisting of NM_007219; AL562528; AL575509; AI760166; U41070; NM_001706; AI538394; AW592242; NM_007246; AW264036; NM_001995; NM_003059; AK025534; AI768563; AW295340; L32185; L13974; NM_006931; NM_000717; NM_005384; W60806; AI084056; S67779; AI452715; NM_018324; NM_004668; AI374686; AL136944; AF177765; AI767388; NM_005239; BC004564; and AL049435, wherein the increased expression of the genes in a biological sample from an individual is indicative of the individual being affected with WG; and more active disease in WG.

[0092] Also, the more expression of genes in Table 1OB was decreased, the higher the BVAS score in patients with WG was. Accordingly, the expression of genes in Table 1OA correlated positively with increased BVAS sdisease activity score, and the expression of genes in Table 1OB correlated negatively with increased BVAS disease activity score. Therefore, expression of any one or all of these genes or any combination of these genes can be used to assess disease activity in an individual affected with WG.

[0093] In one embodiment, if one looks at the expression of interferon activation pathway genes included in the gene signature of the invention, the expression of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10-20 or more transcripts other than interferon activation pathway encoding genes is also measured. [0094] One skilled in the art can readily select genes that are not part of interferon activation pathway based on the list of genes presented in the tables, figures and text, set forth in this description.

[0095] In one embodiment, the expression of at least one other than genes selected from the group consisting of M63835, X54486, L13210, M33882, AA203213, X99699, AJ225089, U22970, ABOOOl 15, AL047596, AB006746, AL022318, U66711, and X55988 is measured.

[0096] The expression of each sample is standardized against a housekeeping gene expression in that sample. The expression is considered increased if it is increased by at least about 5%-10%, 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80- 90%, 90-100%, 100-200%, 200-300%, 300-400%, 400-500% or even more as compared to a standard or baseline sample from another phenotype group, such as a healthy control, a median of healthy controls, an average of healthy controls, or an artificially created baseline control that is based on, for example the expression of the housekeeping gene in the cell or cell mixture of the biological sample. Such cells or cell combinations can be whole blood; white blood cell mixture; purified cells from the blood, such as monocytes, T-cells, B-cells, neutrophils, NK-cells; kidney biopsy; cells isolated from the urine sediment; or cultured cells from such biological sources as blood, kidney, skin, urine sediment or the like.

[0097] The expression is considered similar or comparable to a positive control sample, if the level of expression is similarly elevated. Similar expression, as used herein means that expression is equal to the baseline control. Similar expression also refers to greater or less than the control by about 100-90%, 90-80%, 80-70%, 70-60%, 60-50%, 50-40%, 40-30%, 30-20%, 20-15%, 15-10%, or 10-5% similarity to the baseline sample.

[0098] The biological sample as defined herein can be any biological sample containing nucleic acids from an individual, preferably human. Such biological samples include blood, tisse biopsies, such as kidney or skin biopsies, primary or cultured cells from blood or tissue biopsies, sputum samples, buccal cell samples, urine, particularly cells sedimented from urine, stool, hair follicles, frozen or otherwise preserved samples from any biological sources and so on.

[0099] In one preferred embodiment, the biological sample is a blood leukocyte sample.

[00100] In one preferred embodiment, the biological sample is a kidney biopsy sample.

[00101] In one preferred embodiment, the biological sample is cells present in the urine sediment.

[00102] In one preferred embodiment, the biological sample is whole blood. Whole blood or total blood leukocytes, or white blood cells are preferred because they allow minimal handling of the sample. Handling, such as cell separation, may change the expression in the cells during the sample preparation. Accordingly, it is preferred, although not necessary, to use cells that have been manipulated as little as possible. Whole blood or whole blood white blood cells or urine sediment cells provide thus one optimal biological sample material for analyzing the expression patterns of the present invention.

[00103] In one embodiment, the biological sample is a kidney biopsy or cells from the urine sediment. When the sample is a kidney biopsy or cells from the urine sediment, one preferred embodiment, provides a gene transcript set, or a kidney gene set that comprises at least 1, 2, 3, 4, 5, or 6 transcripts from the group selected from the transcripts corresponding to genes RSAD2/CIG5, Corf29, IFITl, IFIT3, GIP2, and LY6E.

[00104] Transcript level detection methods: The genes identified as being differentially expressed in autoimmune diseases according to the present invention may be used in a variety of nucleic acid detection assays to detect or quantify the expression level of a gene or multiple genes in a given sample. Any hybridization assay format may be used, including solution based and solid support based assay formats. Methods of detecting gene expression are well known to one skilled in the art and include, for example, Northern-blot hybridization, ribonuclease protection assay, and reverse transcriptase polymerase chain reaction (RT-PCR) based methods. The different RT- PCR based techniques are the most suitable quantification method for diagnostic purposes of the present invention, because they are very sensitive and thus require only a small sample size which is desirable for a diagnostic test. A number of quantitative RT-PCR based methods have been described and are useful in measuring the amount of transcripts according to the present invention. These methods include RNA quantification using PCR and complementary DNA (cDNA) arrays (Shalon et al., Genome Research 6(7):639- 45, 1996; Bernard et al., Nucleic Acids Research 24(8): 1435-42, 1996), and 5 'nuclease assay or real-time RT-PCR (Holland et al. Proc Natl Acad Sci USA 88: 7276-7280, 1991).

[00105] Methods using RT-PCR and internal standards differing by length or restriction endonuclease site from the desired target sequence allowing comparison of the standard with the target using gel electrophoretic separation methods followed by densitometric quantification of the target have also been developed and can be used to detect the amount of the transcripts according to the present invention (see, e.g., U.S. Patent Nos. 5,876,978; 5,643,765; and 5,639,606.

[00106] RNA quantification methods based on mass spectrometry, such as MALDI- TOF, can also be used as well known by the skilled artisan (see, for example Sequenom, Inc, CA).

[00107] Also methods based on RNase protection assays (see, e.g., High Throughput Genomics, Inc. Tucson, CA) or amplification of ligatable probes (see, e.g., ILLUMINA®, Illumina Inc., San Diego, CA) can be used.

[00108] For example,use of the qNPA method (High Throughput Genomics Inc., Tucson, AZ ) allows using only reagent addition and washes to the sample, and does not involve any RNA extraction, amplification, purification or biosynthetic steps. All the reagents that bind to the ArrayPlate are synthetic and structurally unaltered by the assay. The qNPA produces a stoichiometric amount of the specific nuclease protection probe for each gene, or a quantative amount of a chemical mirror image. [00109] In another example, the SENTRIX® Human-6 and HumanRef-8 Expression BeadChips enable generation of genome-wide expression profiles for multiple samples on a single BeadChip.

[00110] Methods and assays of the invention are most efficiently designed with array, chip, or bead hybridization based methods designed for detecting the expression levels of a large number of genes. Assays and methods of the invention may utilize available formats to simultaneously screen from, for example, at least about 6 to about 100, preferably about 1000, more preferably about 10,000 and most preferably about 1,000,000 or more different nucleic acid hybridizations. Preferred method of detecting the gene set expression signatures of the invention include nucleic acid chip- or bead- based technologies that are well suited in automation and screening of a large number of genes in a large number of individuals.

[00111] Nucleic acid arrays that are useful in the present invention include, but are not limited to those that are commercially available from Affymetrix (Santa Clara, CA) under the brand name GeneChip7. Example arrays are shown on the website at affymetrix.com.

[00112] Examples of gene expression monitoring, and profiling methods are shown in U.S. Patents Nos. 5,800,992, 6,013,449, 6,020,135, 6,033,860, 6,040,138, 6,177,248 and 6,309,822.

[00113] The nucleic acids from the biological sample may be isolated and purified or analyzed directly. In the preferred embodiment, the nucleic acids are isolated and/or purified using standard nucleic acid isolation and/or purification techniques that are well known and readily available to on skilled in the art. Direct analysis can be performed using, for example, microfluidic chips.

[00114] Methods for conducting polynucleotide hybridization assays have been well developed in the art. Hybridization assay procedures and conditions will vary depending on the application and are selected in accordance with the general binding methods known including those referred to in: Maniatis et al. Molecular Cloning: A Laboratory Manual (2nd Ed. Cold Spring Harbor, N. Y, 1989); Berger and Kimmel Methods in Enzymology, Vol. 152, Guide to Molecular Cloning Techniques (Academic Press, Inc., San Diego, CA, 1987); Young and Davism, P.N.A.S, 80: 1194 (1983). Methods and apparatus for carrying out repeated and controlled hybridization reactions have been described, for example, in US patent 5,871,928, 5,874,219, 6,045,996 and 6,386,749, 6,391,623 each of which are incorporated herein by reference.

[00115] In one embodiment, a FLOW-THRU® chip, such as that disclosed in U.S. Patent No. 5,843,767, which disclosure in incorporated herein by reference in its entirety, is used with present invention. The FLOW-THRU® chip generally comprises an array of micro-channels extending through a solid support. Each micro-channel contains a probe specific for a gene selected from Table 6; and different channels contain different probes for different genes or for the same gene. The hybridization and/or binding reactions take place by providing fluidic flow through of the sample through the chip.

[00116] Alternatively, the transcript expression assay can be conducted using microbeads labeled with different spectral property and/or fluorescent (or colorimetric). Technologies such as CYVERA technology (from ILLUMINA inc.) can be easily optimized to analyze the gene sets or sub-sets of the invention. For example, polystyrene microspheres are provided by Luminex Corp, Austin, Tex. that are internally dyed with two spectrally distinct fluorochromes. Using precise ratios of these fluorochromes, a large number of different fluorescent bead sets (e.g., 100 sets) can be produced. Each set of the beads can be distinguished by its spectral address, a combination of which allows for measurement of a large number of analytes in a single reaction vessel. A third fluorochrome coupled to a reporter molecule quantifies the biomolecular interaction that has occurred at the microsphere surface. These different fluorescent bead sets can be used to label the reference nucleic acids targeting different SNP sites on a test DNA by using standard nucleic acid chemical synthesis methods or by PCR amplification using primers labeled with the beads (e.g., primers modified with 5' amine for coupling to carboxylated microsphere or bead).

[00117] In another embodiment of the present invention, protein and tissue arrays can also be used. In protein arrays, the probes are specific for protein products of the genes of Table 6 or fragments thereof. These probes can be, but are not limited to, antibodies, cell surface receptors, secreted proteins, receptor ligands, irnmunoliposom.es, immunotoxins, cytosolic proteins, nuclear proteins, and functional motifs thereof that specifically bind to the protein products of the genes of Table 6 or fragments thereof. The probes are immobilized on a solid support to form an array and provides a specific binding partner for the protein products of the genes of Table 6 or fragments thereof. The supports can be either plates (glass, plastics, or silicon) or membranes made of nitrocellulose, nylon, or polyvinylidene difluoride (PVDF).

[00118] To use a protein array in studying protein expression patterns, a protein array is incubated with a protein sample prepared under the conditions that native protein- protein interactions are minimized. After incubation, unbound or non-specific binding proteins can be removed with several washes. Proteins specifically bound to their respective binding partners on the array are then detected. Because the binding partners are immobilized in a predetermined order, the identity of the protein captured at each position is therefore known. Measurement of protein amount at all positions on the array thus reflects the protein expression pattern in the sample.

[00119] The quantities of the proteins trapped on the array can be measured in several ways. The amount of proteins bound to each antibody represents the level of the specific protein in the sample. If a specific group of proteins are interested, they can be detected by agents which specifically recognize them. Other methods, like immunochemical staining, surface plasmon resonance, matrix-assisted laser desorption/ionization-time of flight, can also be used to detect the captured proteins.

[00120] Tissue arrays consist of regular arrays of cores of embedded biological tissue arranged in a sectionable block typically made of the same embedding material used originally for the tissue in the cores. The new blocks may be sectioned by traditional means (microtomes etc.) to create multiple nearly identical sections each containing dozens, hundreds or even over a thousand different tissue types.

[00121] In tissue array, the tissue sample is assayed for differential expression of the protein products of the genes of Table 6. When analyzing the intracellular localization of a target protein, standard cytoimmunostaining techniques known to skilled artisans can be employed. Cytoimmunostaining may be performed directly on frozen sections of cells or tissues or, preceded by fixing cells with a fixative that preserves the intracellular structures, followed by permeablization of the cell to ensure free access of the probes. The step of permeablization can be omitted when examining cell-surface antigens. After incubating the cell preparations with a probe such as an antibody specific for the target, unbound antibody is removed by washing, and the bound antibody is detected either directly (if the primary antibody is labeled) or, more commonly, indirectly visualized using a labeled secondary antibody. In localizing a target polypeptide to a specific subcellular structure in a cell, co-staining with one or more marker antibodies specific for antigens differentially present in such structure is preferably performed. A battery of organelle specific antibodies is available in the art. Non-limiting examples include plasma membrane specific antibodies reactive with cell surface receptor Her2, endoplasmic reticulum (ER) specific antibodies directed to the ER resident protein Bip, Golgi specific antibody α-adaptin, and cytokeratin specific antibodies which will differentiate cytokeratins from different cell types (e.g. between epithelial and stromal cells) or in different species. To detect and quantify the immunospecific binding, digital image analysis system coupled to conventional or confocal microscopy can be employed.

[00122] Assays to monitor the expression of a gene or genes of Table 6 may utilize any available means of monitoring for changes in the expression level of the nucleic acids of the invention. As used herein, an agent is said to modulate the expression of a nucleic acid of the invention if it is capable of up or down regulating expression of the nucleic acid in a cell.

[00123] In one assay format, gene chips containing probes to at least two genes selected from Table 6 may be used to directly monitor or detect changes in gene expression in the treated or exposed cell. High density gene chips and their uses are described in U.S. Patent No. 6,040,138 to Lockhart et al., which is incorporated herein by reference. An alternative format to the gene chip is the flow-through chip disclosed in U.S. Patent No. 5,843,767 to Beattie, which is incorporated herein by reference.

[00124] Additional assay formats may be used to monitor the ability of the agent to modulate the expression of one or more genes identified in Table 6. For instance, as described above, mRNA expression may be monitored directly by hybridization of probes to the nucleic acids of Table 6. Cell lines are exposed to the agent to be tested under appropriate conditions and time and total RNA or mRNA is isolated by standard procedures such those disclosed in Sambrook et al. (1989), Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory Press.

[00125] Further, applicants have also discovered that the level of expression is also proportional to the severity of SLE. The higher level of expression corresponds with a higher SLEDAI (Systematic Lupus Erythematosus Disease Activity Index) score which measures disease activity and severity.

[00126] The present inventor has examined tissue samples from normal individuals, SLE, and other autoimmune diseases, such as WG, and RA, to identify a gene set associated with SLE. Changes in gene expression, also referred to as expression profiles or expression pattern, provide useful markers for diagnostic uses as well as markers that can be used to monitor disease states, disease progression, drug toxicity, drug efficacy and drug metabolism.

[00127] Uses for the Gene Expression Patterns of Autoimmune Disease Markers as Diagnostics: As described herein, the expression profiles of the genes of Table 6 may be used as diagnostic markers for the prediction or identification of autoimmune diseases, such as SLE and WG. For instance, a tissue sample, such as blood sample or kidney biopsy or cells from the urine sediment, or other sample from a patient may be assayed by any of the methods described herein or by any other method known to those skilled in the art, and the expression levels from a gene or genes from Table 6 may be compared to the expression levels found in normal sample. Expression profiles generated from the tissue, blood, or other sample that substantially resemble an expression profile from normal or diseased tissue may be used, for instance, to aid in disease diagnosis. Particularly, for example, the genes of Table 1 or Table 4 are upregulated specifically in SLE patients without being upregulated in other rheumatic autoimmune diseases, such as WG or RA. Comparison of the expression data, as well as available sequence or other information may be done by researcher or diagnostician or may be done with the aid of a computer and databases. [00128] Furthermore, the genes of Table 6, Table 7, Table 8, Table 13, Table 14, Table 15, Table 16 and Table 17 can also detect drug-induced lupus. Some drugs can induce a lupus like syndrome as a side effect resulting from long term use, which can be diagnosed with certainty only by resolution of symptoms and their failure to recur after stopping the medication. Lupus-inducing drugs are typically those used to treat chronic diseases. No obvious common factor links the drugs that are likely to cause lupus, which includes medicines used to treat heart disease, thyroid disease, hypertension, neuropsychiatric disorders, certain anti-inflammatory agents and antibiotics. At least eighty (80) drugs currently in use can cause drug-induced lupus. However, most cases have been associated with procainamide (Pronestyl), hydralazine (Apresoline), and quinidine (Quinaglute). The risk for developing lupus-like disease from any of the other seventy seven (77) drugs is low or very low, with some drugs only one or two cases have been reported. Other specific drugs that have been linked to drug-induced lupus include, but are not limited to, Enbrel, Remicade, Celebrex, beta-blockers, penicillin, tetracyclines, dilantin, INH, oral contraceptives, and various vaccines.

[00129] Use of the SLE Markers for Monitoring Disease Progression

[00130] As described above, the genes and gene expression information of Table 6 can also be used as markers for the monitoring of disease activity. For instance, a tissue, blood, or other sample from a patient may be assayed by any of the methods described above, and the expression levels in the sample from a gene or genes from Table 6 may be compared to the expression levels found in normal tissue. The gene expression pattern can be monitored over time to track activity of the disease. Comparison of the expression pattern, as well as available sequence or other information may be done by researcher or diagnostician or may be done with the aid of a computer and databases.

[00131 ] Use of the SLE Markers for Screening Tests

[00132] According to the present invention, the genes identified in Table 6 can be used as markers to evaluate the effects of a candidate drug or agent on a cell, particularly a cell from a SLE tissue sample. [00133] Alternatively, a patient can be treated with a drag candidate and the activity of SLE is monitored over time. This method comprises treating the patient with an agent, obtaining a tissue sample from the patient, extracting a gene product sample from the tissue sample, contacting the gene product sample with probes which specifically bind with gene products of Table 6, and comparing the binding pattern over time to determine the effect of the agent on the activity of SLE.

[00134] In another embodiment, the genes identified in Table 6 can be used as markers to screen agents that can cause SLE or SLE-like conditions. Preferably, the screening is accomplished on a tissue or cellular sample. The method comprises exposing a cell to a test agent, extracting a gene product sample from the tissue sample, contacting the gene product sample with probes which specifically bind with gene products of Table 6, and comparing the binding pattern with normal and SLE cells to determine the effect of the agent on the cell or tissue samples.

[00135] In one embodiment, the invention provides a personalized screen for an SLEAVG patient to select a drug that most effectively normalizes the SLE/WG specific gene expression profile. Here, patient's cells are cultured and exposed to medicines and the expression of the genes, selected from Table 6, are monitored and compared to control and disease samples. The drag that induces improvement in the gene expression profile in the cultured cells from the patient, can then be selected to treat the SLEAVG patient.

[00136] A candidate drag or agent can be screened for the ability to stimulate the transcription or expression of a given marker or markers (drag targets) or to down regulate or counteract the transcription or expression of a marker or markers. According to the present invention, one can also compare the specificity of drags' effects by looking at the number of markers affected by different drags and comparing them. Similar sets of markers identified for two drags indicate similar effects.

[00137] The agents to be screened in the methods of the present invention can be, for example, peptides, small molecules, vitamin derivatives, as well as carbohydrates, dominant negative proteins, DNA encoding these proteins, antibodies to these proteins, peptide fragments of these proteins or mimics of these proteins may be introduced into cells to affect function. "Mimic" as used herein refers to the modification of a region or several regions of a peptide molecule to provide a structure chemically different from the parent peptide but topographically and functionally similar to the parent peptide. A skilled artisan can readily recognize that there is no limit as to the structural nature of the agents of the present invention.

[00138] In another assay format, cells or cell lines are first identified which express the gene products of the invention physiologically. Cell and/or cell lines so identified would be expected to comprise the necessary cellular machinery such that the fidelity of modulation of the transcriptional apparatus is maintained with regard to exogenous contact of a drug or agent with appropriate surface transduction mechanisms and/or the cytosolic cascades. Such cell lines may be, but are not required to be, derived from tissue samples of individuals suffering from SLE. Further, such cells or cell lines may be transduced or transfected with an expression vehicle (e.g., a plasmid or viral vector) construct comprising an operable non translated 5' promoter containing end of the structural gene encoding the instant gene products fused to one or more antigenic fragments, which are peculiar to the instant gene products, wherein said fragments are under the transcriptional control of said promoter and are expressed as polypeptides whose molecular weight can be distinguished from the naturally occurring polypeptides or may further comprise an immunologically distinct tag. Such a process is well known in the art (see Sambrook et al., (1989) Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory Press).

[00139] Cells or cell lines transduced or transfected as outlined above are then contacted with drugs or agents under appropriate conditions. For example, the drug or agent comprises a pharmaceutically acceptable excipient and is contacted with cells in an aqueous physiological buffer such as phosphate buffered saline (PBS) at physiological pH, Eagles balanced salt solution (BSS) at physiological pH, PBS or BSS comprising serum or conditioned media comprising PBS or BSS and serum incubated at 37°C. Said conditions may be modulated as necessary by one of skill in the art. Subsequent to contacting the cells with the drug or agent, said cells will be disrupted and the polypeptides of the lysate are fractionated such that a polypeptide fraction is pooled and contacted with an antibody to be further processed by immunological assay (e.g., .ELISA, immunoprecipitation or Western blot). The pool of proteins isolated from the "agent contacted" sample will be compared with a control sample where only the excipient is contacted with the cells; and an increase or decrease in the immunologically generated signal from the "drug or agent contacted" sample compared to the control will be used to distinguish the effectiveness of the drug or agent.

[00140] Another embodiment of the present invention provides methods for identifying drugs or agents that modulate the levels, concentration or at least one activity of a protein(s) encoded by the genes of Table 6. Such methods or assays may utilize any means of monitoring or detecting the desired activity.

[00141] In one format, the relative amounts of a protein of the invention between a cell population that has been exposed to the drug or agent to be tested compared to an un exposed control cell population may be assayed. In this format, probes such as specific antibodies are used to monitor the differential expression of the protein in the different cell populations. Cell lines or populations are exposed to the drug or agent to be tested under appropriate conditions and time. Cellular lysates may be prepared from the exposed cell line or population and a control, unexposed cell line or population. The cellular lysates are then analyzed with probes, such as specific antibodies.

[00142] The genes which are assayed according to the present invention are typically in the form of mRNA or reverse transcribed mRNA. The genes may or may not be cloned; and the genes may or may not be amplified. The cloning itself does not appear to bias the representation of genes within a population. However, it may be preferable to use polyA+ RNA as a source, as it can be used with less processing steps.

[00143] Probes based on the sequences of the genes described herein may be prepared by any commonly available method. Oligonucleotide probes for assaying the tissue or cell sample are preferably of sufficient length to specifically hybridize only to appropriate, complementary genes or transcripts. Typically the oligonucleotide probes will be at least 10, 12, 14, 16, 18, 20 or 25 nucleotides in length. In some cases longer probes of at least 30, 40, 50, 60 or 70 nucleotides will be desirable. It is preferable that more than one probe specific for each gene is used in the assay.

[00144] Oligonucleotide Probe design

[00145] One of skill in the art will appreciate that an enormous number of array designs are suitable for the practice of this invention. The high density array will typically include a number of probes that specifically hybridize to the sequences of interest. Methods of producing probes for a given gene or genes are disclosed in WO 99/32660, which is incorporated herein by reference. In addition, in a preferred embodiment, the array will include one or more control probes. High density array chips of the invention include "test probes." Test probes may be oligonucleotides that range from about 5 to about 500 or about 10 to about 100 nucleotides, more preferably from about 20 to about 80 nucleotides and most preferably from about 50 to about 70 nucleotides in length. In other particularly preferred embodiments the probes are about 20 to about 25 nucleotides in length. In another preferred embodiment, test probes are double or single strand DNA sequences. DNA sequences are isolated or cloned from natural sources or amplified from natural sources using natural nucleic acid as templates. These probes have sequences complementary to particular subsequences of the genes whose expression they are designed to detect. Thus, the test probes are capable of specifically hybridizing to the target nucleic acid they are to detect.

[00146] In addition to test probes that bind the target nucleic acid(s) of interest, the high density array can contain a number of control probes. The control probes fall into three categories referred to herein as (1) normalization controls; (2) expression level controls; and (3) mismatch controls.

[00147] Normalization controls are oligonucleotide or other nucleic acid probes that are complementary to labeled reference oligonucleotides or other nucleic acid sequences that are added to the nucleic acid sample. The signals obtained from the normalization controls after hybridization provide a control for variations in hybridization conditions, label intensity, "reading" efficiency and other factors that may cause the signal of a perfect hybridization to vary between arrays. In a preferred embodiment, signals (e.g., fluorescence intensity) read from all other probes in the array are divided by the signal (e.g., fluorescence intensity) from the control probes thereby normalizing the measurements.

[00148] Virtually any probe may serve as a normalization control. However, it is recognized that hybridization efficiency varies with base composition and probe length. Preferred normalization probes are selected to reflect the average length of the other probes present in the array, however, they can be selected to cover a range of lengths. The normalization controls can also be selected to reflect the (average) base composition of the other probes in the array, however in a preferred embodiment, only one or a few probes are used and they are selected such that they hybridize well (i. e., no secondary structure) and have minimal cross match with non-specific targets.

[00149] Typical expression level control probes have sequences complementary to subsequences of constitutively expressed housekeeping genes including, but not limited to the 3 actin gene, the transferrin receptor gene, the GAPDH gene, and the like. Examples of other useful housekeeping genes are provided elsewhere in this spacification.

[00150] Mismatch controls are generally not required when using probes of about 60 to about 70 nucleotides. However, when using shorter probes, mismatch controls may also be provided for the probes to the target genes, for expression level controls or for normalization controls. Mismatch controls are oligonucleotide probes or other nucleic acid probes identical to their corresponding test or control probes except for the presence of one or more mismatched bases. A mismatched base is a base selected so that it is not complementary to the corresponding base in the target sequence to which the probe would otherwise specifically hybridize. One or more mismatches are selected such that under appropriate hybridization conditions (e.g., stringent conditions) the test or control probe would be expected to hybridize with its target sequence, but the mismatch probe would not hybridize (or would hybridize to a significantly lesser extent). Preferred mismatch probes contain a central mismatch. Thus, for example, where a probe is a twenty mer, a corresponding mismatch probe will have the identical sequence except for a single base mismatch (e.g., substituting a G, a C or a T for an A) at any of positions 6 through 14 (the central mismatch).

[00151] Mismatch probes thus provide a control for non specific binding or cross hybridization to a nucleic acid in the sample other than the target to which the probe is directed. Mismatch probes also indicate whether a hybridization is specific or not. For example, if the target is present the perfect match probes should be consistently brighter than the mismatch probes. In addition, if all central mismatches are present, the mismatch probes can be used to detect a mutation. The difference in intensity between the perfect match and the mismatch probe provides a good measure of the concentration of the hybridized material.

[00152] However, when using the preferred embodiment of about 60-mer to about 70 mer probes, mismatch probes are not required as the probes are sufficiently long that a single mismatch does not effect an appreciable difference in binding efficiency.

[00153] Nucleic Acid Samples

[00154] As is apparent to one of ordinary skill in the art, nucleic acid samples used in the methods and assays of the invention may be prepared by any available method or process. Methods of isolating total RNA are also well known to those of skill in the art. For example, methods of isolation and purification of nucleic acids are described in detail in Chapter 3 of Laboratory Techniques in Biochemistry and Molecular Biology: Hybridization With Nucleic Acid Probes, Part I - Theory and Nucleic Acid Preparation, Tijssen, (1993) (editor) Elsevier Press. Such samples include RNA samples, but also include cDNA synthesized from a mRNA sample isolated from a cell or tissue of interest. Such samples also include DNA amplified from the cDNA, and an RNA transcribed from the amplified DNA. One of skill in the art would appreciate that it is desirable to inhibit or destroy RNase present in homogenates before homogenates can be used.

[00155] Biological samples may be of any biological tissue or fluid or cells from any organism as well as cells raised in vitro, such as cell lines and tissue culture cells. Frequently the sample will be a "clinical sample" which is a sample derived from a patient. Typical clinical samples include, but are not limited to, sputum, blood, blood cells (e.g., white blood cells or leukocytes), tissue or fine needle biopsy samples, urine, peritoneal fluid, and pleural fluid, or cells therefrom.

[00156] Biological samples may also include sections of tissues, such as frozen sections or formalin fixed sections taken for histological purposes.

[00157] Solid Supports

[00158] Solid supports containing oligonucleotide probes for differentially expressed genes of the invention can be filters, polyvinyl chloride dishes, silicon or glass based chips, etc. Such wafers and hybridization methods are widely available, for example, those disclosed by U.S. Patent No. 6,040,138 to Lockhart et al. and U.S. Patent No. 5,843,767 to Beattie. Any solid surface to which oligonucleotides can be bound, either directly or indirectly, either covalently or non covalently, can be used. A preferred solid support is a high density array or DNA chip. These contain a particular oligonucleotide probe in a predetermined location on the array. Each predetermined location may contain more than one molecule of the probe, but each molecule within the predetermined location has an identical sequence. Such predetermined locations are termed features. There may be, for example, about 2, 10, 100, 1000 to 10,000; 100,000 or 400,000 of such features on a single solid support. The solid support, or the area within which the probes are attached may be on the order of a square centimeter (see, e.g., FLOW-THRU CHIP™, Metrigenix Corporation, Toronto, Canada).

[00159] Oligonucleotide probe arrays for expression monitoring can be made and used according to any techniques known in the art (see for example, Lockhart et al. (1996), Nat. Biotechnol., 14: 1675 1680; McGaIl et al. (1996), PNAS USA, 93:13555-13460). Such probe arrays may contain at least two or more oligonucleotides that are complementary to or hybridize to two or more of the genes described herein. Such arrays may also contain oligonucleotides that are complementary or hybridize to at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 50, 70, 100 or more the genes described herein.

[00160] Methods of forming high density arrays of oligonucleotides with a minimal number of synthetic steps are known. The oligonucleotide analogue array can be synthesized on a solid substrate by a variety of methods, including, but not limited to, light directed chemical coupling, and mechanically directed coupling (U.S. Patent No. 5,143, 854 to Pirrung et al.; U.S. Patent No. 5,800,992 to Fodor et al.; U.S. Patent No. 5,837,832 to Chee et al; which are incorporated herein by reference).

[00161] In brief, the light directed combinatorial synthesis of oligonucleotide arrays on a glass surface proceeds using automated phosphoramidite chemistry and chip masking techniques. In one specific implementation, a glass surface is derivatized with a silane reagent containing a functional group, e.g., a hydroxyl or amine group blocked by a photolabile protecting group. Photolysis through a photolithogaphic mask is used selectively to expose functional groups which are then ready to react with incoming 5' photoprotected nucleoside phosphoramidites. The phosphoramidites react only with those sites which are illuminated (and thus exposed by removal of the photolabile blocking group). Thus, the phosphoramidites only add to those areas selectively exposed from the preceding step. These steps are repeated until the desired array of sequences has been synthesized on the solid surface. Combinatorial synthesis of different oligonucleotide analogues at different locations on the array is determined by the pattern of illumination during synthesis and the order of addition of coupling reagents.

[00162] In addition to the foregoing, additional methods which can be used to generate an array of oligonucleotides on a single substrate are described in U.S. Patent No. 5,677,195 to Winkler et al., which is incorporated herein by reference. High density nucleic acid arrays can also be fabricated by depositing premade or natural nucleic acids in predetermined positions. Synthesized or natural nucleic acids are deposited on specific locations of a substrate by light directed targeting and oligonucleotide directed targeting. Another embodiment uses a dispenser that moves from region to region to deposit nucleic acids in specific spots.

[00163] Hybridization

[00164] Nucleic acid hybridization simply involves contacting a probe and target nucleic acid under conditions where the probe and its complementary target can form stable hybrid duplexes through complementary base pairing (see U.S. Patent No. 6,333,155 to Lockhart et al, which is incorporated herein by reference). The nucleic acids that do not form hybrid duplexes are then washed away leaving the hybridized nucleic acids to be detected, typically through detection of an attached detectable label. It is generally recognized that nucleic acids are denatured by increasing the temperature or decreasing the salt concentration of the buffer containing the nucleic acids.

[00165] Under low stringency conditions (e.g., low temperature and/or high salt) hybrid duplexes (e.g., DNA DNA, RNA RNA or RNA DNA) will form even where the annealed sequences are not perfectly complementary.

[00166] Thus specificity of hybridization is reduced at lower stringency. Conversely, .at higher stringency (e.g., higher temperature or lower salt) successful hybridization requires fewer mismatches. One of skill in the art will appreciate that hybridization conditions may be selected to provide any degree of stringency. In a preferred embodiment, hybridization is performed at low stringency, in this case in 6x SSPE T at 37°C (0.005% Triton x 100) to ensure hybridization and then subsequent washes are performed at higher stringency (e.g., 1 x SSPE T at 37⁰C) to eliminate mismatched hybrid duplexes. Successive washes maybe performed at increasingly higher stringency (e.g., down to as low as 0.25x SSPE-T at 37°C to 50°C) until a desired level of hybridization specificity is obtained. Stringency can also be increased by addition of agents such as formamide. Hybridization specificity may be evaluated by comparison of hybridization to the test probes with hybridization to the various controls that can be present (e.g., expression level control, normalization control, mismatch controls, etc.).

[00167] In general, there is a tradeoff between hybridization specificity (stringency) and signal intensity. Thus, in a preferred embodiment, the wash is performed at the highest stringency that produces consistent results and that provides signal intensity greater than approximately 10% of the background intensity. Thus, in a preferred embodiment, the hybridized array may be washed at successively higher stringency solutions and read between each wash. Analysis of the data sets thus produced will reveal a wash stringency above which the hybridization pattern is not appreciably altered and which provides adequate signal for the particular oligonucleotide probes of interest.

[00168] Signal Detection [00169] The hybridized nucleic acids are typically detected by detecting one or more labels attached to the sample nucleic acids. The labels may be incorporated by any of a number of means well known to those of skill in the art (see U.S. Patent No. 6,333,155 to Lockhart et al, which is incorporated herein by reference). Commonly employed labels include, but are not limited to, biotin, fluorescent molecules, radioactive molecules, chromogenic substrates, chemiluminescent labels, enzymes, and the like. The methods for biotinylating nucleic acids are well known in the art, as are methods for introducing fluorescent molecules and radioactive molecules into oligonucleotides and nucleotides.

[00170] When biotin is employed, it is detected by avidin, streptavidin or the like, which is conjugated to a detectable marker, such as an enzyme (e.g., horseradish peroxidase) or radioactive label (e.g., 32P, 35S, 33P). Enzyme conjugates are commercially available from, for example, Vector Laboratories, Burlingame, CA. Steptavidin binds with high affinity to biotin, unbound stretavidin is washed away, and the presence of horseradish peroxidase enzyme is then detected using a substrate in the presence of peroxide and appropriate buffers. The binding reaction may be detected using a microscope equipped with a visible light source and a CCD camera (Princeton Instruments, Princeton, N.J.).

[00171] Detection methods are well known for fluorescent, radioactive, chemiluminescent, chromogenic labels, as well as other commonly used labels. Briefly, fluorescent labels can be identified and quantified most directly by their absorption and fluorescence emission wavelengths and intensity. A microscope/camera setup using a light source of the appropriate wavelength is a convenient means for detecting fluorescent label. Radioactive labels may be visualized by standard autoradiography, phosphor image analysis or CCD detector. Other detection systems are available and known in the art.

[00172] Databases

[00173] The present invention includes relational databases containing sequence information, for instance for the genes of Table 6, as well as gene expression information for SLE, other rheumatic autoimmune diseases, such as Wegener's Granulomatosus, Rheumatoid Arthritis, and Inflammatory Bowel Disease (Crohn's and Ulcerative Colitis), and normal tissue. Databases may also contain information associated with a given sequence or tissue sample such as descriptive information about the gene associated with the sequence information, or descriptive information concerning the clinical status of the tissue sample, or the patient from which the sample was derived. The database may be designed to include different parts, for instance a sequences database and a gene expression database.

[00174] Methods for the configuration and construction of such databases are widely available, for instance in U.S. Patent 5,953,727 to Akerblom et al., which is herein incorporated by reference.

[00175] The databases of the invention may be linked to an outside or external database. In a preferred embodiment, the external database is GenBank and the associated databases maintained by the National Center for Biotechnology Information (NCBI).

[00176] Any appropriate computer platform may be used to perform the necessary comparisons between sequence information, gene expression information and any other information in the database or provided as an input. For example, a large number of computer workstations are available from a variety of manufacturers, such has those available from Silicon Graphics. Client server environments, database servers and networks are also widely available and appropriate platforms for the databases of the invention.

[00177] The databases of the invention may be used to produce, among other things, electronic Northerns to allow the user to determine the cell type or tissue in which a given gene is expressed and to allow determination of the abundance or expression level of a given gene in a particular tissue or cell.

[00178] The databases of the invention may also be used to present information identifying the expression level in a tissue or cell of a set of genes comprising at least one gene in Table 6 comprising the step of comparing the expression level of at least one gene in Table 6 in the tissue to the level of expression of the gene in the database. Such methods may be used to predict the physiological state of a given tissue by comparing the level of expression of a gene or genes in Table 6 from a sample to the expression levels found in normal tissue or tissues of other rheumatic autoimmune diseases. Such methods may also be used in the drug or agent screening assays as described above.

[00179] Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative examples, make and utilize the compounds of the present invention and practice the claimed methods. The following example is given to illustrate the present invention. It should be understood that the invention is not to be limited to the specific conditions or details described in this example.

[00180] Following is a list of housekeeping genes that are useful in determining the expression levels in individuals according to the present invention derived from the article "Human Housekeeping genes are compact," published in Trends in Genetics 19, 362-365 (2003). Genes designated by asterisk are in popular use as reference in real-time PCR. Any of the known housekeeping genes, such as the genes presented herein by the public accession ID numbers, can be used in the methods of the present invention. A non- limiting list of examples of housekeeping genes include NM_001101; *NM_000034; *NM_002046; *NM_000291; *NM_005566; *NM_002954; *NM_000981; *NM_000975; *NM_007363; *NMJ)04309; *NM_000994; *NM_022551; *NM_007355; NM_004515; NM_004651; NM_004888; NM_003334; NM_001320; NM_003915; NM_001250; NM_001904; NM_003753; NM_004541; NM_001654; NM_002967; NMJ)Ol 183; NM_003526; NM_004718; NM_004436; NM_001207; NM_004907; NM_004889; NM_003769; NM_003910; NMJ)OOlOO; NM_004785; NMJ)Ol 120; NMJ)OOl 82; NM_003377; NM_003576; NM_000918; NM_004584; NM_004952; NM_004308; NM_003190; NM_004640; NM_001064; NM_002117; NM_004161; NM_003339; NM_003969; NM_000516; NM_002819; NMJ)OlOOl; NM_004649; NM_000175; NM_001867; NMJ)Ol 967; NM_001863; NM_001997; NM_002088; NM_001862; NM_004255; NMJXH788; NM_004781; NM_003801; NM_004643; NM_001537; NM_003680; NM_003345; NM_002568; NM_001487; NM_001861; NM_004890; NM_002812; NM_004926; NM_002539; NM_000979; NM_000977; NM_001015; NM_001760; NM_003973; NM_002815; NM_000367; NM_000973; NM_004689; NM_001848; NM_004068; NM_001687; NM_004197; NM_001028; NM_001022; NM_004759; NMJ)01623; NM_004894; NM_002375; NM_001013; NM_003779; NMJ)01296; NM_001009; NM_003021; NM_004285; NM_004142; NM_001950; NM_003815; NMJ)Ol 119; NMJ)OIl 11; NM_003466; NM_001155; NM_003465; NM_003186; NM_000802; NM_004924; NM_002931; NM_000020; NM_001785; NM_004339; NM_003860; NM_000214; NM_002167; NM_001664; NM_003166; NM_001746; NM_001662; NMJW1660; NM_001658; NM_003313; NM_001494; NM_003145; NMJ)Ol 619; NM_001420; NMJ)04930; NMJKM596; NM_004168; NM_004156; NMJ)04910; NM_004517; NM_004494; NM_004121; NMJ)04404; NM_004394; NM_004383; NM_004074; NMJ)04039; NM_001053; NM_001328; NMJXU273; NM_003430; NM_003314; NM_003217; NMJ)03132; NM_000199; NM_002818; NM_002733; NM_002631; NM_002574; NM_002512; NM_002455; NM_002444; NMJ)00529; NM_003573; NM_002315; NM_000884; NM_003641; NM_000841; NM_002070; NM_001493; NMJ)02048; NM_002032; NM_001418; NM_001350; NM_001843; NMJ)01728; NM_001667; NM_001659; NM_003746; NM_002127; NM_004712; NM_003475; NM_004046; NM_001894; NM_003795; NM_001909; NM_002792; NM_002799; NM_002300; NM_004176; NM_002796; NMJ)02794; NM_002793; NM_002473; NMJXU810; NM_002624; NM_004710; NM_001127; NM_002107; NM_003899; NM_003406; NM_002419; NMJ)Ol 130; NM_003379; NM_002636; NM_002622; NM_001823; NM_003405; NM_002939; NM_003562; NM_001916; NM_002823; NM_003096; NM_003321; NM_003404; NM_002946; NM_004356; NM_001743; NM_004231; NM_004893; NM_004146; NM_002128; NM_002002; NM_000858; NM_001469; NM_003766; NM_003906; NM_000757; NM_002149; NM_001694; NM_004047; NM_001696; NM_001865; NM_004373; NM_000801; NM_000992; NM_000988; NM_001004; NM_001003; NM_000405; NM_000967; NM_001428; NM_000999; NM_000997; NM_000995; NM_002948; NM_002952; NM_001026; NM_001020; NMJ)01018; NMJ)Ol 017; NM_000969; NMJ)00985; NM_000937; NMJ)Ol 016; NM_002140; NM_002138; NM_004499; NM_001014; NM_002383; NM_002467; NM_001436; NM_004069; NM_001614; NM_002355; NM_004597; NM_002308; NM_000398; NM_000754; NM_002406; NM_003752; NM_001355; NM_004960; NMJW4729; NM_004587; NM_004552; NM_004450; NM_004048; NM_000239; NM_000269; NM_000431; NM_001247; NM_003365; NM_003329; NM_001069; NM_000356; NM_003134; NM_003131; NM_000454; NM_003091; NM_003089; NM_003016; NM_003952; NM _002950; NM_002743; NM_002686; NM_002654; NM_002648; NM_002635; NM_002494; NM_002488; NM_002434; NM_002415; NM_002227; NM_001536; NMJ)OOl 83; NM_002085; NMJ)01502; NM_002080; NM_001440; NM_003754; NM_003755; NM_003757; NM_001360; NM_001344; NM_001914; NMJ)Ol 834; NM_001833; NM_001281; NM_001749; NM_001697; NM_001689; NMJ)Ol 675; NM_001642; NM_014724; NM_005494; NM_006597; NM_006623; NM_015646; NM_016532; NM_015292; NM_005870; NM_006833; NMJ)05718; NM_005719; NM_006372; NM_005180; NM_018975; NM_005731; NM_020151; NM_005103; NM_012179; NM_020360; NM_014891; NM_005745; NMJ)05418; NM_006262; NM_133476; NM_006570; NM_006333; NM_007285; NM_006354; NM_014302; NM_006118; NM_012100; NM_015680; NM_030796; NM_024069; NMJ) 13234; NMJ) 13310; NMJ) 18507; NMJ) 17670; NMJ) 16292; NMJU4916; NMJH4696; NM_014630; NMJH4761; NM_007286; NM_007263; NM_006349; NM_006004; NM_005787; NM_012412; NM_012401; NM_007262; NM_007273; NM_021009; NM_023009; NM_015456; NM_005053; NM_006830; NM_005682; NM_012102; NM_005550; NM_021960; NM_021959; NMJH4730; NM_014402; NM_007067; NM_006086; NM_014972; NM_024092; NM_021983; NM_006510; NM_006711; NM_006145; NMJB3142; NM_006351; NM_014281; NM_012106; NM_021975; NMJH4874; NMJ)06796; NM_006666; NM_005219; NM_033546; NM_032348; NM_024798; NM_021103; NM_020195; NM_017432; NM_014901; NM_014694; NM_007369; NM_006156; NM_006429; NM_006513; NM_005022; NM_014654; NM_007209; NM_006082; NM_006362; NM_014228; NM_006411; NM_021134; NM_021974; NM_006808; NM_005617; NM_005520; NM_006755; NM_006010; NM_005088; NM_014754; NM_021953; NM_006908; NM_014231; NMJH4833; NM_005157; NMJJ06325; NM_007245; NM_007008; NM_006782; NM_006694; NM_006703; NM_006032; NM_012227; NMJH4604; NM_021642; NM_005354; NM_020529; NM_005561; NM_014774; NM_014390; NM_014623; NM_014453; NM_012127; NMJU2099; NM_006888; NM_006867; NM_006743; NM_006688; NM_006295; NM__006283; NM_006221; NM_006148; NM_005954; NM_ 006003; NM_005998; NM_005997; NM_005629; NM_005548; NM_005545; NM_ _.005507; NM_005381; NM_005439; NM_006445; NM_019059; NM_006039; NM_ 006066; NM_013318; NM_006098; NM_007359; NM_017510; NM_O15399; NM_ _.014508; NM_018955; NM_006368; NM_015024; NM_031420; NM_013232; NM_ _.005917; NM_032801; NM_030662; NM_006268; NM_006826; NM_144582; NM_ _.144565; NM_005984; NM_017828; NM_020150; NM_014610; NM_014225; NM_ 006937; NM_005726; NM_005347; NM_014255; NM_006815; NM_005456; NM_ 005273; NM_007260; NM_007103; NMJH7797; NM_016237; NM_005801; NM_ _.005216; NM_016457; NM_006442; NM_021019; NM_005112; NM_005370; NM_ _.006289; NM_005698; NM_024011; NMJ3O51O5; NM_006013; NM_005786; NM_ 007104; NM_005762; NM_012138; NM_015318; NM_012423; NM_021128; NM_ _.032635; NM_005080; NM_006389; NM_024112; NM_006817; NM_022830; NM_ 019884; NM_021107; NM_021074; NM_014944; NMJ) 14764; NM_015343; NM_ _.014420; NM_005884; NM_012407; NM_012111; NM_007144; NM_007108; NM_ _.007278; NM_007100; NM_006936; NM_006899; NM_006801; NM_006612; NM_ 006659; NM_006595; NM_006401; NM_006423; NM_006460; NM_006356; NM_ _.005891; NM_005839; NM_005594; NM_005340; NM_005175; NM_005165; NM_ 005001; NM_001402; NM_001958; NM_001961; NM_002714; NM_002808; NM_ _.002809; NM_004898; NM_007182, and NM_032378.

[00181] Table 2

Cluster Distribution

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients,, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score chemokine (C- _ON 1405 _i_a C motif) ligand

M21121 0.4111 0.0069 0.1404 -0.58 0.0061 -0.0055 0.1452 -0.3871 0.1184 -0.5527 ribosomal protein L24 ///

200013_ ribosomal NM_0009 - - at protein L24 86 0.4499 0.0641T 0.088 0.3805 -0.0565 0.0502 0.0797 -0.2125 0.075 -0.3499 ribosomal protein S27a ///

200017_ ribosomal NM_0029 - at protein S27a 54 0.2357 -0.0205 0.0533 0.2411 -0.0459 0.0408 0.0567 -0.1512 0.0922 -0.4304

200017 ribosomal NM 0029 0.4258 -0.0524 0.1691 -0.0188 0.0167 0.1037 -0.2767 0.0488 -0.2278

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at protein S27a /// 54 0.4646

4- ribosomal protein S27a

200024_ NMJ)OlO at — 09 0.4504 -0.1132 0.1333 0.2936 -0.1023 0.091 0.0454 -0.121 0.0579 -0.2704 ribosomal protein Ll Oa ///

200036_ ribosomal NM_0071 s_at protein Ll Oa 04 0.459 -0.0663 0.113 0.4079 -0.059 0.0524 0.0844 -0.2251 0.081 -0.3782 ribosomal

200074_ protein L14 /// s at ribosomal U16738 0.3587 -0.0411 0.1519 0.4086 -0.0366 0.0325 0.0923 -0.246 0.082 -0.3825

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus PvA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein Ll 4 ribosomal protein S 6 ///

200081_ ribosomal s at protein S6 BE741754 0.4779 -0.0796 0.0876 0.3675 -0.0698 0.062 0.0729 -0.1943 0.0717 -0.3347 eukaryotic translation initiation factor 3, subunit 10

200596_ theta, s_at 150/17OkDa BE614908 0.3294 0.0723 -0.0698 0.4673 0.0655 -0.0583 0.1421 -0.3789 0.0954 -0.4453

200626 matrin 3 NM 0188 0.2655 0.0393 0.1149 0.035 -0.0311 0.1314 -0.3503 0.1003 -0.468

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s at 34 0.4909 secreted protein, acidic, cysteine-rich

(osteonectin)

/// secreted protein, acidic,

200665_ cysteine-rich NMJ)031 s_at (osteonectin) 18 0.5159 -0.0581 -0.269 -0.121 -0.0527 0.0468 0.0161 -0.0431 0.0237 -0.1108 splicing factor,

200685_ arginine/serine- at rich l l AUl 46237 0.3126 0.0015 0.0695 0.3951 0.0014 -0.0012 0.0986 -0.263 0.0806 -0.3762

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score heat shock

7OkDa protein

-4

200692_ 9B (mortalin- NM_0041 s_at 2) 34 0.3754 0.01 -0.0131 0.4035 0.009 -0.008 0.1072 -0.2859 0.0815 -0.3805 eukaryotic translation

200705_ elongation NMJ)019 s_at factor 1 beta 2 59 0.4497 -0.0883 0.1137 0.3405 -0.0782 0.0696 0.0634 -0.169 0.0668 -0.3117 protein tyrosine

200730_ phosphatase s at type IVA, BF576710 -0.33 0.2695 -0.0772 -0.302 0.2544 -0.2261 0.1441 -0.3842 0.059 -0.2751

Table 6: Group of 1645 genes that are differentially expressed in. healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score member 1 oe ornithine

200790_ decarboxylase NM_0025 at 1 39 0.4175 -0.0099 -0.0629 0.3459 -0.0089 0.0079 0.0867 -0.2313 0.0689 -0.3217

200808_ NMJW34 s at zyxin 61 -0.5254 0.1029 0.0759 0.1974 0.0918 -0.0816 -0.0248 0.0662 -0.0382 0.1781 small nuclear ribonucleoprot ein D2

200826_ polypeptide NM_. _0045 - at 16.5kDa 97 0.4284 -0. 0713 0.0588 0 .3107 -0.0646 0.0574 0.0604 -0.161 0.0619 -0.289

200858 ribosomal NM 0010 0.4234 -0. 0659 0.1289 -0.0584 0.052 0.0812 -0.2166 0.0768 -0.3582

patients.

s at protein S8 12 0,3874 chaperonin containing

200877_ TCPl, subunit NM_0064 at 4 (delta) 30 0.3705 -0.0357 0.0815 0.3675 -0.0321 0.0286 0.0842 -0.2244 0.0739 -0.3451 mannose-6- phosphate receptor

200900_ (cation s_at dependent) AI583537 0.2437 0.0487 0.0844 0.4639 0.0443 -0.0394 0.1332 -0.3551 0.0956 -0.446

200919 polyhomeotic- NM_0044 like 2 27 -0.286 -0.0273 0.0196 0.3504 -0.0251 0.0224 -0.094 0.2507 -0.0718 0.33

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients^ and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(Drosophila) lectin,

-4

O galactoside- binding,

200923_ soluble, 3 NM_0055 at binding protein 67 -0.2068 0.337 -0.2234 0.4689 0.3194 -0.2839 0.1953 -0.5208 0.0915 -0.4268

200937_ ribosomal NM_0009 s_at protein L5 69 0.4422 -0.0961 0.1285 0.3261 -0.0857 0.0761 0.0579 -0.1544 0.0641 -0.299 arginine- glutamic acid

200939_ dipeptide (RE) NM_0121 s_at repeats 02 -0.4486 0.2038 0.064 0.1397 0.193 -0.1715 0.0906 -0.2417 0.0279 -0.1301

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score structure specific

200956_ recognition s_at protein 1 BE795648 0.4182 0.004 0.0043 0.4486 0.0036 -0.0032 0.1138 -0.3033 0.0908 -0.4237

200965_ actin binding NM_0067 s_at LIM protein 1 20 0.5128 -0.0495 0.1185 0.5139 -0.0432 0.0384 0.118 -0.3148 0.1019 -0.4755

200972_ at tetraspanin 3 BC000704 0.3208 -0.0227 0.0525 0.3226 -0.0211 0.0188 0.0752 -0.2006 0.0661 -0.3084

200973_ NM_0057 s_at tetraspanin 3 24 0.3641 0.0144 0.0707 -0.484 0.0131 -0.0116 0.1221 -0.3255 0.0994 -0.4638

200983 CD59 antigen x at pl8-20 BF983379 -0.2841 0.0738 -0.1652 0.2568 0.0681 -0.0605 -0.0472 0.1259 -0.0519 0.2421

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score

(antigen identified by

-4 monoclonal antibodies

16.3A5, EJ16,

EJ30, EL32 and G344) serine (or cysteine) proteinase

200986_ inhibitor, clade NMJ)OOO at G (Cl 62 -0.4688 0.4977 -0.197 0.6514 0.4723 -0.4198 0.298 -0.7947 0.1213 -0.5662

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (topes score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score inhibitor), member 1,

-4

(angioedema, hereditary) cytoskeleton-

200999_ associated NM_0068 s_at protein 4 25 -0.3489 -0.0452 -0.0059 0.4879 -0.0404 0.0359 -0.1348 0.3594 -0.0993 0.4635 lactate

201030_ dehydrogenase NM_0023 x_at B 00 0.4206 -0.0648 0.1677 0.4249 -0.0573 0.051 0.0899 -0.2398 0.0845 -0.3943

201039_ RAD23 ###### s_at homolog A (S. BF572938 0.4116 -0.025 # 0.3602 -0.0225 0.02 0.0858 -0.2289 0.0722 -0.3371

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score cerevisiae) phosphoglucon ate dehydrogenase

/// phosphoglucon

201118_. ate NM_0026 at dehydrogenase 31 -0.3104 -0.0885 0.1116 0.4504 -0.0792 0.0704 -0.1352 0.3604 -0.0911 0.425 progesterone receptor

201120_ membrane s at component 1 AL547946 0.6648 0.0241 -0.3496 0.4171 0.0211 -0.0187 0.1141 -0.3044 0.0808 -0.3772

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, i 3LE patients (lupus score), RA patients, and WG patients_*

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score major histocompatibil ity complex,

201137_ class II, DP NMJ3O21 s_at beta l 21 0.2755 0.0952 -0.0591 0.4827 0.0868 -0.0771 0.1426 -0.3803 0.0991 -0.4626

RAB5C, member RAS

201140_ oncogene NM_0045 s_at family 83 -0.2962 0.0139 0.0476 0.2242 0.0129 -0.0115 -0.0533 0.1422 -0.0456 0.2126

SUMO-I

201177_ activating NM_0054 s at enzyme 99 0.2644 0.0233 0.0761 0.4097 0.0213 -0.019 0.1069 -0.2849 0.0841 -0.3926

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ED Gene Title ID score score score score score 3 score score score score score subunit 2 _<, inositol 1,4,5-

201189_ triphosphate NM_0022 s_at receptor, type 3 24 0.4692 -0.0057 0.0778 0.5464 -0.0051 0.0045 0.1334 -0.3557 0.1114 -0.5197

201258_ ribosomal NMJ)OlO at protein S16 20 0.4629 -0.0799 0.0955 0.3589 -0.0709 0.063 0.0703 -0.1874 0.0707 -0.3297 disabled homolog 2, mitogen- responsive

201279_ phosphoprotein s_at (Drosophila) BC003064 0.4321 -0.0069 0.0284 0.4569 -0.0063 0.0056 0.1102 -0.294 0.0927 -0.4327

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.-

1 2 3 4 5 ^' 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score enolase 2

-4 201313_ (gamma, N NMMJ_0)O0l199 -4 at neuronal) 7 755 0.4017 -0.0519 0.2632 0.5317 -0.047 0.0418 0.1183 -0.3153 0.1086 -0.5068 v-ets erythroblastosi s virus E26 oncogene

201328_ homolog 2 at (avian) A ALL5577555500<9 -0.5219 0.0647 -0.0648 0.4312 0.0567 -0.0504 -0.0912 0.2432 -0.0848 0.3956 v-ets

201329_ erythroblastosi NM_0052 s at s virus E26 39 -0.5236 0.0675 0.0021 0.3609 0.0594 -0.0528 -0.0738 0.1968 -0.0705 0.3289

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score oncogene

-4 homolog 2

OO

(avian)

Rho guanine nucleotide exchange

201334_ factor (GEF) s_at 12 AB002380 0.3794 -0.0949 0.1638 0.2982 -0.0877 0.078 0.0512 -0.1366 0.0603 -0.2812

201406_ ribosomal NM_0210 at protein L36a 29 0.3609 -0.0068 0.1358 0.4869 -0.006 0.0053 0.1199 -0.3198 0.0981 -0.4579

201456_ BUB3 budding s at uninhibited by AU160695 0.3197 -0.0033 0.1312 0.4491 -0.0029 0.0026 0.1126 -0.3002 0.0911 -0.425

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set © Gene Title ID score score score score score 3 score score score score score benzimidazoles

-4 3 homolog

(yeast) nuclear cap binding protein

201521_ subunit2, NM_0073 s_at 2OkDa 62 0.3161 0.0489 -0.0693 0.3915 0.0449 -0.0399 0.1128 -0.3009 0.0801 -0.3739 replication

201528_ protein Al, at 7OkDa BG398414 0.4072 -0.0627 0.1109 0.3617 -0.0562 0.0499 0.0745 -0.1987 0.0721 -0.3363

201554_ NM_0041 x_at glycogenin 30 -0.4542 0.014 -0.0601 0.4916 0.0124 -0.011 -0.1178 0.3142 -0.0988 0.461

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

201571 dCMP s at deaminase AI656493 0.2849 0.0357 0.1183 0.5047 0.0325 -0.0289 0.1325 -0.3533 0.1042 -0.4862

O

201614_ RuvB-like 1 NM_0037 s at (E. coli) 07 0.3767 0.0034 -0.0976 0.3056 0.0031 -0.0028 0.0831 -0.2215 0.0626 -0.2922 fragile X mental retardation,

201635_ autosomal s_at homolog 1 AI990766 0.3753 -0.0108 -0.0269 0.3346 -0.0099 0.0088 0.082 -0.2188 0.0679 -0.317 bone marrow

201641_ stromal cell NM_0043 at antigen 2 35 -0.2349 0.3283 -0.142 0.4953 0.3097 -0.2753 0.2067 -0.5513 0.0971 -0.4529

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (hiptis score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score ubiquitin-

201649_ conjugating N NMMJ 03004422

SC

^ a att enzyme E2L 6 23 -0.3428 0.3232 -0.0935 0.4163 0.303 -0.2693 0.1889 -0.5036 0.0797 -0.372 myristoylated alanine-rich

201669_ protein kinase NM_0023 s_at C substrate 5 566 -0.4645 0.2723 0.0093 0.2535 0.2516 -0.2236 0.139 -0.3707 0.048 -0.224 myristoylated alanine-rich

201670_ protein kinase s_at C substrate M M6688995566 -0.5726 0.297 0.0023 0.2003 0.2739 -0.2435 0.1326 -0.3536 0.0375 -0.1752

201681 discs, large A ABBO0l1111155!5 0.5355 -0.1613 0.1126 -0.1494 0.1328 0.0184 -0.0491 0.0463 -0.2162

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at homolog 5 0.2335

(Drosophila)

201688_ tumor protein 4.00E- s_at D52 BG389015 0.3571 0.0524 04 0.5105 0.0474 -0.0421 0.1432 -0.3819 0.1046 -0.4883

201689_ tumor protein s_at D52 BE974098 0.3043 0.0903 0.0414 -0.596 0.0816 -0.0726 0.1667 -0.4446 0.1234 -0.5758

201694_ early growth NM_0019 s at r reesspnoonnssee 11 64 -0.5135 0.1329 0.2003 0.0149 0.1231 -0.1094 0.0404 -0.1078 0.0029 -0.0137

DNA

(cytosine-5-)-

201697_ methyltransfera NM_0013 s at sel 79 0.2632 0.0763 0.095 0.5679 0.0689 -0.0612 0.1571 -0.419 0.1175 -0.5482

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score neuroepithelial

OO cell

201830_ transforming NM_0058 s_at gene 1 63 0.3028 0.0221 -0.0564 0.3187 0.0209 -0.0186 0.0906 -0.2417 0.0661 -0.3084 heat shock

201841_ 27kDa protein NMJ)015 s_at 1 40 0.2578 0.068 0.0103 0.4586 0.0634 -0.0563 0.1349 -0.3597 0.0954 -0.4453

BCL2/adenovir us ElB 19kDa

201849_ interacting NM_0040 at protein 3 52 0.3668 -0.0423 0.132 0.3946 -0.0383 0.034 0.0878 -0.2341 0.0798 -0.3723

201883 UDP- D29805 0.1086 -0.1118 -0.2654 0.441 -0.1022 0.0909 -0.1397 0.3725 -0.0901 0.4204

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at Gal:betaGlcNA c beta 1,4-

OC galactosyltrans ferase, polypeptide 1 family with sequence

201889_ similarity 3 , NMJ) 148 at member C 88 0.3001 0.1015 0.0574 0.6372 0.0907 -0.0806 0.1804 -0.4811 0.1317 -0.6145 decay

201926_ accelerating s at factor for B BCC0000112288*8 -0.293 -0.0019 -0.057 0.3638 -0.0017 0.0016 -0.0939 0.2503 -0.0743 0.3465

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients_*

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score complement

OO (CD55, Cromer Ul blood group system) chaperonin containing

201946_ TCPl, subunit s at 2 (beta) AL545982 0.3816 0.0321 0.0179 0.4987 0.0287 -0.0255 0.1314 -0.3505 0.1014 -0.473 chaperonin containing

201947_, TCPl. subunit NM_0064 9.00E- -7.00E- s at 2(beta) 31 0.3478 04 0.051 0.4121 04 0.1033 -0.2755 0.0835 -0.3895

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score spen homolog, transcriptional " 201996_ regulator s_at (Drosophila) AL524033 0.2903 -0.1738 -0.0537 0.2142 -0.1666 0.1481 -0.1037 0.2765 -0.0438 0.2043

202018_ NM_0023 s_at lactotransferrin 43 -0.6543 0.1012 -0.4532 0.845 0.0859 -0.0763 -0.1915 0.5106 -0.1675 0.7817 mannosidase,

202032_ alpha, class NM_0061 s at 2A, member 2 22 -0.169 -0.0917 -0.0266 0.4454 -0.084 0.0747 -0.1347 0.3593 -0.0919 0.4288

202074_ NM_0219 - s_at optineurin 80 0.2291 0.101 0.0422 0.5475 0.09 -0.08 0.1644 -0.4385 0.1125 -0.5248

202086_ myxovirus NM_0024 -0.7333 0.6721 -0.2209 -0.819 0.6286 -0.5588 0.3901 -1.0404 0.1402 -0.6544

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus soore), RA patients. and WG patients.

1 o 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set BD Gene Title ID score score score score score 3 score score score score score αe at (influenza 62 virus) resistance 1, interferon- inducible protein p78 (mouse) /// myxovirus (influenza virus) resistance 1 , interferon-

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score inducible protein p78

SC

(mouse) v-ral simian leukemia viral oncogene homolog B (ras related; GTP

202101_ binding NM_0028 s_at protein) 81 -0.4231 0.1311 -0.0548 0.1421 0.1209 -0.1074 -0.0028 0.0074 -0.0281 0.1311

202137_ zinc finger, NM_0066 s at MYND 24 0.2662 0.0635 -0.0358 -0.411 0.0588 -0.0523 0.1228 -0.3275 0.0848 -0.396

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score domain containing 11 lymphocyte antigen 6

202145_ complex, locus NM_0023 at E 46 -0.6258 0.7036 -0.3596 -0.881 0.6733 -0.5985 0.3999 -1.0664 0.1548 -0.7223

202179_ bleomycin NM_0003 at hydrolase 86 0.2508 0.0065 0.1215 0.3945 0.0061 -0.0054 0.1023 -0.2729 0.0816 -0.381

202192_ growth arrest- NM_0058 s_at specific 7 90 -0.1065 -0.1725 0.0018 0.5687 -0.155 0.1378 -0.1849 0.4932 -0.1166 0.5439

202200_ SFRS protein NM_0031 s a ' t kinase 1 37 -0.4941 0.0258 -0.0041 0.4475 0.0227 -0.0202 -0.1063 0.2834 -0.0888 0.4144

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

ADP-

202206 ribosylation AW45036

O at factor-like 7 3 0.4458 -0.0101 0.1718 0.6008 -0.0087 0.0077 0.1486 -0.3963 0.1203 -0.5616 ADP- ■

202207_ ribosylation at factor-like 7 BG435404 0.3555 0.0336 0.213 0.6635 0.0291 -0.0258 0.174 -0.4639 0.1352 -0.6308 ADP-

202208_ ribosylation s_at factor-like 7 BC001051 0.4089 0.0557 0.1153 0.6835 0.048 -0.0427 0.1832 -0.4884 0.1391 -0.6493 pescadillo

202212_ homolog 1, NM_0143 at containing 03 0.4195 -0.1324 0.0574 0.1374 -0.1249 0.1111 0.0013 -0.0034 0.0278 -0.1296

TaWe 6: Group of 1645 genes that are differentially expressedia healthy dønørø, SLE pafeats (luptts score)_* RA patients and WG patients.

2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score

BRCT domain (zebrafish)

SO

^ tribbles

202241_ homoløg 1 NMJ251 at (DrosopMla) 95 -0.6946 0.2133 0.1198 0.0363 0.1887 -0.1677 0.0458 -0.1221 -0.0067 0.0314

RAB13, member RAS

202252_ oncogene NM_0028 at family 70 -0.1679 -0.1065 -0.0615 0.5175 -0.0976 0.0868 -0.1566 0.4175 -0.1073 0.5009 guanykte

202269_ binding protein - x_at 1, interferon- BC002666 -0.3558 0.4047 -0.1033 0,6109 0,3806 -0.3383 0-2597 -0.6925 0.1177 -0.5491

Table 6: Group of 1645 genes that are differentially expressed in liealfhy donors_* SLE patients (lupus score), RA patients, and WG patients. ^|

I 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score inducible, 67kDa/// guanylate binding protein 1, interferon- inducible, 67kDa guanylate binding protein 1, interferon-

202270_^ inducible, NM_0020 at 67kDa/// 53 -0.5481 0.4638 -0.0591 0.6115 0.4325 -0.3844 0.2766 -0.7377 0.1131 -0.528

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score to guanylate binding protein 1, interferon- inducible, 67kDa glucose-6-

202275_ phosphate NM_0004 at dehydrogenase 02 -0.3088 -0.0316 0.0913 0.3165 -0.0289 0.0257 -0.0879 0.2343 -0.0642 0.2995 tumor- associated

202286_ calcium signal s at transducer 2 J04152 -0.2271 -0.0669 -0.1956 0.6022 -0.0612 0.0544 -0.1753 0.4674 -0.1257 0.5866

Table 6: Group of 1645 genes that are differentially expressed in healthy donors _» SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score transporter 1, ATP-binding cassette, sub¬

202307_ family B NM_0005 s_at (MDR/TAP) 93 -0.5139 0.3347 -0.1548 0.2105 0.3138 -0.2789 0.1427 -0.3804 0.0392 -0.1832 HLA-B

202326_ associated NM_0067 at transcript 8 09 0.326 0.0014 0.1272 0.4644 0.0013 -0.0012 0.1123 -0.2994 0.0953 -0.4448 natural killer- tumor ^~

202379_ recognition s at sequence AI361805 0.5116 -0.1524 -0.046 0.0801 -0.1421 0.1263 -0.0191 0.0509 0.0159 -0.0742

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score interferon, vO 202411 alpha-mducible NM_ _0055

'Jl at protein 27 32 -0.4947 0.5674 -0.5073 0.5116 0.5513 -0.49 0.268 -0.7147 0.0925 -0.4316

202430_ phospholipid NM_ _0211 s_at scramblase 1 05 -0.8062 0.4873 -0.2147 0.2567 0.4497 -0.3997 0.1893 -0.5048 0.0444 -0.2073 v-myc myelocytomato sis viral oncogene

202431_ homolog NM_ _0024 s_at (avian) 61 0.3304 0.0173 0.0886 0.4741 0.0156 -0.0139 0.1295 -0.3452 0.097 -0.4528

202437 cytochrome N NMM 00000011 -0.3312 0.0014 0.303 0.0479 0.0013 -0.0011 -0.0124 0.0332 -0.0096 0.0446

Table 6: Group of 1645 genes that are differentially expressed in healthy donors* SLE patients (lupus score), RA patients, and WG patients. <

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at P450, family 1, 04 subfamily B,

ON polypeptide 1 iduronate 2- sulfatase

202438_ (Hunter x_at syndrome) BF346014 -0.3137 0.104 -0.031 0.0777 0.0988 -0.0878 0.0068 -0.0181 -0.0159 0.074

202446_ phospholipid s_at scramblase 1 AI825926 -0.8752 0.5084 -0.262 0.1959 0.4622 -0.4108 0.1827 -0.4873 0.0329 -0.1536

202458_ protease, NM_0071 at serine, 23 73 0.2989 -0.0476 0.3083 -0.48 -0.0436 0.0388 0.1093 -0.2915 0.0985 -0.4597

202464 6- NM 0045 -0.3512 -0.0485 -0.0249 0.5174 -0.0437 0.0389 -0.1446 0.3855 -0.1061 0.4952

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients. "

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at phosphorructo- 66

VO 2- -4 kinase/fructose

-2,6- biphosphatase

3 tribbles

202478_ homolog 2 NM_0216 at (Drosophila) 43 0.2822 0.0844 0.0874 0.6018 0.0749 -0.0666 0.171 -0.4561 0.1239 -0.5782 tribbles

202479_ homolog 2 s_at (Drosophila) BC002637 0.3826 0.0728 0.0741 0.6623 0.0643 -0.0571 0.1779 -0.4744 0.1361 -0.635

TaMe 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus scored RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score dehydrogenase/ reductase 202481_ (SDR family) NM_0047 at member 3 53 0.4827 -0.0781 0.0704 0.3599 -0.0705 0.0626 0.0708 -0.1888 0.0717 -0.3347

S solute carrier family 2

(facilitated glucose

202497_ transporter), x_at member 3 AI631159 -0.5776 0.1493 0.0198 0.1817 0.1347 -0.1197 -0.0086 0.0229 -0.0351 0.1638

202498_ solute carrier s_at family 2 BE550486 -0.4639 0.1093 0.0122 0.1778 0.1008 -0.0896 -0.0176 0.0469 -0.0354 0.165

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(facilitated glucose transporter), member 3 solute carrier family 2 (facilitated glucose

202499_. transporter), NM_0069 s_at member 3 31 -0.5664 0.1323 -0.0093 0.2437 0.118 -0.1049 -0.0293 0.0782 -0.047 0.2194

202500_ DnaJ (Hsp40) NM_0067 at homolog, 36 0.3068 -0.0607 0.1485 0.2992 -0.0564 0.0502 0.0595 -0.1588 0.0611 -0.285

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score subfamily B,

O member 2 O discs, large

202514_ homolog 1 AWl 3913 at (Drosophila) 1 0.2749 -0.0087 0.1526 0.4089 -0.008 0.0071 0.0985 -0.2627 0.0841 -0.3924 sparc/osteonect in, cwcv and kazal-like domains

202524_ proteoglycan NM_0147 s_at (testican) 2 67 0.4135 -0.0485 0.142 0.4363 -0.0427 0.038 0.0977 -0.2605 0.0869 -0.4055

202530 mitogen- NM 0013 -0.4147 -0.015 -0.0537 0.5218 -0.0131 0.0116 -0.1352 0.3605 -0.1048 0.4891

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WO patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at activated 15 protein kinase

14 myosin, light polypeptide kinase /// myosin, light

202555_ polypeptide NM_0059 s_at kinase 65 0.6994 -0.1367 -0.1612 0.2054 -0.1224 0.1088 0.0173 -0.0462 0.0395 -0.1845 tumor necrosis

202687_ factor (ligand) s at superfamily, U57059 -0.5992 0.381 -0.1231 -0.276 0.3532 -0.314 0.1694 -0.4518 0.0499 -0.233

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG δ Set ID Gene Title ID score score score score score 3 score score score score score member 10 /// tumor necrosis factor (ligand) superfamily, member 10 tumor necrosis factor (ligand) superfamily, member 10 /// tumor necrosis

202688 factor (ligand) NMJ3O38 superfamily, 10 -0.6177 0.3194 -0.1206 -0.095 0.2888 -0.2567 0.1093 -0.2916 0.017 -0.07

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score member 10

O protein kinase

(cAMP- dependent, catalytic)

202732_ inhibitor NMJ3O7O 4.00E- -3.00E- at gamma 66 0.313 04 0.0472 -0.371 04 0.091 -0.2426 0.0761 -0.3551 protein kinase, cAMP-

202741_ dependent, at catalytic, beta AA130247 0.4136 -0.0174 0.1231 0.5012 -0 .0153 0 .0136 0.1205 -0.3214 0.1007 -0.4698

202742 nrotein kinase. NM 0027 0.3696 0.0205 0.1125 _ 0 .0183 -0 .0163 0.141 -0.376 0.1118 -0.5219

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (tupϊts score), RA patients, and, WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s at cAMP- 31 0.5462 dependent, catalytic, beta integral

20274ό_ membrane at protein 2A AL021786 0.2247 0.1301 0.0717 0.6489 0.1152 -0.1024 0.1968 -0.5249 0.134 -0.6253 integral

202747_ membrane NM_0048 s_at protein 2 A 67 0.3633 0.0946 0.1065 0.7315 0.0829 -0.0737 0.2058 -0.5487 0.151 -0.7045 family with

202771_ sequence NM_0147 at similarity 38, 45 0.2953 0.0029 0.0861 -0.397 0.0027 -0.0024 0.0986 -0.2631 0.0816 -0.380'

Table 6: Group of 1645 genes that are differential y expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score member A

202780 3-oxoacid CoA NM 0004

* at transferase 1 36 0.3371 0.0516 0.0891 0.5731 0.0462 -0.041 0.1532 -0.4085 0.1178 -0.5497

202789_ phospholipase at C, gamma 1 AL022394 0.2605 0.0376 0.0472 0.4157 0.0346 -0.0307 0.1173 -0.3127 0.0857 -0.4001

TAR (HIV)

202813_ RNA binding NM_0056 at protein 1 46 0.3615 0.0686 -0.0657 0.4945 0.0617 -0.0549 0.1415 -0.3772 0.1008 -0.4702

202837_ FLN29 gene NM_0067 - at product 00 -0.6076 0.3193 -0.0193 0.2028 0.2985 -0.2653 0.1395 -0.3721 0.0385 -0.1795

202859_ NM_0005 x at interleukin δ 84 -0.2117 0.2387 0.2109 -0.62 0.221 -0.1965 0.2304 -0.6145 0.127 -0.5927

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

202863 nuclear antigen NM_0031 μ- at

O SpIOO 13 -0.5443 0.3358 -0.1399 0.1962 0.3106 -0.2761 0.1353 -0.3609 0.0358 -0.1668

202864 nuclear antigen NMJ)031 s at SpIOO 13 -0.441 0.37 -0.2419 0.2963 0.3509 -0.3119 0.1725 -0.4601 0.0552 -0.2576

2',5'- oligoadenylate

202869_ synthetase 1, NMJ) 168 at 40/46kDa 16 -0.5342 0.623 -0.3074 0.8113 0.5928 -0.527 0.3681 -0.9816 0.1459 -0.6807

202900_ nucleoporin NM_0025 s_at 88kDa 32 0.2279 0.1324 0.1058 0.6913 0.1168 -0.1038 0.1995 -0.5319 0.1431 -0.6677

202912_. NMJ)OIl at adrenomedullin 24 -0.4962 0.1989 -0.0488 0.0311 0.1844 -0.1639 0.0433 -0.1155 -0.0061 0.0283

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (hipus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score family with

O sequence -4

202916_ similarity 20, NMJH48 s at member B 64 0.3048 -0.053 0.1987 0.3662 -0.0486 0.0432 0.0772 -0.2059 0.0745 -0.3477 v-yes-1 Yamaguchi sarcoma viral

202932_ oncogene NM_0054 at homolog 1 33 0.5666 -0.1527 0.1068 0.2832 -0.1387 0.1233 0.0323 -0.0861 0.0555 -0.259 v-yes-1

202933_ Yamaguchi NM_0054 s at sarcoma viral 33 0.5668 -0.127 0.0775 0.3239 -0.1162 0.1033 0.0491 -0.1308 0.0645 -0.3008

₀₈₁

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score oncogene homolog 1 glycophorin C

202947_ (Gerbich blood NM_0021 s_at group) 01 0.4658 -0.0919 0.0457 0.2818 -0.0829 0.0737 0.0478 -0.1274 0.0556 -0.2596

202948_ interleukin 1 NM_0008 at receptor, type I 77 -0.3268 -0.0161 -0.1325 0.5095 -0.0146 0.013 -0.1328 0.3541 -0.1048 0.4893 dual-specificity tyrosine-(Y)- phosphorylatio

202968_ n regulated s at kinase 2 Y09216 0.4042 -0.024 0.2662 0.6115 -0.021 0.0187 0.1456 -0.3884 0.1237 -0.5772

Table 6: Group of 1645 genes that are differentially expressed iϊi healthy donors. SLB patients (lupus score), RA patients, aacl WG patients_*

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Dual-

O ¹O specificity tyrosine-(Y)- phosphorylatio

202969_ n regulated at kinase 2 AI216690 0.3317 0.02 0.1429 0.5349 0.0177 -0.0157 0.1395 -0.3721 0.109 -0.5086 dual-specificity tyrosine-(Y)- phosphorylatio

202971_ n regulated NMJ)064 s at kinase 2 82 0.5484 -0.0546 -0.009 0.4145 -0.05 0.0445 0.0963 -0.2568 0.0839 -0.3917

202990__ phosphorylase, NMJ)028 -0.3865 -0.0356 0.1038 0.3959 -0.032 0.0284 -0.1076 0.287 -0.0797 0.3718

Table 6: Group of 1645 genes that are differentially expressed in liealtliy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at glycogen; liver 63

(Hers disease, glycogen storage disease type VI) secretory leukocyte protease inhibitor

203021_ (antileukoprote NM_0030 at inase) 64 -0.4342 -0.0098 -0.0924 0.5654 -0.0086 0.0077 -0.1478 0.3941 -0.1145 0.5342

203084 transforming NMJ3OO6 -0.1607 -0.0553 -0.1492 0.4577 -0.0515 0.0458 -0.134 0.3573 -0.0955 0.445*

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at growth factor, 60 beta l

(Camurati-

Engelmann disease) ubiquitin

203117_ specific NM_0148 s at protease 52 71 0.3953 -0.0712 0.1244 -0.34 -0.0646 0.0574 0.0662 -0.1767 0.0682 -0.3185 serine palmitoyltransf

203127_ erase, long s at chain base BC005123 -0.4119 0.0839 -0.0802 0.2807 0.0756 -0.0672 -0.049 0.1308 -0.0555 0.2592

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score subunit 2

B-cell

CLL/lymphom a 6 (zinc finger protein 51) ///

B-cell

CLL/lymphom

203140_ a 6 (zinc finger NMJ)Ol 7 at protein 51) 06 -0.3972 0.0101 -0.008 0.3926 0.009 -0.008 -0.0978 0.2607 -0.0785 0.3663 interferon-

203153_ induced protein NM_0015 at with 48 -0.777 0.7551 -0.1725 1.0417 0.6938 -0.6167 0.4624 -1.233 0.1763 -0.8226

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score tetratricopeptid e repeats 1 ///

W interferon- induced protein with tetratricopeptid e repeats 1 fflV-1 rev

203203_ binding protein NM_0070 s_at 2 43 0.2677 0.0663 0.1125 0.5628 0.0602 -0.0535 0.1544 -0.4116 0.1167 -0.5444

203234_ uridine NM_0033 at phosphorylase 64 -0.3062 -0.0191 -0.0614 0.4276 -0.0174 0.0154 -0.1127 0.3004 -0.0875 0.4083

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients. ~

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

1 developmentall y regulated

203267_ GTP binding s_at protein 2 BF223206 0.4644 -0.0448 0.1291 0.4866 -0.0404 0.0359 0.1108 -0.2956 0.0987 -0.4605 interferon

203275_ regulatory NM_0021 at factor 2 99 -0.6485 0.2389 0.0617 0.0239 0.2124 -0.1888 0.0694 -0.1851 0.0044 -0.0205

203375_ tripeptidyl NM_0032 - s_at peptidase II 91 0.2898 0.0366 0.0403 0.4369 0.0331 -0.0294 0.1204 -0.3209 0.0894 -0.4171

203386_ TBCl domain - at family, AI650848 0.349 -0.0035 0.1138 0.4622 -0.0031 0.0028 0.116 -0.3094 0.0939 -0.4381

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score member 4

NEL-like 2

(chicken) ///

203413_ NEL-like 2 N NMM__00006611 at (chicken) 5599 0.4426 0.0047 0.0271 0.4976 0.0042 -0.0037 0.1293 -0.3448 0.0999 -0.4664 monocyte to macrophage

203414_ differentiation- NM_0123 at associated 29 0.6812 -0.0937 -0.1589 0.3036 -0.0811 0.0721 0.0544 -0.1451 0.0575 -0.2685 family with

203420_ sequence NM_0162 at similarity 8, 55 -0.5034 0.2744 -0.08 0.1327 0.252 -0.224 0.103 -0.2747 0.0246 -0.1148

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score member Al tumor protein

S 203421_ p53 inducible NM_0060 at protein 11 34 - -00..44335566 00..00444488 -0.1155 0.4436 0.0409 -0.0364 -0.104 0.2772 -0.0904 0.4219

ASFl anti- silencing function 1

203427_ homolog A (S. NM_0140 at cerevisiae) 34 0.2548 0.0483 0.1994 -0.585 0.0432 -0.0384 0.1571 -0.4189 0.1207 -0.5632 membrane

203434_ metallo- s at endopeptidase AI433463 -0.3466 0.1628 0.1544 0.2235 0.1531 -0.1361 0.0966 -0.2577 0.045 -0.2099

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (tojras score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set JGD Gene Title ID score score score score score 3 score score score score score

(neutral endopeptidase, enkephalinase, CALLA, CDlO) ATP-binding cassette, sub¬ family A

203504_ (ABCl), NMJ3O55 s_at member 1 02 -0.5991 0.2472 -0.1279 0.0853 0.2236 -0.1987 0.0413 -0.1102 -0.0159 0.0743

203505_^ ATP-binding at cassette, sub- AF285167 -0.7017 03491 -0.1534 0.0554 0.3194 -0.2839 0.1025 -0.2734 0.0101 -0.047

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score family A

(ABCl), member 1

CD4 antigen

203547_ (p55) /// CD4 at antigen (p55) U47924 0 0..22336666 00..00009933 0.2091 0.4715 0.0084 -0.0075 0.1185 -0.316 0.0967 -0.4514 mitogen- activated protein kinase

203553_ kinase kinase NM_0065 s_at kinase 5 75 0 0..22552288 00..00550022 0.0139 0.4095 0.0461 -0.041 0.1158 -0.3087 0.0843 -0.3933

203574 nuclear factor. NM 0053 -0.6754 0.1876 0.0337 0.1677 0.1652 -0.1469 0.005 -0.0133 -0.0313 0.1461

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score),, RA patients, and WG patients_*

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at interleukin 3 84 regulated

VO branched chain aminotransfera

203576_ se 2, NMJ)OI l at mitochondrial 90 0.4487 -0.1174 0.0682 -0.218 -0.1096 0.0974 0.0256 -0.0683 0.0439 -0.205 interferon- induced protein with

203595_ tetratricopeptid s_at e repeats 5 N47725 -0.5502 0.5511 -0.1809 0.7247 0.5136 -0.4565 0.3219 -0.8585 0.1292 -0.6029

203596 interferon- NM 0124 -0.5836 0.5797 -0.2278 0.5439 -0.4835 0.3284 -0.8756 0.1272 -0.5937

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at induced protein 20 0.7212 with

O tetratricopeptid e repeats 5 muscleblind-

203640_ Iike 2 at (Drosophila) BE328496 0.3316 -0.0459 0.2134 0.4269 -0.0419 0.0373 0.0934 -0.2491 0.087 -0.4062

203645_ NM_0042 s_at CD 163 antigen 44 -0.3537 -0.0033 -0.1029 0.4749 -0.003 0.0027 -0.119 0.3173 -0.0968 0.4519

203678_ KIAA1018 NM_0149 at protein 67 0.3029 0.0116 0.0916 0.4333 0.0105 -0.0093 0.1118 -0.2982 0.0884 -0.4127

203680_ protein kinase, NM_0027 0.5836 -0.151 -0.1658 -0.043 -0.1377 0.1224 -0.0274 0.0731 0.0084 -0.039

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at cAMP- 36 dependent, regulatory, type II, beta vascular endothelial

203683_ growth factor NM_0033 s_at B 77 0.3286 0.0176 0.1314 0.5143 0.0161 -0.0143 0.1316 -0.3511 0.1062 -0.4954

B-cell

203685_ CLL/lymphom NM_0006 at a 2 33 0.2866 0.0352 0.1668 0.5518 0.0312 -0.0277 0.1476 -0.3936 0.1129 -0.527

203725 growth arrest NM 0019 -0.2188 -0.156 -0.1078 0.7468 -0.1376 0.1223 -0.229 0.6108 -0.1551 0.7237

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients_? and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at and DNA- 24 κ> κ> damage- inducible, alpha carcinoembryo nic antigen- related cell adhesion molecule 6 (non-specific

203757_ cross reacting s at antigen) BC005008 -0.4772 0.0322 -0.4134 0.8072 0.0276 -0.0245 -0.193 0.5145 -0.1635 0.7629

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (luptis score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

NAD(P)H ^ 203814_ dehydrogenase, NM_0009 s_at quinone 2 04 -0.4392 0.0769 -0.0869 0.334 0.0699 -0.0621 -0.0664 0.177 -0.0669 0.312

IGF-II mRNA- 203819_ binding protein s_at 3 AU160004 0.3513 0.0832 -0.2994 0.2978 0.0768 -0.0683 0.0987 -0.2632 0.0601 -0.2804 interleukin 32

203828_ /// interleukin NM_0042 s_at 32 21 0.1996 0.1195 0.1429 0.6633 0.1074 -0.0954 0.1936 -0.5162 0.1381 -0.6442 small nuclear

203832_ ribonucleoprot NM_0030 at ein polypeptide 95 0.4383 -0.0291 0.0127 0.3891 -0.0259 0.023 0.0929 -0.2477 0.0776 -0.362

patients.

adenosine deaminase,

RNA-specific,

203865_ Bl (REDl NM_0158 s_at homolog rat) 33 0.3171 0.0236 0.2328 0.6159 0.0214 -0.019 0.1583 -0.4221 0.1279 -0.5967 mitochondrial

20393 !_„ ribosomal NMJJ029 s_at protein L 12 49 0.3097 0.0468 0.0091 0.4548 0.0422 -0.0375 0.1268 -0.3383 0.0928 -0.433 matrix

203936_ mstalloproteπia NMJ3G49 s at se 9 (gelatinase 94 -0.3731 -0.0763 0.0263 0.5651 -0.069 0.0614 -0.1598 0.4261 -0.1162 0.5425

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

B, 92kDa

Is) gelatinase,

92kDa type IV collagenase)

203948_ myeloperoxida s_at se J02694 -0.3771 -0.0013 -0.2333 0.6191 -0.0012 0.001 -0.1533 0.4088 -0.1281 0.5977

203949_ myeloperoxida NM_0002 at se 50 -0.3806 -0.0201 -0.1937 0.6349 -0.0179 0.0159 -0.1637 0.4365 -0.1305 0.6088 hemoglobin, alpha 1 ///

204018_ hemoglobin, NM_0005 x at alpha 1 /// 58 0.6812 -0.185 -0.1846 0.0354 -0.1664 0.1479 -0.0379 0.1011 0.0067 -0.0314

Table 6; Group of 1645 genes that are differentially expressed iii healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hemoglobin, alpha 2 /// hemoglobin, alpha 2 SH3 domain containing,

204019_, Ysc84-like 1 NM 0156 -4.00E- 3.00E- s_at (S. cerevisiae) 77 0.3686 04 0.1116 0.4887 04 0.1238 -0.3302 0.0996 -0.4647

204040_ ring finger NM_0147 at protein 144 46 0.1628 0.1231 0.0832 0.5771 0.1128 -0.1002 0.1816 -0.4842 0.1202 -0.561

204070_ retinoic acid NM_0045 at receptor 85 0.2951 0.041 0.054 0.4672 0.0367 -0.0327 0.1279 -0.3411 0.0954 -0.4452

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score responder

KJ

(tazarotene induced) 3 neurogranin

(protein kinase

204081_ C substrate, NMJ)061 at RC3) 76 0.5381 -0.1474 -0.1468 0.0237 -0.1351 0.1201 -0.032 0.0854 0.0046 -0.0216 mitogen- activated

204089_ protein kinase NM_0067 x_at kinase kinase 4 24 0.3041 -0.0086 0.0844 0.3735 -0.0079 0.007 0.0887 -0.2366 0.0763 -0.356

204115_ guanine NM_0041 0.7531 -0.1147 -0.2462 - -0.1001 0.089 0.0321 -0.0855 0.045 -0.2099

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at nucleotide 26 0.2382 binding protein

(G protein), gamma 11 tyrosylprotein

204140_ sulfotransferas NM_0035 at e l 96 -0.1601 -0.0916 -0.0816 0.4888 -0.0854 0.0759 -0.1422 0.3791 -0.1021 0.4765 enolase

204142_ superfamily NM_0175 at member 1 12 0.492 -0.1391 0.0494 0.1868 -0.1299 0.1154 0.0119 -0.0317 0.0374 -0.1746

204143_ enolase NMJ) 175 -8.00E- 7.00E- s at superfamily 12 0.461 04 0.0335 0.5082 04 0.125 -0.3333 0.103 -0.4806

Table 6: Group of 1645 genes that are differentially expressed in healthy donorSj SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score member 1 manic fringe

^ 204152 homolog s_at (Drosophila) AI738965 0.4126 -0.0863 0.046 0.2419 -0.0804 0.0714 0.0389 -0.1037 0.049 -0.2285 runt-related

204198_ transcription s at factor 3 AA541630 0.3098 0.0171 0.1767 0.5369 0.0149 -0.0133 0.141 -0.3759 0.1089 -0.5082 eukaryotic translation initiation factor

204211_ 2-alpha kinase NM_0027 x at 2 59 -0.4149 0.362 -0.2555 0.2891 0.345 -0.3066 0.1652 -0.4406 0.0545 -0.2544

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score peptidyl prolyl

204228_ isomerase H NM_0063

O at (cyclophilin H) 47 0.2913 -0.0092 0.0576 0.3329 -0.0086 0.0076 0.0817 -0.2179 0.0684 -0.3193

204244_ activator of S NM_0067 s_at phase kinase 16 0.3222 -0.007 0.0219 0.3366 -0.0065 0.0057 0.0807 -0.2152 0.069 -0.3221 estrogen receptor binding site

204278 associated, NM 0042 s_at antigen, 9 15 0.2023 0.0593 0.1772 0.5385 0.054 -0.048 0.1472 -0.3926 0.1118 -0.5216

204285_ phorbol-12- s at myristate-13- AI857639 -0.3459 0.2875 0.1469 0.5495 0.2656 -0.2361 0.2127 -0.5671 0.109 -0.5089

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SJLE patients (lupus score), RA patients., and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score acetate-induced protein 1

W phorbol-12- myristate-13-

204286_ acetate-induced NM_0211 s_at protein 1 27 -0.4361 0.3443 0.1147 0.5763 0.3167 -0.2815 0.2307 -0.6152 0.1115 -0.5204

204326_ metallothionein NM__0024 x_at IX 50 -0.0378 0.2402 -0.1647 0.4428 0.2257 -0.2006 0.1906 -0.5083 0.0893 -0.417

SlOO calcium

204351_ binding protein NM_0059 at P 80 -0.0889 -0.1674 0.1885 0.357 -0.1611 0.1432 -0.1335 0.356 -0.0743 0.3466

204352_ TNF receptor- NM_0046 0.3548 0.0242 0.0668 0.0217 -0.0193 0.1279 -0.3411 0.1013 -0.4725

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at associated 19 0.4969 factor 5

204388_ monoamine NM_0002 s_at oxidase A 40 -0.038 -0.1797 -0.1953 0.7067 -0.1653 0.147 -0.228 0.6081 -0.1482 0.6918 interferon, alpha-inducible

204415_ protein (clone NM_0228 at IFI-6-16) 73 -0.3831 0.4088 -0.2234 0.4777 0.3918 -0.3483 0.2236 -0.5962 0.0915 -0.4269 hemoglobin, gamma A ///

204419_ hemoglobin, NMJ)OOl x at gamma A /// 84 0.7972 -0.1687 -0.149 0.2333 -0.1496 0.133 0.0172 -0.0458 0.0443 -0.2066

Table 6: Group of 1645 genes that are differentially expressed unhealthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hemoglobin, gamma G /// hemoglobin, gamma G solute carrier family 2

(facilitated glucose/fructos

204430_ e transporter), NM_0030 s_at member 5 39 -0.3123 0.022 -0.2752 0.5301 0.0202 -0.018 -0.1254 0.3343 -0.1096 0.5114

204439_ interferon- NM_0068 at induced protein 20 -0.8455 0.8266 -0.2978 1.0407 0.7786 -0.6921 0.4831 -1.2884 0.1737 -0.8106

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

44-like zinc finger

4- 204453_ protein 84 NM_0034 at (HPF2) 28 0.3192 -0.0429 0.0913 0.3045 -0.0401 0.0356 0.0657 -0.1752 0.0624 -0.2914 synuclein, alpha (non A4 component of amyloid precursor) /// synuclein,

204466_, alpha (non A4 s at component of BG260394 0.4849 -0.1741 -0.1119 0.0693 -0.1604 0.1426 -0.0664 0.177 -0.0135 0.063

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score amyloid precursor)

Ul synuclein, alpha (non A4 component of amyloid precursor) /// synuclein, alpha (non A4 component of

204467_ amyloid NM_0003 s at precursor) 45 0.4917 -0.1665 -0.1543 0.0826 -0.154 0.1368 -0.0664 0.177 -0.0162 0.0757

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score chemokine (C-

X-C motif) ligand 1

(melanoma growth

204470_ stimulating NM_0015 at activity, alpha) 11 -0.4587 0.1389 0.27 0.1548 0.1275 -0.1134 0.0798 -0.2129 0.0305 -0.1421 zinc finger

204523_ protein 140 NM_0034 at (clone pHZ-39) 40 0.2644 0.0334 0.0553 0.4166 0.0308 -0.0274 0.1112 -0.2966 0.086 -0.4014

204642_ endothelial NM_0014 at differentiation, 00 0.3204 0.0013 0.1302 0.4611 0.0012 -0.0011 0.1141 -0.3044 0.0942 -0.4394

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score sphingolipid G-protein-

-4 coupled receptor, 1

204655_ NM_0029 at 85 0.3969 -0.0137 0.1113 0.4823 -0.0123 0.0109 0.118 -0.3146 0.0981 -0.458

CD52 antigen (CAMPATH-I antigen) /// CD52 antigen

204661_, (CAMPATH-I NMJ)Ol 8 at antigen) 03 0.3402 -0.0122 0.0663 0.3842 -0.0111 0.0098 0.0926 -0.247 0.0781 -0.3643

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

204669_. ring finger NM_0072 s_at protein 24 19 -0.8744 0.2582 0.1358 0.0874 0.2261 -0.201 0.0479 -0.1277 -0.0159 0.0743

OO intercellular

204683_ adhesion NM_0008 -2.00E- 2.00E- at molecule 2 73 0.352 04 0.101 0.4617 04 0.1153 -0.3075 0.0935 -0.4363 interferon

204698_ stimulated NM_0022 at gene 2OkDa 01 -0.4275 0.2931 -0.1929 0.1525 0.2765 -0.2458 0.1145 -0.3054 0.029 -0.1355 coagulation factor V

204714_ (proaccelerin, NMJ)OOl s at labile factor) 30 -0.515 0.0301 0.1742 0.2861 0.027 -0.024 -0.066 0.1761 -0.0564 0.263

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), MA patients.. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score mterferon- induced protein with

204747_ tetratricopeptid NM_0015 at e repeats 3 49 -0.8957 0.7108 -0.2024 0.7716 0.6549 -0.5822 0.3891 4.0376 0.1258 -0.5871 prostaglandin- endoperoxide synthase 2

(prostaglandin

G/H synthase

204748_ and NM_0009 at cyclooxygenas 63 -0.6182 0.2313 0.2823 0.2476 0.21 -0.1867 0.1273 -0.3394 0.0474 -0.2211

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score e) mal, T-cell ^β 204777_. differentiation NM_0023 s at protein 71 0.2462 0.0162 0.1763 0.4682 0.0147 -0.0131 0.1235 -0.3293 0.0963 -0.4495

G protein- coupled receptor associated

204793_ sorting protein NM_0147 at 1 10 0.5548 -0.1144 0.0727 0.3404 -0.1019 0.0906 0.0569 -0.1517 0.0665 -0.3102

204811_ calcium NM_0060 s at channel, 30 0.3759 -0.2012 0.2324 0.0769 -0.1916 0.1703 -0.0312 0.0832 0.0154 -0.0719

Table 6: Group of 1645 genes that are differentially expressed in healthy dønørø, SLE patients (lupus score), RA patients,, and WG patients,

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score voltage- dependent, alpha 2/delta subunit 2 butyropnilin,

204821_, subfamily 3, NM_0069 at member A3 94 0.0487 0.2284 -0.0282 0.6324 0.2061 -0.1832 0.2162 -0.5766 0.Ϊ29 -0.6022

204838_ mutL homolog NMJ) 143 s_at 3 (E. coli) 81 0.6738 -0.0414 -0.1212 0.4718 -0.0354 0.0315 0.1111 -0.2964 0.0907 -0.4233 hemoglobin,

204848_ gamma A /// NM_0005 x at hemoglobin, 59 0.8267 -0.2185 -0.164 0.1168 -0.1979 0.1759 -0.0265 0.0708 0.0223 -0.104

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score gamma A MADl mitotic arrest

204857_ deficient-like 1 NM_0035 at (yeast) 50 0.1749 0.128 -0.0053 0.5176 0.1184 -0.1052 0.1594 -0.4251 0.1075 -0.5017 baculoviral

204860_ IAP repeat- s_at containing 1 AI817801 -0.4629 0.1961 -0.0968 0.0503 0.1837 -0.1633 0.036 -0.0961 -0.0099 0.0463 lymphocyte-

204890_ specific protein s_at tyrosine kinase U07236 0.3881 0.0475 0.0879 0.6139 0.0411 -0.0366 0.1682 -0.4485 0.1244 -0.5807

204891 lymphocyte- NM 0053 0.3935 0.0366 0.1825 0.0317 -0.0282 0.1766 -0.4708 0.1391 -0.649

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), JRA patients, and WG patients.

3 4 5 6 7 10 11 12 13

Representa Healthy tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title I IDD score score score score score 3 score score score score score s_at specific protein 5 566 0.6814 tyrosine kinase

W sin3 -associated

204900_ polypeptide, NM _0038 x_at 3OkDa 64 -0.3776 0.0442 -0.0548 0.3264 0.041 -0.0364 -0.0706 0.1882 -0.0666 0.3108

B-cell

204908_ CLL/lymphom NM _0051 s_at a 3 78 -0.651 0.1647 0.0831 0.1558 0.1464 -0.1301 0.0024 -0.0064 -0.0295 0.1376

204924_ toll-like NM _0032 at receptor 2 64 -0.4499 0.0914 -0.0816 0.3014 0.0825 -0.0734 -0.0534 0.1425 -0.0597 0.2785

204951_ ras homolog NM _0043 at gene family, 10 0.3416 0.0114 0.0144 0.3985 0.0102 -0.0091 0.1034 -0.2758 0.0807 -0.3764

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (Itjpus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

4- 4- member H protein tyrosine phosphatase, receptor type,

204960_ C-associated NM_0056 at protein 08 0.3797 0.0048 0.0906 0.4939 0.0043 -0.0038 0.1258 -0.3354 0.1006 -0.4694

2 -5'- oligoadenylate

204972_ synthetase 2, NM_0168 at 69/7IkDa 17 -0.5255 0.6049 -0.2579 0.8199 0.5699 -0.5066 0.3594 -0.9584 0.1472 -0.68:

204994 myxoviras NM 0024 -0.4731 0.339 -0.1843 0.3173 -0.282 0.1471 -0.3922 0.0434 -0.202

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe rive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at (influenza 63 0.2358 virus)

CΛ resistance 2

(mouse)

205003_ dedicator of NM_0147 at cytokinesis 4 05 -0.4773 0.2592 -0.0099 0.1868 0.2429 -0.2159 0.1126 -0.3002 0.0361 -0.1686

N-

205006_ myristoyltransf NM_0048 s_at erase 2 08 0.2744 0.0344 0.1368 -0.508 0.0309 -0.0275 0.1347 -0.3592 0.1043 -0.4866 transforming

205016_ growth factor, NM_0032 at alpha 36 -0.4255 0.0871 -0.0667 0.2732 0.0791 -0.0703 -0.0469 0.125 -0.0543 0.2534

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score muscleblmd-

0.2098 0.0865 0.103 0.5475 0.0795 -0.0706 0.1628 -0.434 0.114 -0.5322 defensin, alpha

1, myeloid- related sequence /// defensin, alpha

205033_ 3, neutrophil- NM_0040 s_at specific 84 -0.4409 -0.0133 -0.2603 0.7433 -0.0117 0.0104 -0.1916 0.5111 -0.1528 0.7131

205040_ NM_0006 at orosomucoid 1 07 -0.3259 -0.1465 0.0775 0.6539 -0.1351 0.1201 -0.2215 0.5906 -0.1364 0.6367

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients_* and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe live Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set BD Gene Title ID score score score score score 3 score score score score score orosomucoid 1

205041_ /// NM_0006 s_at orosomucoid 2 07 -0.299 -0.1311 0.0249 0.6356 -0.1207 0.1073 -0.2086 0.5564 -0.1327 0.6194

CD79A antigen

(immunoglobul in-associated alpha) ///

CD79A antigen

205049_ (immunoglobul NMJ)017 s at in-associated 83 0.3517 0.0062 -0.0926 0.2922 0.0058 -0.0052 0.0766 -0.2043 0.0597 -0.2788

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score alpha) solute carrier family 26 (sulfate

S

205097_ transporter), at membei 2 AI025519 0.4292 -0.0549 -0.0667 0.2346 -0.0507 0.0451 0.0473 -0.1262 0.0473 -0.2208 cheniokine (C-

205098_ C motif) at receptor 1 AI421071 -0.5454 0.3679 0.0236 0.4382 0.3398 -0.302 0.2015 -0.5373 0.0818 -0.3816 chemokine (C-

205099_ C motif) NM_0012 s at receptor 1 95 -0.5211 0.4109 -0.0301 0.5263 0.3827 -0.3401 0.2395 -0.6387 0.0984 -0.4591

Table 6; Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (hipm score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score chemokine (C- C motif) ligand

O 3 /// chemokine (C-C motif) ligand 3-like 1 /// chemokine (C-C motif)

205114_ ligand 3-like, NMJ)029 s_at centromeric 83 -0.3599 0.1867 0.0649 0.1872 0.1778 -0.158 0.0965 -0.2574 0.0378 -0.1764 prostaglandin-

205127_ endoperoxide NM_0009 at synthase 1 62 0.5199 -0.1027 -0.1046 0.1645 -0.0955 0.0849 0.0158 -0.0421 0.0329 -0.1537

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(prostaglandin G/H synthase

O and cyclooxygenas e) protein tyrosine phosphatase, non-receptor type 4

205171_ (megakaryocyt NM__0028 at e) 30 0.4244 -0.0017 0.0215 0.4564 -0.0015 0.0013 0.1152 -0.3071 0.0911 -0.4252

Table 6: Group of 1645 genes that are differentially expressed ia healthy døaots, SLE patients (tapis score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score glutaminyl- £ ' peptide cyclotransferas

205174_ e (glutaminyl NMJH24 s_at cyclase) 13 -0.6987 0.1002 0.1289 0.3331 0.0868 -0.0771 -0.0595 0.1586 -0.0632 0.295 rabphilin 3 A

205230_ homolog NMJ3149 at (mouse) 54 -0.4066 0.1949 -0.0855 0.0158 0.1857 -0.165 0.0531 -0.1415 0.0032 -0.0148

SCO cytochrome

205241 oxidase NM — 0051 - at deficient 38 -0.5045 0.3655 -0.1184 0.3374 0.3426 -0.3045 0.182 -0.4852 0.0626 -0.2924

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients,, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score homolog 2

K)

(yeast) early growth response 2

(Krox-20

205249_ homolog, NM__0003 at Drosophila) 99 - -00..883355'7 0.3275 0.2671 0.2638 0.2919 -0.2594 0.156 -0.4159 0.0483 -0.2252 transcription factor 7 (T-cell

205254_ specific, HMG- AW02735 x_at box) 9 0.2419 0.0419 0.1412 0.4985 0.0377 -0.0335 0.1376 -0.3669 0.1025 -0.4782

205255 transcription NM 0032 0.3709 1.00E- 0.0474 - ####### -1.00E- 0.1089 -0.2904 0.0873 -0.4073

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus seøre)_> RA patients, and WG patients. ,

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score x_at factor 7 (T-cell 02 04 0.4305 04 specific, HMG-

Ul

W box) nuclear receptor subfamily 3,

205259_ group C, NM_0009 - at member 2 01 0.3767 -0.0014 0.0522 0.4373 -0.0012 0.0011 0.1102 -0.2939 0.0898 -0.4189 acylphosphatas

205260_ e 1, erythrocyte NMJ)OIl s_at (common) type 07 0.2318 0.0542 0.1694 -0.548 0.0496 -0.044 0.1478 -0.3941 0.1139 -0.5317

205267 POU domain, NM 0062 0.2462 0.0885 -0.1148 _ 0.0825 -0.0733 0.1175 -0.3134 0.0784 -0.366

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at class 2, 35 0.3808 associating factor 1 interleukin 2 receptor, beta

205291_. /// interleukin 2 NM_0008 at receptor, beta 78 0.4484 -0.129 0.0792 0.1974 -0.1178 0.1047 0.0179 -0.0477 0.0388 -0.1812 spleen focus forming virus

(SFFV)

205312_ proviral NM_0031 at integration 20 -0.5169 0.1114 0.0408 0.1997 0.1026 -0.0912 -0.0228 0.0609 -0.0397 0.1853

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score oncogene spil

205353 prostatic NM_0025

'Jl

¹^ s_at binding protein 67 0.3089 0.0574 0.1696 0.6368 0.0513 -0.0456 0.1702 -0.454 0.1317 -0.6145 pleomorphic

205372_ adenoma gene NM_0026 at 1 55 0.5029 -0.0803 -0.1154 0.1963 -0.0747 0.0664 0.0294 -0.0783 0.0395 -0.1844

Wiskott-

Aldrich syndrome

(eczema-

205400_ thrombocytope NM_0003 at nia) 77 -0.5501 0.1243 0.0814 0.1608 0.1119 -0.0994 -0.0096 0.0255 -0.0311 0.1453

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score interleukin 1

205403_ receptor, type NM_0046 at II 33 -0.3668 -0.0281 -0.0428 0.4964 -0.0258 0.0229 -0.128 0.3413 -0.1025 0.4783 reversion- inducing- cysteine-rich

205407_ protein with NM_0211 at kazal motifs 11 0.2975 0.0082 0.0828 -0.41 0.0075 -0.0067 0.1023 -0.2728 0.0843 -0.3932 Epstein-Barr virus induced

205419_ gene 2 NM_0049 at (lymphocyte- 51 0.2985 0.0345 0.1249 0.5218 0.0312 -0.0277 0.1396 -0.3723 0.1074 -0.5013

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score specific G protein-

Ul -4 coupled receptor)

205437_ zinc finger NM_0063 at protein 211 85 0.3942 -0.0796 0.1743 0.3642 -0.0717 0.0637 0.07 -0.1866 0.0727 -0.3392

205442_ NM_0216 at — 47 0.571 -0.1445 -0.1145 0.0965 -0.1303 0.1158 -0.0124 0.0331 0.0186 -0.0867 platelet-derived growth factor

205463_ alpha NM_0026 s_at polypeptide 07 0.4636 -0.0936 -0.0896 0.1448 -0.0871 0.0774 0.0126 -0.0335 0.029 -0.1355

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score dachshund

205471_ homolog 1 AW77208

OO s_at (Drosophila) 2 -0.2219 -0.0449 0.0268 0.324 -0.0416 0.0369 -0.0929 0.2477 -0.0665 0.3105 interferon, alpha-inducible

205483_ protein (clone NM_0051 s_at IFI-15K) 01 -0.7435 0.7396 -0.2888 0.9232 0.6939 -0.6168 0.431 -1.1492 0.1556 -0.7261 granzyme A

(granzyme 1, cytotoxic T-

205488_ lymphocyte- NM_0061 at associated 44 0.3405 0.0071 0.0747 0.4439 0.0065 -0.0058 0.1135 -0.3025 0.0909 -0.4243

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SEE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score serine esterase

3) /// granzyme

A (granzyme 1, cytotoxic T- lymphocyte- associated serine esterase

3)

205495_, granulysin /// NM_0064 s_at granulysin 33 0.4926 -0.1164 0.2425 0.4338 -0.1056 0.0939 0.0796 -0.2123 0.0868 -0.4051

205513_ transcobalamin NMJ)OlO at I (vitamin B12 62 -0.4871 0.0049 -0.1713 0.6569 0.0042 -0.0038 -0.1603 0.4275 -0.132 0.6162

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score binding protein, R binder family) Gl to S phase transition 2 ///

205541_ Gl to S phase NMJ)180 s at transition 2 94 0.3545 0.048 0.0889 0.5814 0.0427 -0.038 0.1561 -0.4163 0.1192 -0.5561 2 ',5 - oligoadenylate

205552_ synthetase 1, NM_0025 s_at 40/46kDa 34 -0.7121 0.6812 -0.2974 0.7916 0.6468 -0.5749 0.3737 -0.9964 0.1366 -0.6373

205557 bactericidal/per NM_0017 -0.4085 -0.0138 -0.3136 0.7623 -0.0121 0.0108 -0.193 0.5146 -0.1573 0.7342

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at meability- 25 increasing protein lysosomal- associated

205569_. membrane NM_0143 at protein 3 98 -0.5121 0.4811 -0.309 0.4543 0.4641 -0.4125 0.2508 -0.6688 0.0844 -0.394 RAS guanyl releasing protein 1

205590_ (calcium and NM_0057 at DAG- 39 0.3618 0.0088 0.1057 0.5006 0.0079 -0.007 0.1265 -0.3373 0.1022 -0.4768

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score regulated)

^ 205627 — cytidine NM — 0017 at deaminase 85 -0.3846 0.0032 0.0427 0.349 0.003 -0.0026 -0.0872 0.2326 -0.0706 0.3293

RALBPl associated Eps

205645_ domain NM_0047 at containing 2 26 -0.272 -0.0323 0.0558 0.3144 -0.03 0.0267 -0.0863 0.2302 -0.0646 0.3016

205653_ NM_0019 at cathepsin G 11 -0.4075 0.0214 -0.1727 0.5319 0.0194 -0.0173 -0.1265 0.3372 -0.1092 0.5096

2'-5'-

205660_ oligoadenylate NM_0037 at synthetase-like 33 -0.6469 0.5792 -0.2888 0.5956 0.5495 -0.4885 0.2939 -0.7837 0.104 -0.4854

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

205681_ BCL2-related NM_0040

^ at protein Al 49 -0.601 0.1901 0.0422 0.0757 0.1711 -0.1521 0.0292 -0.0778 -0.0144 0.067

©\

W

A kinase

(PRKA)

205771_ anchor protein s_at 7 ALl 37063 0.2696 0.02 0.1363 0.4642 0.0182 -0.0162 0.12 -0.3201 0.0955 -0.4455 interleukin 7 receptor ///

205798_ interleukin 7 NM__0021 - at receptor 85 0.5908 -0.0702 0.0543 0.4776 -0.0627 0.0558 0.1051 -0.2803 0.0952 -0.4443

205808_ aspartate beta- NM_0043 at hydroxylase 18 -0.1965 -0.0392 -0.1853 0.4867 -0.0364 0.0324 -0.1312 0.3498 -0.1015 0.4735

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score killer cell lectin-like receptor

205821. subfamily K, NM_0073 at member 1 60 0.4341 -0.0417 0.0885 -0.424 -0.0373 0.0332 0.0959 -0.2556 0.0851 -0.3969 myomesin (M- protein) 2, 165kDa /// myomesin (M-

205826_ protein) 2, NM_0039 at 165kDa 70 0.3401 0.0261 -0.0614 0.3632 0.0247 -0.022 0.1074 -0.2863 0.0756 -0.353

205831 CD2 antigen NM 0017 0.3223 0.0192 0.1577 0.0171 -0.0152 0.1386 -0.3697 0.1097 -0.512

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at (p50), sheep 67 0.5373 red blood cell

'Jl receptor /// CD2 antigen (p50), sheep red blood cell receptor

205844_ vanin 1 /// NM_0046 at vanin 1 66 -0.5806 0.1137 0.0279 0.2721 0.1041 -0.0925 -0.0418 0.1116 -0.054 0.2521 Spi-B

205861_ transcription NM_0031 at factor (Spi- 21 0.2958 0.0361 -0.0849 0.3214 0.0337 -0.03 0.0922 -0.2458 0.0661 -0.3085

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

1/PU.l related) /// Spi-B transcription factor (Spi- 1/PU.l related) SlOO calcium binding protein A12

(calgranulin C) /// SlOO

205863_ calcium NM 0056 at binding protein 21 -0.3938 -0.0566 0.1041 0.4591 -0.0508 0.0451 -0.1298 0.3461 -0.0928 0.4331

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

A12

(calgranulin C)

-4 three prime

205875_ repair NM_0163 s_at exonuclease 1 81 -0.258 0.3927 -0.2483 0.5407 0.3737 -0.3322 0.2398 -0.6394 0.1045 -0.4877

POU domain, class 6,

205878_ transcription NM_0027 at factor 1 02 0.3554 -0.0581 0.0889 0.2992 -0.0537 0.0477 0.0599 -0.1598 0.0607 -0.2834 integrin, alpha

205884_ 4 (antigen NM_0008 at CD49D, alpha 85 -0.0138 0.1797 0.0896 0.5512 0.1666 -0.1481 0.1833 -0.4887 0.1142 -0.5331

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

4 subunit of VLA-4

OO receptor) integrin, alpha 4 (antigen CD49D, alpha 4 subunit of

205885_ VLA-4 s_at receptor) L12002 0.1149 0.1765 0.03 0.6188 0.1611 -0.1432 0.2032 -0.5419 0.1283 -0.5988 solute carrier

205896_ family 22 NM 0030 at (organic cation 59 -0.5291 0.1031 -0.0203 0.2933 0.0921 -0.0819 -0.0476 0.1269 -0.0573 0.2674

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score transporter), member 4

"° chemokine (C-

205898_ X3-C motif) at receptor 1 U20350 0.1695 0.0284 0.2373 -0.48 0.0259 -0.023 0.1295 -0.3454 0.0991 -0.4622

205936_ hexokinase 3 NM_0021 s_at (white cell) 15 -0.4268 -0.0388 0.0963 0.4533 -0.0341 0.0303 -0.1246 0.3322 -0.0904 0.4218

205987_ CDlC antigen, NM_0017 at c polypeptide 65 0.4609 -0.0928 0.0475 0.2762 -0.0873 0.0776 0.0455 -0.1214 0.0564 -0.2631 tumor necrosis

206025_ factor, alpha- AWl 8819 s_at induced protein 8 -0.6608 0.4126 -0.1289 -0.291 0.3869 -0.3439 0.1826 -0.4869 0.0533 -0.2487

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

tumor necrosis

O factor, alpha-

206026_ induced protein NM_0071 s_at 6 15 -0.6494 0.3821 -0.0916 0.2572 0.3558 -0.3163 0.1646 -0.4389 0.0472 -0.2205 small nuclear ribonucleoprot ein polypeptide

N /// SNRPN

206042_ upstream NM_0228 x_at reading frame 04 0.5322 -0.0351 0.0729 0.5286 -0.0306 0.0272 0.1243 -0.3316 0.105 -0.4901

206055 small nuclear NM 0030 0.2296 0.0355 0.1261 - 0.0327 -0.0291 0.1218 -0.3249 0.0941 -0.4391

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at ribonucleoprot 90 0.4542 ein polypeptide A' zinc finger protein 91

206059_ ( (HHPPFF77,, NM_0034 at H HTTFFllOO)) 30 0.3718 -0.0828 0.1308 0.2909 -0.0761 0.0676 0.0534 -0.1423 0.0586 -0.2736

206099_ protein kinase NM_0062 at C C,, e ettaa 5555 0.3482 0.0013 0.0849 0.4463 0.0012 -0.0011 0.1153 -0.3076 0.0907 -0.4232

206110_ N NMM__00003355 at h hiissttoonnee 11,, H H33hh 3366 0.5449 -0.0325 -0.1854 0.2998 -0.029 0.0258 0.0702 -0.1872 0.0588 -0.2743

206111_ ribonuclease, NM_0029 -0.352 0.01 -0.0405 0.3774 0.0092 -0.0081 -0.0951 0.2536 -0.077 0.3594

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at RNase A 34

-4 family, 2 (liver, eosinophil- derived neurotoxin)

206115_ early growth NM_0044 at response 3 30 -0.4303 0.1311 0.1432 0.0412 0.1223 -0.1087 0.0456 -0.1217 0.0082 -0.0384

XIAP

206133_ associated NMJ)175 at factor- 1 23 -0.5166 0.5833 -0.2821 -0.748 0.5544 -0.4928 0.3428 -0.9141 0.1353 -0.6316

206150_ tumor necrosis NM_0012 at factor receϋtor 42 0.4636 0.0161 0.0314 0.5539 0.014 -0.0124 0.1456 -0.3881 0.1111 -0.5185

superfamily, member 7 ///

-4 tumor necrosis factor receptor superfamily, member 7 pentraxin- related gene,

206157_ rapidly induced NM_0028 at by IL-I beta 52 -0.3337 0.0078 -0.1601 0.4793 0.0071 -0.0063 -0.1187 0.3166 -0.0983 0.4587

206175_, zinc finger NM_0133 x at protein 222 60 -0.38 0.2547 0.0299 0.3138 0.2416 -0.2147 0.1569 -0.4184 0.0625 -0.2915

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

206177_ NMJ)OOO s_at arginase, liver 45 -0.5834 -0.0623 -0.1034 0.8708 -0.0533 0.0473 -0.2309 0.6158 -0.1777 0.8294

206208_ carbonic NMJ0OO7 at anhydrase rV 17 -0.4691 -0.0279 -0.0184 0.5786 -0.0247 0.022 -0.1562 0.4164 -0.1174 0.548

206209_ carbonic NM_0007 s_at anhydrase rV 17 -0.2775 -0.0596 0.0523 0.3964 -0.0548 0.0487 -0.1139 0.3038 -0.0813 0.3793

RAS p21

206220_ protein NM_0073 s_at activator 3 68 0.3263 -0.0151 -0.0013 0.2968 -0.0142 0.0126 0.0731 -0.1948 0.0612 -0.2856 complement

206244_ component NM_0005 at (3b/4b) 73 -0.6033 0.088 0.1572 0.2397 0.0789 -0.0701 -0.0415 0.1108 -0.0467 0.2181

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score receptor 1, including

-4

Knops blood group system epidermal growth factor

206254_ (beta- NMJ)019 at urogastrone) 63 0.3435 -0.1344 -0.1898 0.185 -0.1262 0.1122 -0.0885 0.2359 -0.0373 0.1741

206255_ B lymphoid NM_0017 at tyrosine kinase 15 0.5524 -0.0822 0.1586 0.5064 -0.0742 0.0659 0.109 -0.2906 0.102 -0.4762

206267_ megakaryocyte NM_0023 s at -associated 78 0.5191 -0.1211 0.1055 -0.317 -0.1103 0.098 0.0484 -0.1292 0.0629 -0.2935

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set E) Gene Title ID score score score score score 3 score score score score score tyrosine kinase

206271 toll-like NM_0032

-4 at receptor 3 65 0.3788 -0.0655 0.0776 0.2929 -0.0607 0.0539 0.0573 -0.1529 0.0595 -0.2775 mitogen- activated protein kinase

206296_ kinase kinase NM_0071 x at kinase 1 81 0.2959 0.0394 0.1116 0.5194 0.0363 -0.0323 0.1404 -0.3743 0.1079 -0.5037 interferon, gamma-

206332_ inducible NM_0055 s at protein 16 31 -0.5887 0.3907 -0.1745 0.2634 0.3612 -0.3211 0.1685 -0.4494 0.0467 -0.2182

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score). RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other ' Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score chemokine (C-

C motif)

-4 -4 receptor 7 /// chemokine (C-

206337_ C motif) NM_0018 at receptor 7 38 0.6084 -0.0037 0.0544 0.6735 -0.0031 0.0028 0.1704 -0.4545 0.133 -0.6204 suppressor of

206359_ cytokine at signaling 3 BG035761 -0.5108 0.1176 0.011 0.2055 0.1089 -0.0968 -0.0244 0.0651 -0.041 0.1915

206366_ chemokine (C x_at motif) ligand 2 U23772 0.4128 -0.1244 0.0997 0.1925 -0.1171 0.1041 0.0168 -0.0449 0.039 -0.182

206371 folate receptor NM_0008 -0.3086 0.1021 -0.1333 0.176 0.0975 -0.0866 -0.0189 0.0505 -0.0362 0.169

Table 6: Group of 1645 genes ftat are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at 3 (gamma) 04 ankyrin 3, node

∞ 206385_ ofRanvier NM_0209 s_at (ankyrin G) 87 0.3177 0.0262 0.1979 0.5899 0.0237 -0.0211 0.152 -0.4053 0.1221 -0.5697 platelet factor 4

(chemokine

206390_ (C-X-C motif) NM_0026 x_at Iigand 4) 19 0.6184 -0.1303 -0.291 0.0137 -0.1169 0.1039 -0.03 0.0801 0.0026 -0.0123

206440_ lin-7 homolog NM_0046 at A (C. elegans) 64 -0.3364 0.04 0.0098 0.2328 0.0373 -0.0331 -0.0496 0.1322 -0.0474 0.2214

206445 HMTl hnRNP NM 0015 - s_at methyltransfera 36 0.3809 -0.0068 0.1001 0.4732 -0.0061 0.0054 0.1156 -0.3084 0.0955 -0.4455

patients_*

^ cerevisiae)

"° 206461_ metallothionein NM_0059 x_at IH 51 -0.2806 0.3766 -0.2699 0.4533 0.3604 -0.3203 0.2237 -0.5966 0.0875 -0.4085

BMX non-

206464_ receptor NM_0017 at tyrosine kinase 21 -0.5425 0.0257 0.0856 0.4116 0.0232 -0.0206 -0.1007 0.2684 -0.0825 0.3848 maltase- glucoamylase

206522_ (alpha- NM_0046 at glucosidase) 68 -0.2467 -0.071 0.1387 0.3117 -0.0668 0.0594 -0.0931 0.2482 -0.0643 0.3001

206553 — 2'-5'- NM — 0025 -0.2358 0.5208 -0.1495 - 0.471 -0.4187 0.3786 -1.0096 0.1918 -0.8951

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at oligoadenylate 35 1.0003 synthetase 2,

OO O

69/7IkDa

THUMP

206555_ domain NMJ)177 s_at containing 1 36 0.2794 0.0184 0.1603 0.4932 0.0168 -0.0149 0.1264 -0.3371 0.1017 -0.4747

206584_ lymphocyte NM_0153 at antigen 96 64 -0.5692 0.2673 -0.0318 -0.092 0.2445 -0.2173 0.091 -0.2428 0.0172 -0.0801

206617_^ renin binding NM_0029 s_at protein 10 -0.4175 -0.0544 0.201 0.3844 -0.0497 0.0442 -0.109 0.2908 -0.0778 0.3632

206618_ interleukin 18 NM_0038 at receptor 1 55 -0.4155 0.0607 -0.1372 0.401 0.056 -0.0498 -0.0825 0.22 -0.0819 0.382

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score glycoprotein Ib

206655_ (platelet), beta NM_0004 s_at polypeptide 07 0.4999 -0.1046 -0.2617 0.0127 -0.0969 0.0861 -0.0302 0.0805 -0.0025 0.0118 granzyme K

(serine protease, granzyme 3; tryptase II) /// granzyme K

(serine

206666_ protease, NM_0021 at granzyme 3; 04 0.3367 0.0393 -0.047 0.4087 0.0365 -0.0325 0.1078 -0.2873 0.0844 -0.394

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score tryptase II)

OO fins-related

206674_ tyrosine kinase NM_0041 at 19 -0.0697 -0.1342 -0.091 0.5179 -0.1253 0.1114 -0.1632 0.4352 -0.1082 0.5048 carcinoembryo nic antigen- related cell

206676_ adhesion at molecule 8 M33326 -0.5552 0.0352 -0.374 0.842 0.0303 -0.0269 -0.2029 0.541 -0.1709 0.7974

206697_ NM_0051 s_at haptoglobin 43 -0.3047 -0.0717 -0.1307 0.633 -0.0645 0.0573 -0.1911 0.5097 -0.1313 0.6128

206710 erythrocyte NM 0123 -0.0402 0.2196 0.1627 0.1994 -0.1772 0.23 -0.6132 0.1449 -0.676

Table 6: Group of 1645 genes that are differentially expressed m. healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at membrane 07 0.7006 protein band 4.1 -like 3 Fc fragment of IgE, low affinity II,

206759_ receptor for NM_0020 at (CD23A) 02 0.3999 -0.061 -0.052 -0.202 -0.0577 0.0513 0.036 -0.096 0.0415 -0.1934

206761_ NM_0058 at CD96 antigen 16 0.3455 -0.0575 0.1964 0.3941 -0.0524 0.0466 0.0824 -0.2198 0.08 -0.3731

206785_ killer cell NM_0022 s at lectin-like 60 0.551 -0.0707 0.138 0.5158 -0.0638 0.0567 0.1101 -0.2936 0.1041 -0.486

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score receptor

00 subfamily C, member 1 /// killer cell lectin-like receptor subfamily C, member 2

206828_ TXK tyrosine NM_0033 at kinase 28 0.5399 -0.0889 0.0416 0.3629 -0.0785 0.0698 0.0693 -0.1847 0.0709 -0.3309

206834_ hemoglobin, NM_0005 at delta /// 19 0.3896 -0.1467 -0.1795 0.1599 -0.1377 0.1224 -0.0831 0.2215 -0.0321 0.1499

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hemoglobin, delta ribonuclease,

RNase A family, 3

(eosinophil

206851_ cationic NM_0029 at protein) 35 -0.4176 -0.0039 -0.1149 0.5541 -0.0035 0.0031 -0.1448 0.3862 -0.1136 0.5302

206871_ elastase 2, NMJ)Ol 9 at neutrophil 72 -0.5426 -0.0275 -0.2767 0.9026 -0.0237 0.0211 -0.2326 0.6203 -0.1858 0.8671

206877_ MAX NM_0023 at dimerization 57 -0.3415 0.2 -0.0703 0.1115 0.1911 -0.1698 0.0792 -0.2112 0.0224 -0.1045

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein 1

OO leukocyte

O\ immunoglobuli n-like receptor, subfamily A

(without TM

206881_ domain), NM_0068 s_at member 3 65 -0.3056 0.0829 0.0649 0.0335 0.0793 -0.0705 0.0139 -0.0372 -0.0069 0.0321

206965_ Kruppel-like NMJ) 162 at factor 12 85 0.487 -0.0793 -0.05 0.2454 -0.0734 0.0653 0.0429 -0.1145 0.0494 -0.2306

206991_ chemokine (C- NM_0005 s at C motif) 79 0.1574 0.105 0.1419 0.5798 0.0953 -0.0847 0.174 -0.4639 0.1205 -0.5623

TaWe 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients. {

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score receptor 5 protein

-4 phosphatase 3

(formerly 2B), catalytic subunit, gamma isoform

207000_ (calcineurin A NM_0056 s_at gamma) 05 0.4288 0.0743 0.1128 0.7514 0.065 -0.0577 0.2022 -0.5392 0.1547 -0.7221

207053_ solute carrier NM_0210 at family 8 97 -0.2884 -0.0644 0.1173 0.3577 -0.0605 0.0538 -0.1074 0.2864 -0.0741 0.3456

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(sodium/calciu m exchanger),

00 member 1 solute carrier family 16

(monocarboxyl ic acid

207057_ transporters), NM_0047 at member 7 31 0.4217 -0.1247 -0.0393 0.0668 -0.118 0.1049 -0.015 0.04 0.0135 -0.0631 interleukin 18

207072_ receptor NM_0038 at accessory 53 -0.4143 0.0249 -0.1222 0.4809 0.0226 -0.0201 -0.116 0.3093 -0.0981 0.4577

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein

OO colony stimulating factor 2 receptor, alpha, low-affinity

207085_ (granulocyte- NM_0061 x_at macrophage) 40 -0.2244 -0.0785 0.0514 0.3926 -0.0722 0.0642 -0.1253 0.3342 -0.0806 0.376 arachidonate

207206_ 12- NM_0006 s_at lipoxygenase 97 0.4256 -0.0495 -0.1827 0.1332 -0.0461 0.041 0.023 -0.0614 0.0268 -0.1253

207269 defensin. alϋha NM 0019 -0.4223 -0.059 -0.2757 0.8608 -0.051 0.0453 -0.2218 0.5914 -0.178 0.8304

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at 4, corticostatin 25 acyl-CoA

O synthetase long-chain

207275_ family member NM_0019 s at 1 95 -0.5389 0.0951 0.0332 0.2733 0.0851 -0.0757 -0.0453 0.1209 -0.0534 0.2493 matrix metalloproteina

207329_. se 8 (neutrophil NM_0024 at collagenase) 24 -0.4939 0.0644 -0.4265 0.7511 0.0556 -0.0494 -0.1731 0.4615 -0.151 0.7045

207341_ proteinase 3 NM_0027 at (serine 77 -0.2825 -0.109 -0.2106 0.7865 -0.0968 0.086 -0.2341 0.6243 -0.1643 0.767

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus scorej, RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score proteinase, neutrophil,

Wegener granulomatosis autoantigen) peptidoglycan

207384_ recognition NM_0050 at protein 1 91 -0.468 -0.1619 0.1408 0.7815 -0.1438 0.1278 -0.228 0.608 -0.1605 0.7491

207387_ NMJ)OOl s_at glycerol kinase 67 -0.4831 0.2536 -0.0016 0.1739 0.2349 -0.2088 0.112 -0.2988 0.0331 -0.1546

207460_ granzyme M NM_0053 at (lymphocyte 17 0.4085 0.0273 0.0849 0.5781 0.0242 -0.0215 0.1518 -0.4049 0.118 -0.5508

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLB patients (lupus score), RA patients,. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score met-ase 1) caspase 5,

VO apoptosis-

207500_ related cysteine NM_0043 at protease 47 -0.4233 0.2728 -0.1745 0.1203 0.2586 -0.2299 0.098 -0.2615 0.0233 -0.1088 solute carrier family 4, sodium bicarbonate

207604_ cotransporter, NM_0036 -9.00E- s_at member 7 15 0.5243 -0.1473 -0.0075 0.1437 -0.1369 0 .1217 04 0 .0025 0. 0285 -0 .1331

207610 egf-like NM 0134 -0.3589 0.0038 0.0764 0.2884 0.0035 -0 .0031 -0.075 0.2 -0 .0583 0. 2718

patients.

s at module 47 containing, mucin-like, hormone receptor-like 2

G protein-

207651_ coupled NMJH33 at receptor 171 08 0.1819 0.1511 0.036 0.6262 0.1355 -0.1204 0.1982 -0.5286 0.1294 -0.6038

Fc fragment of

207674_ IgA, receptor NMJ3020 at for 00 -0.5196 0.1238 0.121 0.0922 0.1139 -0.1012 0.0084 -0.0225 -0.0182 0.0847

207723 killer cell NM 0022 0.3489 -0.0018 0.1824 -0.0016 0.0014 0.1343 -0.3582 0.1096 -0.5115

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s at lectin-like 61 0.5329 receptor subfamily C, member 3

207777_ SP 140 nuclear NM_0072 s at body protein 37 -0.2189 0.355 -0.1984 0.5287 0.3325 -0.2956 0.2249 -0.5996 0.1016 -0.4743 killer cell lectin-like receptor

207795_ subfamily D, s_at member 1 AB009597 0.4127 -0.0705 0.129 0.3643 -0.0636 0.0566 0.0738 -0.1969 0.0729 -0.3404

207796 killer cell NM 0073 0.3661 -0.0488 0.1052 -0.0443 0.0394 0.0761 -0.2029 0.0708 -0.3303

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x_at lectin-like 34 0.3508

VO receptor Ul subfamily D, member 1 cysteine-rich

207802_ secretory NM_0060 at protein 3 61 -0.7796 0.1093 -0.2151 0.7241 0.0943 -0.0839 -0.1574 0.4197 -0.1426 0.6654

207815_ platelet factor 4 NM_0026 at variant 1 20 0.4574 0.1246 -0.2999 0.5178 0.1116 -0.0992 0.1648 -0.4394 0.1036 -0.4835

207831_ deoxyhypusine NM_0134 x_at synthase 07 0.3388 -0.0734 0.1849 0.3337 -0.0682 0.0606 0.0676 -0.1802 0.0682 -0.3181

207840 CD 160 antigen NM_0070 0.526 -0.1056 0.1386 -0.0948 0.0843 0.0736 -0.1963 0.0787 -0.3673

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at 53 0.3973 matrix Os 207890_ metalloproteina NM_0227 -6.00E- 5.00E- s_at se 25 18 -0.3354 04 0.061 0.2907 ####### 04 -0.0736 0.1961 -0.059 0.2755

CD40 ligand

(TNF superfamily, member 5,

207892_ hyper-IgM NM_0000 at syndrome) 74 0.2761 -0.0037 0.2891 0.5548 -0.0033 0.003 0.1383 -0.3688 0.1143 -0.5334

207979_ CD8 antigen, NM_0049 s at beta 31 0.2916 0.0722 -0.0541 0.4428 0.0657 -0.0584 0.1341 -0.3575 0.0906 -0.4229

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score polypeptide 1

(p37)

VO -4 Z-DNA binding protein

1 /// Z-DNA

208087_ binding protein NM_0307 s_at 1 76 -0.5413 0.4673 -0.3521 0.3457 0.4481 -0.3983 0.2097 -0.5593 0.0631 -0.2947 signal

208095_ recognition NM_0012 s_at particle 72kDa 22 0.1951 0.09 0.0879 -0.527 0.0821 -0.073 0.1526 -0.4071 0.1093 -0.5099

208168_ chitinase 1 NM_0034 s at (chitotriosidase 65 -0.1257 -0.1121 -0.3017 0.7197 -0.1008 0.0896 -0.205 0.5468 -0.1503 0.7014

TaMe 6: Group of 1645 genes that are differentially expressed in healthy donors, SUE patients (lupus score), RA patients, md WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

H ^e- 208185 — NMJ) 164 x_at — 15 0.4113 -0.0478 -0.1024 0.2004 -0.0446 0.0396 0.0391 -0.1044 0.0406 -0.1896 mucosa associated lymphoid tissue lymphoma

208309_ translocation NM_0067 s_at gene 1 85 0.2028 0.0379 0.088 0.3962 0.0354 -0.0314 0.108 -0.288 0.0823 -0.3839

208406_ GRB2-related NM_0048 s at adaυtor υrotein 10 0.6706 -0.0807 -0.1069 0.3774 -0.0724 0.0643 0.0798 -0.2129 0.0743 -0.3469

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

interferon

208436_ regulatory NM_0040 s_at factor 7 30 -0.6819 0.5264 -0.2783 0.4287 0.4937 -0.4389 0.2407 -0.6419 0.0736 -0.3437 related RAS viral (r-ras)

208456_ oncogene NM_0122 4.00E- -3.00E- s_at homolog 2 50 0.4716 04 0.0548 0.5429 ####### 04 0.1364 -0.3637 0.1109 -0.5176 haptoglobin ///

208470_ haptoglobin- NM_0209 s_at related protein 95 -0.3225 -0.0331 -0.2498 0.6632 -0.0299 0.0266 -0.1929 0.5144 -0.1379 0.6436

208488 complement N NMM 00000066 -0.4059 0.0094 0.1015 0.2982 0.0086 -0.0076 -0.075 0.2001 -0.0602 0.281

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s at component 51

O (3b/4b) O receptor 1, including Knops blood group system growth factor independent IB (potential regulator of

208501_, CDKNlA, NM_0041 at translocated in 88 0.3677 0.015 0.1269 0.5436 0.0136 -0.0121 0.1437 -0.3833 0.1117 -0.5211

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

CML) g 208581_ metallothionein NM_0059 x_at IX 52 -0.2702 0.42 -0.2579 0.5913 0.4002 -0.3558 0.2652 -0.7072 0.1142 -0.5328 tubulin, beta 1

208601_ /// tubulin, beta NM_0307 s_at 1 73 0.5819 -0.0163 -0.3046 0.2668 -0.0147 0.0131 0.0651 -0.1737 0.0526 -0.2457 serine/arginine 208610_ repetitive s_at matrix 2 AI655799 0.433 -0.1701 -0.1368 0.1365 -0.1597 0.1419 -0.0807 0.2153 -0.0272 0.127 protein

208612 disulfide - at isomerase- D83485 0.3408 0.0042 0.0591 0.4214 0.0037 -0.0033 0.1092 -0.2913 0.0853 -0.3982

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set E) Gene Title ID score score score score score 3 score score score score score associated 3

at PRO2640 AFl 16710 0.4017 -0.0987 0.176 0.3228 -0.0894 0.0795 0.0564 -0.1505 0.0642 -0.2998

CD24 antigen

(small cell lung carcinoma

208650_ cluster 4 s at antigen) BG327863 -0.2685 -0.0253 -0.2183 0.5562 -0.023 0.0205 -0.1411 0.3763 -0.1152 0.5375

CD24 antigen

(small cell lung

208651_, carcinoma x at cluster 4 M58664 -0.2535 -0.0157 -0.2908 0.5848 -0.0141 0.0125 -0.1484 0.3957 -0.1205 0.5623

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score antigen) κ>

O tetratricopeptid

208661_ e repeat AW51069 s_at domain 3 6 0.411 -0.0185 0.0478 0.4231 -0.0168 0.0149 0.1011 -0.2697 0.0861 -0.4018 tetratricopeptid 208662_ e repeat s_at domain 3 AI885338 0.4472 -0.0375 0.0562 0.4178 -0.0336 0.0298 0.0959 -0.2556 0.0837 -0.3907 tetratricopeptid 208663_ e repeat - s_at domain 3 AI652848 0.4863 -0.0459 0.0212 0.4022 -0.0424 0.0377 0.0928 -0.2474 0.082 -0.3825

208744 heat shock - x at 105kDa/110kD BG403660 0.3901 0.0281 -0.1058 0.3774 0.0261 -0.0232 0.1067 -0.2845 0.0775 -0.3617

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score a protein 1 g 208749_ x at flotillin l AF085357 -0.3741 -0.002 0.0154 0.3786 -0.0018 0.0016 -0.0962 0.2566 -0.0758 0.3538

N- ethylrnaleimide

-sensitive factor

208751_ attachment at protein, alpha BC001165 -0.2445 0.3083 -0.0994 0.4729 0.2875 -0.2556 0.1971 -0.5256 0.0918 -0.4282 nucleosonie

208752_ assembly x at protein 1 -like 1 AI888672 0.3905 -0.0457 0.11 0.3892 -0.0405 0.036 0.0853 -0.2276 0.0776 -0.3619

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score nucleosome g 208754 assembly s at protein 1 -like 1 AL162068 0.3519 -0.0165 0.1131 0.4297 -0.0149 0.0133 0.1025 -0.2734 0.0873 -0.4073

5- aminoimidazol e-4- carboxamide ribonucleotide formyltransfera

208758_ se/IMP at cyclohydrolase D89976 0.3883 0.0169 0.0191 0.4662 0.015 -0.0133 0.1214 -0.3238 0.0939 -0.4383.

208791 clusterin M25915 0.4912 -0.0929 -0.165 -0.0866 0.0769 0.0026 -0.007 0.0206 -0.0962

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, andWG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at (complement 0.1028

O lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone- repressed prostate message 2, apolipoprotein

J)

208792 clusterin M25915 0.4414 -0.096 -0.231 0.0207 -0.0888 0.0789 -0.031 0.0826 -0.0041 0.0192

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s at (complement

O lysis inhibitor, -4 SP-40,40, sulfated glycoprotein 2, testosterone- repressed prostate message 2, apolipoprotein

J)

208798 golgin-67 AF204231 0.4338 -0.0507 0.0512 -0.0458 0.0407 0.0786 -0.2097 0.0729 -0.3403

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x_at 0.3639

K O. 208808 - high-mobility

OO s_at group box 2 BC000903 -0.4868 0.0526 -0.0125 0.3767 0.0468 -0.0416 -0.0817 0.2178 -0.0747 0.3484 cisplatin resistance- associated

208835_ overexpressed AW08967 s_at protein 3 0.3928 -0.0101 -0.0615 0.3212 -0.0092 0.0082 0.0792 -0.2111 0.0648 -0.3024 likely ortholog of mouse

208858_ membrane s at bound C2 BC004998 0.3407 0.0445 0.2106 0.6746 0.039 -0.0347 0.1732 -0.462 0.1387 -0.6473

Table 6: Group of 1645 genes that are differentially expressed in heal thy donors „ SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score domain

O containing protein alpha thalassemia/me ntal retardation syndrome X- linked (RAD54

208859_. homolog, S. s_at cerevisiae) AI650257 0.3081 -0.0539 -0.0492 0.1283 -0.0514 0.0457 0.0207 -0.0553 0.0264 -0.1234

208879_^ chromosome x at 20 open BG469030 0.5264 -0.1492 0.1106 0.2544 -0.1393 0.1238 0.0262 -0.0698 0.051 -0.2382

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score reading frame 14

O major histocompatibil ity complex, class II, DR alpha /// major histocompatibil ity complex,

208894_ class II, DR at alpha M60334 0.3575 0.0097 0.0697 0.4639 0.0087 -0.0078 0.1168 -0.3114 0.0943 -0.4398

208896 DEAD (Asp- X98743 0.1808 0.0873 0.0791 0.0798 -0.0709 0.1454 -0.3878 0.1028 -0.4797

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients* and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at Glu-Ala-Asp) 0.4965 box polypeptide 18 complement component 1, q

208910_^ subcomponent s at binding protein L04636 0.2886 0.0116 0.0789 0.4062 0.0106 -0.0094 0.1049 -0.2796 0.0832 -0.3882 interferon, gamma-

208965_ inducible s_at protein 16 BG256677 -0.2274 0.3179 -0.1985 0.4208 0.304 -0.2702 0.1882 -0.502 0.0832 -0.3883

208966_ interferon, AF208043 -0.6164 0.3884 -0.1664 0.3569 -0.3172 0.1632 -0.4352 0.0417 -0.1944

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score)., RA patients_> and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x_at gamma- 0.2362 inducible

K) protein 16

F-box and

209005_ leucine-rich at repeat protein 5 AF 157323 -0.6632 0.1855 0.1097 0.0875 0.1603 -0.1425 0.0255 -0.0681 -0.0159 0.0744

209017_ protease, s_at serine, 15 U02389 0.3749 -0.0809 0.0972 0.2666 -0.0758 0.0674 0.0468 -0.1248 0.0544 -0.2541 synaptotagmin binding,

209024_ cytoplasmic s at RNA AI472757 0.4156 -0.0472 -0.0397 -0.267 -0.0438 0.039 0.0551 -0.1469 0.0543 -0.2532

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score interacting protein ral guanine nucleotide

209051_ dissociation s_at stimulator AF295773 0.412 0.0293 0.0908 0.5929 0.0262 -0.0233 0.157 -0.4186 0.1216 -0.5673

209072_ myelin basic at protein M13577 -0.3807 0.0098 -0.0735 0.4395 0.0088 -0.0078 -0.1123 0.2994 -0.0888 0.4144

SH3-domain

209091_ GRB2-like s_at endophilin Bl AF263293 -0.4686 0.0831 0.0153 0.2496 0.0746 -0.0663 -0.0418 0.1116 -0.049 0.2285

209113 high-mobility AF288679 0.4526 -0.0997 -0.0199 - -0.0931 0.0828 0.0216 -0.0576 0.0372 -0.1735

Table 6; Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at group 2OB 0.1843 hemoglobin, beta ///

209116_ hemoglobin, x_at beta M25079 0.6504 -0.1628 -0.214 0.0344 -0.1473 0.1309 -0.0325 0.0867 0.0066 -0.0309

209135_ aspartate beta- at hydroxylase AF289489 -0.5062 0.1055 -0.1375 0.3759 0.096 -0.0854 -0.0683 0.1823 -0.0752 0.3508

Immunoglobuli

209138_ n lambda x_at variable 3-21 M87790 0.2059 0.11 -0.2086 0.3061 0.1043 -0.0927 0.1068 -0.2849 0.0632 -0.2948

209153_ transcription s_at factor 3 (E2A M31523 0.3929 0.058 -0.0071 0.5553 0.0527 -0.0468 0.1566 -0.4175 0.1143 -0.5335

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score immunoglobuli n enhancer

(Jl binding factors

E12/E47)

209156_ collagen, type s_at VI, alpha 2 A AYY002299220088 00..448833 -0.1583 0.243 0.3128 -0.1443 0.1283 0.038 -0.1013 0.0617 -0.2877 aldo-keto reductase family 1, member C3 (3-

209160_ alpha at hydroxysteroid ABOl 8580 0.5928 -0.1593 0.2493 0.4301 -0.1437 0.1277 0.0711 -0.1896 0.0848 -0.3956

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score dehydrogenase, type II)

PRP4 pre- mRNA processing factor 4

209162_, homolog s_at (yeast) U82756 0.3896 -0.0231 0.0062 0.3484 -0.0212 0.0189 0.0817 -0.218 0.0709 -0.3306

209184_ insulin receptor s_at substrate 2 BF700086 -0.142 -0.1156 0.0443 0.4129 -0.1078 0.0958 -0.1305 0.3481 -0.0854 0.3985

209185_ insulin receptor s at substrate 2 AF073310 -0.2391 -0.1337 0.107 0.5015 -0.1226 0.109 -0.1587 0.4231 -0.1031 0.4809

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

MADS box transcription

-4 enhancer factor

2, polypeptide

C (myocyte

209200_ enhancer factor at 2C) AL536517 0.3473 -0.0295 0.0833 0.3618 -0.0276 0.0245 0.0819 -0.2185 0.0746 -0.3481

209234_ kinesin family at member IB BF939474 -0.4241 -0.0641 0.079 0.5347 -0.0558 0.0496 -0.1524 0.4063 -0.107 0.4992

CDC42

209286_ effector protein at (Rho GTPase AI754416 -0.6256 0.1994 -0.0015 0.1184 0.1767 -0.1571 0.021 -0.056 -0.022 0.1029

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score binding) 3

CDC42

OO effector protein 209287_ (Rho GTPase s_at binding) 3 AF104857 -0.5234 0.176 0.0442 0.0309 0.1606 -0.1427 0.0365 -0.0974 -0.0059 0.0278

209301_ carbonic at anhydrase ll M36532 0.6274 -0.0413 -0.2459 0.3038 -0.0366 0.0326 0.069 -0.1841 0.0591 -0.276 major histocompatibil ity complex,

209312_ class II, DR 7.00E- -6.00E- x_at beta 1 /// major U65585 0.3821 04 -0.0044 0.3939 04 0.0974 -0.2597 0.0795 -0.3711

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score histocompatibil ity complex,

VO class II, DR beta l

209369_ at annexin A3 M63310 -0.8009 0.1907 -0.1208 0.4382 0.1649 -0.1466 -0.0628 0.1674 -0.0824 0.3846 immunoglobuli

209374_ n heavy s_at constant mu BC001872 0.3562 0.0256 -0.1604 0.2831 0.0239 -0.0212 0.0776 -0.207 0.058 -0.2706 growth factor

209409_ receptor-bound at protein 10 D86962 -0.2873 -0.0979 -0.1989 0.7505 -0.0859 0.0764 -0.2065 0.5507 -0.1557 0.7266

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score growth factor

209410_ receptor-bound

K)

O s_at protein 10 AF000017 -0.2897 -0.0353 -0.1633 0.5518 -0.0317 0.0282 -0.1436 0.383 -0.1135 0.5298 interferon-

2091417 '_ induced protein s at 35 BC001356 -0.4716 0.4253 -0.1795 0.4721 0.4027 -0.358 0.2244 -0.5984 0.0878 -0.4097 mutS homolog

2, colon cancer,

209421_ nonpolyposis at type 1 (E. coli) U04045 0.2391 0.1121 -0.005 -0.542 0.1007 -0.0895 0.1658 -0.442 0.1114 -0.5196

209458 hemoglobin, AF 105974 0.7088 -0.1962 -0.1885 - -0.1758 0.1562 -0.042 0.1119 0.0057 -0.0268

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x at alpha 1 /// 0.0304 hemoglobin,

K) alpha 1 /// hemoglobin, alpha 2 /// hemoglobin, alpha 2

209486_ disrupter of at silencing 10 BC004546 0.4293 -0.0323 0.1158 0.4706 -0.0295 0.0262 0.1081 -0.2882 0.0963 -0.4494 carcinoembryo

209498_ nic antigen- at related cell X16354 -0.5803 0.2147 -0.1881 0.2104 0.1944 -0.1728 0.0011 -0.0029 -0.0402 0.1874

Table 6; Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score adhesion molecule 1

K) κ> (biliary glycoprotein) zinc finger

209538_ protein 32 at (KOX 30) U69645 0.3106 0.0099 0.0819 0.4274 0.0091 -0.008 0.1105 -0.2948 0.0876 -0.4089

209546_ apolipoprotein s_at L, 1 AF323540 -0.2873 0.3001 -0.0116 0.4912 0.2825 -0.2511 0.2109 -0.5625 0.0976 -0.4555

CD36 antigen

209555_ (collagen type I s at receotor. M98399 - -00..00115544 00..00225555 0.338 0.3775 0.0233 -0.0207 0.1039 -0.2772 0.0769 -0.3591

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score thrombospondi n receptor)

K) RRSl ribosome biogenesis regulator

209567_ homolog (S. at cerevisiae) BC001811 0.336 0.0983 0.0657 0.6739 0.0861 -0.0765 0.1962 -0.5233 0.1384 -0.6459 torsin family 1,

209593_ member B s at ( (ttoorrssiinn B B)) AF317129 -0.5068 0.3559 -0.1507 0.2783 0.3336 -0.2966 0.1595 -0.4252 0.0515 -0.2402

209602_ GATA binding AI796169 0.2433 0.0673 0.2879 -0.709 0.0601 -0.0534 0.1898 -0.5061 0.1475 -0.6884

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at protein 3

ATP-binding

K) cassette, sub¬ family B

209620_ (MDR/TAP), s_at member 7 AB005289 0.3375 -0.0527 0.1021 0.3077 -0.0489 0.0434 0.0633 -0.1687 0.0627 -0.2927 phosphatidylin

209625_ ositol glycan, at class H BC004100 0.1956 0.0701 0.0651 0.4525 0.0644 -0.0572 0.1312 -0.3498 0.0936 -0.4368 heat shock

209657_ transcription s at factor 2 M65217 0.4523 -0.0624 0.1133 0.4118 -0.0556 0.0494 0.0861 -0.2296 0.0821 -0.3832

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set E) Gene Title ID score score score score score 3 score score score score score

CDC 16 cell division cycle

209658_ 16 homolog (S. at cerevisiae) A AFF 1166445598 0.3824 -0.011 0.0081 0.3751 -0.01 0.0089 0.0904 -0.241 0.0762 -0.3558

T cell receptor alpha constant

/// T cell

209670_ receptor alpha at constant M M1122995599 0.3131 0.0968 0.0815 0.6614 0.0853 -0.0759 0.1898 -0.5061 0.1362 -0.6358

T cell receptor

209671_ alpha locus /// x at T cell receptor Ml 2423 0.3295 0.0633 0.102 0.6086 0.0567 -0.0504 0.1706 -0.455 0.1257 -0.5864

Table 6: Group of 1645 g enes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients. >

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score alpha locus /// T cell receptor

K) alpha constant /// T cell receptor alpha constant cryptochrome

209674_ 1 (photolyase- at like) D83702 0.3062 -0.02 0.1667 0.4248 -0.0181 0.0161 0.0999 -0.2664 0.0867 -0.4046

Cas-Br-M

209682_ (murine) at ecotropic U26710 0.5034 -0.0458 0.0142 0.4136 -0.0404 0.0359 0.0954 -0.2544 0.0817 -0.3812

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score retroviral transforming

K) -4 sequence b nuclear receptor subfamily 1,

209750_ group D, at member 2 N32859 0.456 -0.0947 -0.049 0.1732 -0.0879 0.0781 0.0195 -0.052 0.0348 -0.1622

209762_ SPI lO nuclear x_at body protein AF280094 -0.5071 0.2998 -0.1348 0.1437 0.2762 -0.2455 0.1144 -0.305 0.0264 -0.123

209771_ CD24 antigen x at (small cell lung AA761181 -0.25 -0.1019 -0.2833 0.8039 -0.0883 0.0785 -0.2228 0.594 -0.1667 0.7778

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score carcinoma cluster 4

QC antigen) CD24 antigen (small cell lung carcinoma

209772_ cluster 4 s at antigen) X69397 -0.3106 -0.0327 -0.2696 0.669 -0.0295 0.0262 -0.1775 0.4733 -0.1391 0.6492 T cell receptor gamma

209813_ constant 2 /// T x at cell receptor Ml 6768 0.3995 -0.0242 -0.0278 0.3229 -0.0223 0.0198 0.0776 -0.2069 0.0655 -0.3058

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients' (lupus score)₄ RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score gamma

K) constant 2 /// T cell receptor gamma variable 9 /// T cell receptor gamma variable 9 /// similar to T- cell receptor gamma chain C region PT-

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score gamma- 1/2 /// similar to T-

O cell receptor gamma chain C region PT- gamma-1/2 /// TCR gamma alternate reading frame protein /// TCR gamma alternate

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score reading frame

W protein

--

Patched

209815_ homolog - at (Drosophila) BG054916 0.3572 -0.0522 0.2509 0.4729 -0.0466 0.0414 0.1049 -0.2798 0.0953 -0.4448 leucine rich

209840_ repeat neuronal - s_at 3 AI221950 0.4996 -0.006 0.0539 0.5539 -0.0054 0.0048 0.1396 -0.3724 0.1125 -0.5249 leucine rich

209841_ repeat neuronal - s_at 3 AL442092 0.4337 0.0288 -0.0815 0.4482 0.026 -0.0231 0.1263 -0.3369 0.0907 -0.4231

209870_ amyloid beta AW57158 0.7094 -0.0943 -0.0146 _ -0.082 0.0729 0.0935 -0.2494 0.091 -0.4245

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s at (A4) precursor 0.4701 protein-

K) binding, family A, member 2 (XIl -like) linker for

209881_ activation of T s_at cells AF036905 0.4266 -0.0071 -0.0258 0.3987 -0.0064 0.0057 0.1 -0.2667 0.0809 -0.3777 complement

209906_ component 3 a at receptor 1 U62027 -0.4399 0.1028 -0.0307 0.2116 0.0952 -0.0846 -0.0271 0.0721 -0.0424 0.198

209930 nuclear factor L13974 -0.541 0.0815 0.0094 0.3348 0.0721 -0.0641 -0.0641 0.1709 -0.0653 0.305

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at (erythroid- derived 2),

45kDa

6- phosphofracto-

2- kinase/fructose

-2,6-

209992_ biphosphatase at 2 AB044805 -0.0915 -0.1267 0.572 -0.0831 0.0739 -0.1637 0.4364 -0.1188 0.5544

209993_ ATP-binding at cassette, sub- AF016535 0.4226 -0.0544 0.1114 0.4005 -0.0484 0.043 0.0869 -0.2318 0.0799 -0.3727

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score family B (MDR/TAP), member 1 ATP-binding cassette, sub¬ family B (MDR/TAP), member 1 /// ATP-binding cassette, sub¬

209994_ family B s at (MDR/TAP), AF016535 0.4678 -0.0442 0.1444 0.5063 -0.04 0.0356 0.1186 -0.3164 0.103 -0.4808

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score member 4

T-cell

'Jl leukemia/lymp homa lA /// T- cell

209995_ leukemia/lymp s_at homa lA BC003574 0.359 -0.0307 -0.054 0.2384 -0.0288 0.0256 0.0516 -0.1375 0.0488 -0.2277

CD3Z antigen, zeta polypeptide 210031_ (TiT3 at complex) J04132 0.7155 -0.1267 0.1637 0.5618 -0.1063 0.0945 0.1112 -0.2965 0.1064 -0.4966

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

SH3 -domain

^ 210101 GRB2-like x at endophilin Bl AF257318 -0.4186 0.0492 0.02 0.2834 0.0442 -0.0393 -0.0592 0.1579 -0.0561 0.262

SH2 domain protein IA,

Duncan's disease

(lymphoprolife

210116_ rative at syndrome) AF072930 0.4015 0.0359 0.1153 -0.623 0.0318 -0.0282 0.1597 -0.4258 0.1276 -0.5955

210128_ leukotriene B4 s at receptor U41070 -0.4022 0.003 -0.0318 0.4396 0.0027 -0.0024 -0.1124 0.2997 -0.0886 0.4136

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

210140 cystatin F

K ^at (leukocystatin) AF031824 -0.2865 -0.0423 -0.0707 0.4779 -0.0386 0.0343 -0.1276 0.3402 -0.0986 0.4601

-4

210142_ x at flotillin l AF117234 -0.4298 -0.0158 0.0579 0.4322 -0.014 0.0124 -0.1145 0.3054 -0.0861 0.4018 granzyme B

(granzyme 2, cytotoxic T- lymphocyte- associated serine esterase

210164_ 1) /// granzyme at B (granzyme 2, J03189 0.4644 -0.0245 0.163 0.5731 -0.0215 0.0191 0.139 -0.3706 0.1155 -0.5388

Table 6; Group of 1645 genes that are differential y expressed in healthy donors, SLE patients (iupαs score)_* RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score cytotoxic T- lymphocyte- associated serine esterase

1)

210166_ toll-like at receptor 5 A AFF005511115511 --00..339944^3 0.0477 -0.0848 0.3633 0.0431 -0.0383 -0.0798 0.2128 -0.0731 0.3409

FUS interacting

210178_ protein (seriαe- x_at arginine rich) l AF047448 0.3265 0.0014 0.0601 0.4003 0.0013 -0.0012 0.1005 -0.2679 0.0827 -0.3861

210202 bridging U87558 0.52 -0.0128 0.1221 -0.0112 0.01 0.1488 -0.3967 0.1255 -0.5858

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients .(lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at integrator 1 0.6226 cathelicidin

VO

210244_ antimicrobial at peptide U19970 -0.4231 0.0041 -0.2801 0.6977 0.0036 -0.0032 -0.1701 0.4536 -0.1428 0.6664 membrane- spanning A- domains, subfamily A, member 3

210254_ (hematopoietic at cell-specific) L35848 -0.3572 -0.046 -0.1565 0.6439 -0.0412 0.0366 -0.1692 0.4511 -0.133 0.6208

210262 cysteine-rich M25532 -0.1799 -0.0056 -0.3449 0.5336 -0.0051 0.0046 -0.1399 0.373 -0.1105 0.5158

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set H) Gene Title ID score score score score score 3 score score score score score at secretory

* protein 2

O- G protein-

210279_ coupled at receptor 18 AF261135 0.5765 -0.0405 0.0502 -0.538 -0.0359 0.0319 0.1201 -0.3203 0.1076 -0.5023

210281_ zinc ringer s_at protein 198 AL136621 0.4095 -0.1274 0.0334 -0.117 -0.1204 0.107 -0.0026 0.0069 0.0237 -0.1105

210282_ zinc finger at protein 198 AL136621 0.2245 -0.0697 -0.0319 0.0163 -0.067 0.0596 -0.0149 0.0397 0.0034 -0.0157 membrane-

210356_ spanning 4- x at domains, BC002807 0.4354 -0.0284 -0.0654 0.3128 -0.0263 0.0234 0.0711 -0.1897 0.0637 -0.2971

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score subfamily A, member 1

210357_ spermine s at oxidase BC000669 0.3045 -0.0916 -0.2699 0.1884 -0.0853 0.0758 -0.0746 0.1989 -0.038 0.1773 solute carrier family 11 (proton- coupled divalent metal ion

210423_ transporters), s at member 1 L32185 -0.314 -0.0461 0.0209 0.4285 -0.0419 0.0373 -0.119 0.3174 -0.0876 0.4087

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

210425

£ x_at golgin-67 AF164622 0.5519 -0.1043 0.0738 0.3652 -0.0922 0.082 0.0678 -0.1808 0.0712 -0.3322 κ> RAR-related

210426_ orphan x_at receptor A U04897 0.3152 -0.004 0.1024 0.4147 -0.0037 0.0033 0.1011 -0.2697 0.085 -0.3966 purinergic receptor P2X,

210448_ ligand-gated s_at ion channel, 5 U49396 0.3706 0.021 -0.1172 0.3276 0.0194 -0.0172 0.0874 -0.2331 0.0666 -0.3108 hypothetical

210463_ protein x at FLJ20244 BC002492 0.4222 -0.0788 0.0723 0.2974 -0.0728 0.0647 0.0567 -0.1513 0.0601 -0.2807

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

RAR-related

Ig 210479_ orphan s at receptor A L14611 0.3176 0.0074 0.0477 0.3951 0.0068 -0.006 0.0993 -0.2648 0.0809 -0.3776 peptidylprolyl

210502_ isomerase E s_at (cyclophilin E) AF042386 0.462 -0.042 0.0937 0.4574 -0.0374 0.0332 0.1024 -0.2732 0.0917 -0.4281 baculoviral

210538_ LAP repeat- s_at containing 3 U37546 0.2345 0.0756 0.0244 0.4682 0.0691 -0.0614 0.1382 -0.3685 0.0966 -0.4508 killer cell

210606_ lectin-like x at receptor U30610 0.4248 -0.0464 0.135 0.4469 -0.0415 0.0369 0.1005 -0.2681 0.0899 -0.4196

Table 6: Group of 1645 genes that are differentially expressed in healthy donors j, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score subfamily D, member 1 fms-related

210607_ tyrosine kinase at 3 1igand U03858 0.2579 0.1226 0.0646 0.6567 0.1101 -0.0979 0.1976 -0.527 0.1363 -0.6361 tumor protein 210609_ p53 inducible s_at protein 3 BC000474 -0.4279 0.0608 -0.1417 0.418 0.0551 -0.049 -0.0988 0.2634 -0.0844 0.3939 cyclin- dependent

210622_ kinase (CDC2- x at like) 10 AF153430 0.4233 0.0098 -0.0824 0.3857 0.0088 -0.0078 0.1028 -0.2741 0.0778 -0.3628

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

A kinase

(PRKA)

" 210625 anchor protein s at 1 U34074 0.3985 -0.0518 -0.015 0.2607 -0.0479 0.0426 0.053 -0.1413 0.0528 -0.2464 tetratricopeptid

210645_ e repeat s at domain 3 D83077 0.4241 -0.0496 0.1769 0.4779 -0.044 0.0391 0.1067 -0.2845 0.0959 -0.4477 iduronate 2- sulfatase

210666_ (Hunter at syndrome) AF050145 0.3887 -0.2456 0.0415 0.2117 -0.2369 0.2106 -0.1246 0.3322 -0.0427 0.1994

210705 tripartite motif- AF220028 -0.4544 0.3555 -0.1677 0.3371 -0.2996 0.1703 -0.454 0.0596 -0.2781

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at containing 5 0.3154

Ig 210717_. 5.00E- at AFl 16659 0.3758 -0.1223 -0.0632 0.0026 -0.1166 0.1036 -0.0308 0.0821 04 -0.0025 formyl peptide receptor-like 1 /// formyl

210773_ peptide s_at receptor-like 1 U81501 -0.4212 0.1502 -0.0353 0.0703 0.1404 -0.1248 0.0204 -0.0545 -0.014 0.0652 SARIa gene

210790_ homolog 1 (S. s_at cerevisiae) BC003658 0.3235 -0.0152 -0.0887 0.2095 -0.0145 0.0128 0.0521 -0.139 0.0433 -0.2019

210797 2'-5'- AF063612 -0.6192 0.5016 -0.1897 - 0.4711 -0.4187 0.2547 -0.6793 0.0911 -0.4253

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients-

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at oligoadenylate 0.5129

4- synthetase-like -4 solute carrier family 8

(sodium/calciu

210804_ m exchanger), x_at member 1 A AFF112288552244 -0.282 0.0049 -0.0751 0.3515 0.0046 -0.0041 -0.0927 0.2473 -0.0723 0.3375 tumor necrosis factor receptor superfamily,

210847_ member 25 /// x_at putative NFkB AF026071 0.4258 0.0524 0.0979 0.6755 0.0469 -0.0416 0.1883 -0.5021 0.1395 -0.6511

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score activating protein

OO apolipoprotein

B mRNA editing enzyme, catalytic

210873_ polypeptide- x_at like 3A U03891 -0.5612 0.1931 -0.1044 0.1675 0.1768 -0.1571 0.0074 -0.0198 -0.0324 0.1514 Fc fragment of

210889_ IgG, low s at affinity lib, M31933 -0.4559 0.2409 -0.2258 0.0478 0.2228 -0.198 0.0505 -0.1346 -0.0091 0.0424

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score receptor

(CD32)

K*

210896_ aspartate beta- s_at hydroxylase AF306765 -0.4267 0.0709 -0.1065 0.3561 0.0647 -0.0575 -0.0711 0.1896 -0.0718 0.3349

210915_ T cell receptor x_at beta constant 1 M15564 0.3708 0.046 0.1378 0.6399 0.0402 -0.0357 0.1691 -0.4508 0.1307 -0.6101 lysosomal

210943_ trafficking s_at regulator U84744 0.3594 -0.1376 -0.1454 0.1342 -0.129 0.1147 -0.0705 0.188 -0.0269 0.1257 lymphoid

210948 — enhancer- - s_at binding factor AF294627 0.4515 0.0567 0.0507 0.6684 0.0501 -0.0445 0.1823 -0.4862 0.1369 -0.6386

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

T cell receptor

O alpha locus ///

210972_ T cell receptor x_at alpha constant Ml 5565 0.3244 0.0641 0.1167 0.6198 0.0567 -0.0504 0.1712 -0.4565 0.1274 -0.5944 major histocompatibil ity complex,

210982_ class II, DR s_at alpha M60333 0.3643 -0.0177 0.0534 -0.382 -0.0161 0.0143 0.09 -0.24 0.0774 -0.3612

210992_ Fc fragment of x at IgG, low U90939 -0.4504 0.206 -0.0978 0.0118 0.1912 -0.17 0.0501 -0.1337 -0.0023 0.0107

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score affinity Hc,

Ul receptor for (CD32) growth factor

210999_. receptor-bound s_at protein 10 U66065 -0.3813 -0.0592 -0.1806 0.7271 -0.0523 0.0465 -0.1901 0.5069 -0.1504 0.7018 linker for

211005_ activation of T at cells AF036906 0.4263 -0.0426 0.117 0.4412 -0.0378 0.0336 0.0997 -0.2658 0.0884 -0.4124

211012_ promyelocytic s_at leukemia BC000080 -0.9629 0.49 -0.0544 0.2557 0.4377 -0.3891 0.2093 -0.558 0.0434 -0.2023

211087 mitogen- Z25432 -0.3211 0.0758 -0.1169 0.2434 0.072 -0.064 -0.0439 0.1171 -0.0502 0.2343

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x at activated protein kinase

K) 14 /// mitogen- activated protein kinase 14

PRP4 pre- mRNA processing factor 4

211090_ homolog B s at (yeast) /// Z25435 0.1847 0.0619 0.0644 0.4186 0.0575 -0.0511 0.12 -0.32 0.0869 -0.4056

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set BD Gene Title ID score score score score score 3 score score score score score

PRP4 pre- κ> mRNA processing factor 4 homolog B

(yeast)

T cell receptor

211144_, gamma x_at constant 2 M30894 0.3771 -0.0275 -0.0262 0.2924 -0.0253 0.0225 0.0686 -0.1829 0.0593 -0.2766

211275_ s_at glycogenin AF087942 -0.4286 -0.0249 -0.0086 0.5192 -0.0219 0.0195 -0.1356 0.3616 -0.1045 0.4877

211282 tumor necrosis U94506 0.4273 0.0541 0.149 - 0.0464 -0.0413 0.1902 -0.5072 0.149 -0.6953

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x_at factor receptor 0.7308 superfamily, member 25

Fc fragment of

211307_ IgA, receptor s_at for U43677 -0.5216 0.1194 0.0828 0.1429 0.1115 -0.0991 -0.0064 0.0171 -0.0287 0.1338

211339_ IL2-inducible s_at T-cell kinase D13720 0.3826 0.0171 0.168 -0.604 0.0148 -0.0132 0.1545 -0.4121 0.1224 -0.571

CDKNlA

211358_ interacting zinc s_at finger protein 1 AF234161 0.3485 -0.0262 0.0856 -0.374 -0.0241 0.0214 0.0846 -0.2256 0.0764 -0.3565

211367_ caspase 1, U13699 -0.4306 0.2928 -0.0448 -0.291 0.2716 -0.2414 0.1482 -0.3953 0.0548 -0.2556

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s at apoptosis-

Ul related cysteine protease (interleukin 1, beta, convertase) interleukin 1

211372_ receptor, type s_at II U64094 -0.3344 -0.0468 -0.0625 0.5318 -0.0431 0.0384 -0.1402 0.3739 -0.1105 0.5158

Fc fragment of

211395_ IgG, low x at affinity Hc, U90940 -0.4043 0.1884 -0.0337 0.0506 0.1764 -0.1568 0.0606 -0.1615 0.01 -0.0465

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients,, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score receptor for (CD32) immunoglobuli n heavy locus III immunoglobuli n heavy constant gamma 1 (GIm marker) ///

211430_ immunoglobuli s at n heavy M87789 0.1015 0.1378 -0.1293 0.3483 0.1328 -0.1181 0.1238 -0.33 0.0729 -0.3401

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score constant

Ul gamma 2 (G2m -4 marker) /// immunoglobuli n heavy constant gamma 3 (G3m marker) /// immunoglobuli n heavy constant mu

211456 Similar to 60S AF333388 -0.2334 0.3658 -0.1182 0.3462 -0.3077 0.2733 -0.7287 0.1232 -0.5748

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x at ribosomal 0.6196 κ> protein L35 dipeptidylpepti dase 4 (CD26, adenosine deaminase

211478_ complexing s at protein 2) M74777 0.321 0.0054 0.1186 0.4615 0.005 -0.0044 0.116 -0.3094 0.0953 -0.4446 eukaryotic translation

211501 initiation factor s at 3, subunit 9 BCOOl 173 0.3692 -0.0225 -0.0159 0.3075 -0.0206 0.0183 0.0705 -0.188 0.0622 -0.2903

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, t md WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score eta, 116kDa

B 211506 s_at interleukin δ AF043337 -0.3 0.2584 0.2776 0.6454 0.2382 -0.2117 0.2555 -0.6813 0.1311 -0.6118

211513_ opioid growth 1.00E- 1.00E- s_at factor receptor AF172449 0.3192 -0.0946 -0.082 04 -0.0905 0.0804 -0.0249 0.0665 0 04 chromosome

19 open

211563_ reading frame s_at 2 AB006572 0.3508 0.0624 0.0695 0.5972 0.0551 -0.049 0.1618 -0.4315 0.1222 -0.5704 natural

211583_ cytotoxicity - x_at triggering AF031136 0.4727 -0.0539 0.0556 0.3999 -0.0482 0.0428 0.0846 -0.2256 0.0797 -0.3718

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score receptor 3 mitochondrial

O ribosomal protein L9 /// mitochondrial

211594_ ribosomal s_at protein L9 AB0496 0.256 0.0611 0.0362 0.4633 0.0566 -0.0503 0.1362 -0.3631 0.0962 -0.4488

211623_ fibrillarin /// s_at fibrillarin M30448 0.4404 -0.1034 0.1578 0.3329 -0.0924 0.0821 0.0575 -0.1533 0.0655 -0.3056 immunoglobuli

211634_ n heavy x at constant mu /// M24669 0.3685 0.0447 -0.1796 0.3283 0.0415 -0.0369 0.0929 -0.2478 0.0671 -0.3132

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score immunoglobuli n heavy constant mu IgM rheumatoid factor RF-TTl, variable heavy chain /// IgM rheumatoid factor RF-TTl,

211635_ variable heavy x at chain M24670 0.3347 0.047 -0.1192 0.3578 0.0438 -0.0389 0.1012 -0.2699 0.0735 -0.3432

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Immunoglobuli κ> n heavy chain κ>

V region (Humha448) /// Immunoglobuli n heavy chain

211637_ V region x at (Humha448) L23516 0.2846 0.1718 -0.3313 0.4342 0.1611 -0.1432 0.1545 -0.4121 0.0887 -0.414 Anti-rabies virus

211644_ immunoglobuli x at n rearranged L 14458 0.2273 0.153 -0.2333 -0.419 0.1443 -0.1283 0.1474 -0.393 0.0864 -0.4032

Table 6; Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score kappa chain V- region /// Anti- rabies virus immunoglobuli n rearranged kappa chain V- region /// HRV Fab O27-VL /// HRV Fab 027- VL /// HRV Fab O26-VL /// HRV Fab 026-

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

VL ///

Antibody light chain variable region to HIY- l gpl20 (339bp) /// Antibody light chain variable region to HIV- l gpl20 (339bp) /// Clone 125fl2

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score anti-tetanus toxoid imniunoglobuli n light chain variable region (IGL@) mRNA, partial cds /// Clone 125fl2 anti¬ tetanus toxoid immunoglobuli n light chain

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score variable region CGL@) mRNA, partial cds ///

Immunoglobuli n kappa constant /// Immunoglobuli n kappa constant /// Clone JLCD5 immunoglobuli

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score n kappa chain (IgK) mRNA,

-4 VKIII-JKl region, partial cds. /// Clone JLCD5 immunoglobuli n kappa chain (IgK) mRNA, VKIII-JKl region, partial cds. /// Ig

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score germline

ON kappa-chain QO gene Vk3 region, 13kl l and l3kl2 /// Ig germline kappa-chain gene Vk3 region, 13kll and l3kl2 /// Ig germline kappa-chain

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score gene Vk3

O\ region, 13kO4 /// Ig germline kappa-chain gene Vk3 region, 13kO4 /// Clone 136dO9 anti¬ tetanus toxoid immunoglobuli n light chain variable region

Table 6; Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(IGL@) mRNA, partial

O cds /// Clone 136dO9 anti¬ tetanus toxoid immunoglobuli n light chain variable region (IGL@) mRNA, partial cds /// Immunoglobuli

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score n heavy

-4 constant mu /// Immunoglobuli n heavy constant mu /// Immunoglobuli n kappa light chain VJ region (ID KPOLYC13) III Immunoglobuli

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score n kappa light chain VJ

K) region (ID KPOLYC13) III

Immunoglobuli n kappa light chain VJ region (ID POMOl 5) /// Immunoglobuli n kappa light

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patieϊits., and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score chain VJ

KJ region (ID

POMOl 5) ///

Immunoglobuli n kappa variable 1-5 ///

Immunoglobuli n kappa variable 1-5

IgM VDJ-

211650_ region /// IgM x at VDJ-region L34164 0.2099 0.1587 -0.2884 0.3632 0.1509 -0.1342 0.1366 -0.3643 0.0748 -0.3492

Table 6: Group of 1645 genes that are differentially expressed in- healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score major

-4 histocompatibil ity complex, class II, DQ beta 1 /// major histocompatibil ity complex,

211654_ class II, DQ x_at beta l M17565 0.4986 -0.0735 -0.0583 0.2649 -0.0673 0.0598 0.0498 -0.1327 0.0529 -0.247 carcinoembryo

211657_ nic antigen- at related cell M18728 -0.3034 -0.0599 -0.3409 0.8025 -0.0516 0.0459 -0.2089 0.557 -0.1654 0.7719

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLEpatie αts (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score adhesion molecule 6 (non-specific cross reacting antigen) /// carcinoembryo nic antigen- related cell adhesion molecule 6 (non-specific cross reacting

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

3 4 5 10 11 12 13

Representa Healthy tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score antigen) κ> peroxiredoxin

2111

211658_ peroxiredoxin at 2 L19185 0.3995 -0.1007 0.1046 0.2464 -0.0933 0.0829 0.0365 -0.0975 0.0496 -0.2314 ribosomal protein L3 ///

211666_ ribosomal x_at protein L3 L22453 0.5719 -0.1256 0.1037 0.3579 -0.11 0.0978 0.0588 -0.1567 0.0688 -0.3211 hemoglobin,

211696_ beta /// x_at hemoglobin, AF349114 0.5629 -0.1574 -0.1894 0.0185 -0.1436 0.1276 -0.0446 0.1189 -0.0036 0.0167

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score beta hemoglobin,

-4 alpha 1 /// hemoglobin, alpha 1 /// hemoglobin, alpha 2 ///

211699_ hemoglobin, x_at alpha 2 AF349571 0.734 -0.1745 -0.2005 0.1028 -0.1557 0.1384 -0.0183 0.0488 0.0195 -0.0909

Fc fragment of

211734_ IgE, high s at affinity I, BC005912 0.3238 0.0782 0.2637 0.7982 0.0685 -0.0609 0.2136 -0.5695 0.1658 -0.7739

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score receptor for; alpha polypeptide /// Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide hemoglobin,

211745_ alpha 1 /// x at hemoglobin, BC005931 0.6857 -0.1887 -0.1732 0.0412 -0.1697 0.1508 -0.0374 0.0998 0.0078 -0.0366

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score alpha 1 ///

-4 hemoglobin, alpha 2 /// hemoglobin, alpha 2 prostaglandin D2 synthase 2IkDa (brain) III prostaglandin

211748_ D2 synthase x at 2IkDa (brain) BC005939 0.5379 -0.1487 0.1888 -0.343 -0.1358 0.1207 0.0522 -0.1392 0.068 -0.3173

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

211796_ T cell receptor

£ s_at beta constant 1 AF043179 0.4136 0.0342 0.1024 0.6188 0.0301 -0.0267 0.1617 -0.4312 0.1261 -0.5885

TRAF2 and

NCK

211828_ interacting s_at kinase AF172268 0.2805 0.0743 0.0689 0.5552 0.0663 -0.0589 0.1603 -0.4276 0.1141 -0.5324 tumor necrosis factor receptor

211841_ superfamily, - s_at member 25 U94510 0.4992 0.0114 0.1228 0.6664 0.0101 -0.009 0.1688 -0.4502 0.1361 -0.6352

211893_ - x_at CD6 antigen U66145 0.4362 -0.0294 0.0306 0.4034 -0.027 0.024 0.0973 -0.2594 0.0823 -0.3839

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

211900 g ^x-^at CDo antigen U66146 0.4468 -0.0529 0.0645 0.3845 -0.0475 0.0422 0.0861 -0.2297 0.0769 -0.359

211902_ T cell receptor x_at alpha locus L34703 0.361 0.0465 0.0528 0.5491 0.0412 -0.0366 0.1489 -0.3972 0.1119 -0.5223

211948_ BAT2 domain x_at containing 1 BG261071 0.3975 -0.0666 -0.0475 0.1888 -0.0628 0.0559 0.0314 -0.0839 0.0386 -0.1801 nucleolar and coiled-body

211951_ phosphoprotein at 1 D21262 0.3115 0.0563 0.0233 0.4955 0.0503 -0.0447 0.1372 -0.3658 0.1011 -0.4718

211955_ RAN binding NM_0022 at protein 5 71 0.3525 -0.0141 0.0796 0.4045 -0.0128 0.0114 0.0971 -0.2591 0.0822 -0.3837

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score zinc finger

OO protein 36,

211965_ C3H type-like -7.00E- at 1 BE620915 -0.4667 0.1194 0.1684 0.0034 0.1108 -0.0985 0.0304 -0.0812 04 0.0032 pro-oncosis receptor inducing

211967_ membrane at injury gene BG538627 -0.1822 0.3662 -0.1653 0.6284 0.3376 -0.3001 0.2492 -0.6646 0.1212 -0.5654 leucine-rich

211971_ PPR-motif s at containing AI653608 0.3324 0.0029 0.0651 0.4153 0.0026 -0.0023 0.1044 -0.2784 0.0841 -0.3925

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

G protein- g 211979 coupled at receptor 107 AB046844 -0.2865 -0.0106 -0.0339 0.358 -0.0098 0.0087 -0.1003 0.2674 -0.0737 0.344 major histocompatibil ity complex,

211991_ class II, DP s_at alpha 1 M27487 0.2284 0.0501 0.0636 0.4319 0.0462 -0.0411 0.1185 -0.316 0.0893 -0.4168 mitogen- activated

212046_ protein kinase x at 3 X60188 -0.5473 0.0094 0.1879 0.3615 0.0084 -0.0074 -0.0914 0.2438 -0.0711 0.3318

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

G protein-

212070_ coupled at receptor 56 AL554008 0.3793 -0.055 0.2588 0.4959 -0.0496 0.0441 0.1079 -0.2876 0.1007 -0.4699 glutamate receptor, ionotropic, N- methyl D- asparate- associated protein 1

212090_ (glutamate at binding) AL571424 -0.4162 0.013 0.0585 0.3405 0.0118 -0.0104 -0.0847 0.2258 -0.0682 0.3183

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

DEAH (Asp- Glu-Ala-His)

212105_ box -4.00E- 3.00E- s_at polypeptide 9 BF313832 0.3024 04 -0.1311 0.1863 04 0.0491 -0.1308 0.0384 -0.1791

212185_ metallothionein NM_0059 x_at 2A 53 -0.2395 0.328 -0.2081 0.4259 0.3121 -0.2775 0.2044 -0.545 0.0832 -0.3883 prostaglandin

212187_ D2 synthase NM_0009 x_at 2IkDa (brain) 54 0.5719 -0.1394 0.2129 0.4263 -0.1239 0.1101 0.074 -0.1974 0.0834 -0.3891

212229_ F-box protein s_at 21 AKOO1699 0.4246 -0.0746 0.0751 0.3137 -0.0678 0.0603 0.0606 -0.1615 0.0628 -0.2929

212268 serine (or NM 0306 -0.4771 0.1021 -0.1253 0.343 0.0903 -0.0803 -0.0597 0.1593 -0.0669 0.3124

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at cysteine) 66 proteinase inhibitor, clade B (ovalbumin), member 1

212285_ AW00805 s at agrin 1 -0.2432 0.3592 -0.2643 0.4511 0.3414 -0.3035 0.2101 -0.5604 0.0868 -0.4052 amine oxidase

(flavin

212348_ containing) s_at domain 2 ABOl 1173 0.3623 0.0052 0.006 0.3954 0.0047 -0.0042 0.1008 -0.2687 0.0802 -0.3743

212380 KIAA0082 D43949 -0.1502 0.3178 -0.1159 0.296 -0.2631 0.2208 -0.5888 0.1151 -0.5371

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ED Gene Title ID score score score score score 3 score score score score score at 0.5801

K OO. 212386 — Transcription - at factor 4 BF592782 0.2614 0.0848 -0 .0157 0.4821 0.0776 -0.069 0.1413 -0.3768 0.0994 -0.464 chromosome 9

212400_ open reading - at frame 132 AL043266 0.4442 -0.0183 0. 0405 0.4507 -0.0161 0.0143 0.1098 -0.2928 0.0897 -0.4188

IMP4, U3 small nucleolar ribonucleoprot

212411_ ein, homolog - at (yeast) BE747342 0.3414 0.0066 0. 0516 0.4213 0.0059 -0.0052 0.1071 -0.2857 0.0854 -0.3984

212462 ___ AUl 44267 0.4372 -0.0793 0. 0518 -0.0719 0.0639 0.0532 -0.1419 0.0581 -0.2712

Table 6: Group of 1645 genes that are differentially expressed in healthy donors,. SLE patients (hipus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at 0.2919

^ FYN oncogene

212486_ related to SRC, s_at FGR₅ YES N20923 0.3229 0.0401 0.1532 0.5895 0.0352 -0.0313 0.1554 -0.4143 0.1204 -0.5618 lipocalin 2

212531_ (oncogene NM_0055 at 24p3) 64 -0.3693 -0.0029 -0.5063 0.8783 -0.0025 0.0022 -0.217 0.5786 -0.1792 0.8363

212538_ dedicator of at cytokinesis 9 AL576253 0.3406 0.0498 0.0966 -0.579 0.0449 -0.0399 0.1576 -0.4203 0.1195 -0.5578

212589 Sterol carrier - at protein 2 AI753792 0.5439 -0.0731 0.0245 0.3927 -0.0659 0.0586 0.0784 -0.209 0.0783 -0.3653

212592 ~ Immunoglobuli AV733266 0.175 0.1839 -0.2774 - 0.1745 -0.1551 0.1574 -0.4198 0.0832 -0.3883

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at n J 0.4046

OO polypeptide,

VO linker protein for immunoglobuli n alpha and mu polypeptides autism

212599_ susceptibility at candidate 2 AK025298 0.4028 -0.0446 0.0759 0.3718 -0.0403 0.0359 0.0833 -0.2221 0.0748 -0.3491

212621_ KIAA0286 at protein AB006624 0.3428 0.0108 0.0581 0.4402 0.0097 -0.0087 0.1112 -0.2966 0.0896 -0.4181

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients_*

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

212634_ AW29809

£ at KIAA0776 2 0.372 -0.0151 -0.1338 0.2167 -0.0139 0.0123 0.0553 -0.1474 0.0436 -0.2037

O

WW domain containing E3 212638 _ ubiquitin s_at protein ligase l BF131791 0.3503 -0.0335 0.1083 0.3783 -0.0303 0.0269 0.0882 -0.2352 0.0765 -0.3572

EH domain

212653_ binding protein s at 1 AB020710 0.3172 -0.0756 0.1787 0.2994 -0.0702 0.0624 0.0555 -0.148 0.061 -0.2845 interleukin 1 212657_ receptor s_at antagonist U65590 -0.7733 0.4197 -0.1218 0.2001 0.3808 -0.3385 0.1594 -0.4251 0.0349 -0.1628

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score major histocompatibil

^o ity complex, class II, DQ alpha 1 /// major histocompatibil ity complex,

212671_ class II, DQ s_at alpha 2 BG397856 0.4022 -0.1261 0.3007 0.3703 -0.1159 0.1031 0.0611 -0.163 0.0744 -0.3473

212692_ LPS- s_at responsive W60686 0.4454 -0.0433 0.0339 0.3789 -0.0385 0.0342 0.0857 -0.2286 0.0752 -0.3511

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients., and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score vesicle trafficking,

K> beach and anchor containing

212709_. nucleoporin at 16OkDa D83781 0.2283 0.0629 0.1095 0.5099 0.0576 -0.0512 0.1397 -0.3726 0.1057 -0.4935 protein phosphatase 1, regulatory

212750_ (inhibitor) at subunit 16B AB020630 0.2935 0.0692 0.1974 0.6791 0.0618 -0.0549 0.1879 -0.501 0.141 -0.6578

<

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

212768 s_at olfactomedin 4 AL390736 -0 .6532 0.0268 -0.4167 1. 0074 0.0224 -0.0199 -0.2503 0.6673 -0.2037 0.9508 κ> dishevelled associated activator of

212793_ morphogenesis at 2 BF513244 -0 .1411 -0.105 -0.1366 0 .558 -0.098 0.0871 -0.1612 0.4299 -0.1172 0.5468 solute carrier family 25

(mitochondrial

212826_ carrier; adenine - s at nucleotide AI961224 0.3965 -0.0935 0.2019 0.3564 -0.0839 0.0746 0.0656 -0.1748 0.0708 -0.3302

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score translocator),

VO member 6 immunoglobuli n heavy constant mu /// immunoglobuli

212827_ n heavy at constant mu X17115 0.3279 -0.022 -0.0406 0.2424 -0.0207 0.0184 0.0544 -0.1452 0.0499 -0.2329

212846_ at KIAA0179 AA811192 0.3361 -0.011 0.1276 0.4421 -0.0098 0.0087 0.1077 -0.2871 0.0897 -0.4186

212885_ M-phase at phosphoprotein AL545921 0.3813 0.0539 0.0607 0.5976 0.0484 -0.043 0.1662 -0.4433 0.123 -0.5741

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

10 (U3 small nucleolar

Ul ribonucleoprot ein)

212966_ hypermethylate at d in cancer 2 AL043112 0.2731 0.0248 0.1132 0.4582 0.0226 -0.0201 0.1199 -0.3197 0.0944 -0.4406 major histocompatibil ity complex, class II, DQ

212998_ beta 1 /// major x_at histocompatibil AI583173 0.3951 0.0923 0.0267 0.6816 0.082 -0.0729 0.1899 -0.5064 0.1405 -0.6556

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score ity complex,

VO class II, DQ beta l Bobby sox

213015_ homolog at (Drosophila) BF448315 0.3343 -0.0277 -0.0855 0.1906 -0.0258 0.0229 0.0436 -0.1162 0.0387 -0.1807 GTPase activating

213049_. Rap/RanGAP at domain-like 1 BG436400 0.3521 -0.002 0.0586 0.4163 -0.0018 0.0016 0.1033 -0.2754 0.0853 -0.398

213057_ ATP synthase AWl 1860 at mitochondrial 8 0.2785 0.0263 -0.0531 0.3077 0.0246 -0.0219 0.0865 -0.2306 0.0635 -0.2962

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Fl complex assembly

-4 factor 2

T-cell lymphoma

213135_ invasion and at metastasis 1 U90902 0.2381 -0.0178 0.2808 0.4698 -0.0159 0.0142 0.1119 -0.2983 0.0955 -0.4458

Splicing factor,

213152_ arginine/serine- s_at rich, 46kD AI343248 0.2997 0.0113 0.1126 0.4495 0.0103 -0.0091 0.1139 -0.3037 0.092 -0.4294

213193_ T cell receptor x at beta constant 1 AL559122 0.3977 0.0015 0.1456 0.5565 0.0013 -0.0011 0.1381 -0.3684 0.1125 -0.5252

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

III T cell ^ receptor beta constant 1

213293_ tripartite motif- s_at containing 22 AA083478 -0.5638 0.3394 -0.2035 0.1246 0.3146 -0.2796 0.1183 -0.3156 0.0227 -0.1061

Hypothetical 213294_ protein at FLJ38348 AV755522 -0.7545 0.496 -0.1584 0.3876 0.4553 -0.4047 0.2245 -0.5987 0.0663 -0.3093

213459_ ribosomal - at protein L37a AU155515 0.3116 0.0434 -0.0604 0.3806 0.0396 -0.0352 0.1058 -0.2821 0.0776 -0.362

213515_ hemoglobin, - x_at gamma K ill AI133353 0.6798 -0.1745 -0.1082 0.1354 -0.1567 0.1393 -0.0105 0.028 0.0258 -0.1205

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hemoglobin, gamma A ///

VO hemoglobin, gamma G /// hemoglobin, gamma G

Poly(rC)

213517_ binding protein AWl 0342 at 2 2 0.426 -0.1831 -0.1342 0.1757 -0.1701 0.1512 -0.0938 0.2503 -0.0346 0.1615 putative

213524_ lymphocyte NM_0157 s at G0/G1 switch 14 -0.3428 0.1686 0.2312 0.3167 0.1586 -0.141 0.1396 -0.3723 0.0642 -0.2996

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score gene

O PAS domain O containing

213534_ serine/threonin s_at e kinase D50925 0.4917 -0.0531 0.0312 0.3984 -0.0476 0.0423 0.0869 -0.2318 0.0794 -0.3708

CD3D antigen, delta polypeptide

213539_ (TiT3 NM_0007 at complex) 32 0.3665 0.031 0.089 0.5483 0.0275 -0.0245 0.146 -0.3892 0.112 -0.5225

213541_ v-ets s_at erythroblastosi AI351043 -0.1245 -0.0646 -0.2241 0.5172 -0.0593 0.0527 -0.1575 0.4199 -0.1075 0.5017

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupws score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s virus E26 oncogene like

O (avian) lactate

213564_ dehydrogenase x at B BE042354 0.4068 -0.0442 0.1594 0.4575 -0.0391 0.0348 0.1028 -0.274 0.0916 -0.4274 serine (or cysteine) proteinase inhibitor, clade

213572_ B (ovalbumin), s at member 1 AI554300 -0.4229 0.0728 -0.0511 0.2935 0.0653 -0.058 -0.0552 0.1473 -0.058 0.2705

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

213575_ Transformer-2

O a att alpha A AAA8833111177(0 0.5241 -0.125 -0.1182 0.0964 -0.1162 0.1033 -0.0076 0.0203 0.0192 -0.0896 hypothetical protein

LOC146712 ///

UDP-

GlcNAc:betaG al beta-l,3-N- acetylglucosam

213589_ inyltransferase- AW46820 s_at like 1 1 -0.2662 -0.0052 0.1678 0.1284 -0.005 0.0044 -0.0338 0.0902 -0.0265 0.1238

213593 Transformer-2 AW97889 0.3991 -0.103 -0.0119 -0.0968 0.0861 0.0065 -0.0173 0.0259 -0.1206

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients,, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at alpha 0.1277

O intercellular

213620_ adhesion s_at molecule 2 AA126728 0.3675 -0.0533 0.1359 0.3699 -0.0484 0.043 0.0792 -0.2112 0.0746 -0.3482

213622_ collagen, type at LX, alpha 2 AI733465 -0.2073 -0.0398 -0.1181 0.4348 -0.0365 0.0324 -0.1176 0.3135 -0.0897 0.4188 splicing factor,

213649_. arginine/serine- at rich 7, 35kDa AA524053 0.5932 -0.1256 0.0386 0.3176 -0.1106 0.0983 0.0501 -0.1336 0.0611 -0.285

213653_ methyltransfera AW06929 at se like 3 0 0.287 0.0252 0.0694 0.4317 0.023 -0.0204 0.1113 -0.2969 0.0885 -0.4132

213670 Williams- AI768378 0.3782 -0.0127 -0.0097 -0.349 -0.0116 0.0103 0.0848 -0.2262 0.0708 -0.3304

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set DD Gene Title ID score score score score score 3 score score score score score x_at Beuren

Syndrome critical region protein 20 copy

B immunoglobuli 213674_ n heavy x_at constant delta AI858004 0.2727 0.0272 -0.0502 0.3071 0.0259 -0.023 0.0813 -0.2168 0.064 -0.2986 hypothetical protein

213701_ DKFZp434N2 AW29924 at 030 5 0.3891 -0.0318 0.0257 0.3433 -0.0295 0.0262 0.0771 -0.2057 0.0702 -0.3277

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score splicing factor,

« 213742 arginine/serine- AW24175

Ul at rich 11 2 0.3634 -0.1284 0.0617 0.0938 -0.1208 0.1073 -0.0093 0.0248 0.0189 -0.0881 golgi associated, gamma adaptin ear containing,

213772_ ARF binding s_at protein 2 BF196572 0.4284 -0.0772 -0.1595 0.0848 -0.0715 0.0636 0.002 -0.0053 0.017 -0.0792

213792_ s_at insulin receptor AA485908 -0.1739 -0.1183 -0.0326 0.5271 -0.1084 0.0964 -0.168 0.4479 -0.1093 0.5101

213797 radical s- AI337069 -0.9422 0.8498 -0.3474 - 0.8028 -0.7136 0.4733 -1.2621 0.1542 -0.7196

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients., and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at adenosyl 0.9545 meunonme domain containing 2

213813_ x_at — AI345238 -0.193 -0.0139 -0.1862 0.4165 -0.0128 0.0114 -0.1155 0.3079 -0.0861 0.402

CDNA

FLJ13601 fis, clone

213817_ PLACE101006 at 9 AL049435 -0.35 -0.0977 0.0035 0.6201 -0.0868 0.0771 -0.182 0.4854 -0.1272 0.5937

213830_ T cell receptor AW00775 0.6151 -0.0349 0.1672 -0.03 0.0267 0.1669 -0.4451 0.1409 -0.6577

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (hipϊts score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at delta locus /// 1 0.7057

T-cell receptor- delta mRNA, 3' end. v-myb myeloblastosis viral oncogene

213906_ homolog AW59226 at (avian)-like 1 6 0.4493 -0.0308 0.2611 0.6352 -0.027 0.024 0.1492 -0.3977 0.1284 -0.5993 hypothetical

213908_. protein at LOC339005 AI824078 0.5178 -0.0737 0.0622 0.4004 -0.0662 0.0589 0.0811 -0.2162 0.0798 -0.3725

Table 6: Gi'oup of 1645 genes fliat are differentially expressed in healthy donors₅ SLE patients, (lupus øcore), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

213947 nucleoporin

O s at 21OkDa AI867102 0.5073 -0.1056 0.1482 0.3871 -0.0954 0.0848 0.0684 -0.1824 0.077 -0.3593 centrosome-

213956_ associated AW29929 at protein 350 4 0.3344 -0.162 -0.1128 0.1937 -0.1522 0.1353 -0.0941 0.251 -0.0389 0.1814

213958_ CD6 antigen /// AWl 3482 at CD6 antigen 3 0.3479 -0.0266 0.078 -0.365 -0.0243 0.0216 0.0842 -0.2246 0.0742 -0.3461 chromosome 19 open

213986_ reading frame s_at 6 AI805266 0.3917 -0.0925 -0.0358 -0.125 -0.087 0.0773 0.0084 -0.0223 0.0253 -0.1182

214011 hypothetical BE314601 0.3849 -0.0328 -0.026 -0.0307 0.0273 0.0655 -0.1747 0.0587 -0.2741

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at protein 0.2867

O HSPCl I l

214020_ x at Integrin, beta 5 BE138575 0.4079 -0.1145 -0.1407 0.0179 -0.1085 0.0964 -0.0354 0.0943 -0.0036 0.0169 zeta-chain

(TCR) associated

214032_ protein kinase at 7OkDa AI817942 0.5249 -0.0228 0.0997 0.5797 -0.0196 0.0174 0.1407 -0.3753 0.1151 -0.5373

214049_. CD7 antigen x_at (p41) AI829961 0.353 -0.0015 0.1286 0.4858 -0.0014 0.0012 0.1227 -0.3271 0.0997 -0.4652

214059 Interferon- BE049439 -0.7265 0.6386 -0.3896 0.6137 -0.5455 0.308 -0.8213 0.0993 -0.4633

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (luptts score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at induced protein 0.5742

44

O serine hydroxymethyl

214096_ transferase 2 AWl 9031 s_at (mitochondrial) 6 0.3572 -0.0156 0.1382 -0.462 -0.014 0.0124 0.1097 -0.2927 0.0939 -0.4381

PDZ and LIM

214121_ domain 7 x_at (enigma) AA086229 -0.3649 0.1029 0.0209 0.0839 0.0971 -0.0863 0.0047 -0.0125 -0.017 0.0794 pro-platelet

214146_ basic protein s at (chemokine R64130 0.5592 -0.1555 -0.2496 0.075 -0.1418 0.126 -0.0593 0.158 -0.0146 0.0679

Table 6; Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(C-X-C motif)

W ligand 7) chromosome

19 open

214173_ reading frame AW51490 x at 2 0 0.3497 0.0475 0.0373 0.5254 0.0426 -0.0379 0.144 -0.384 0.1075 -0.5017 complement component 1, q

214214_ subcomponent s_at binding protein AU151801 0.2971 0.0676 0.0157 0.5034 0.0607 -0.0539 0.1423 -0.3796 0.1031 -0.4811

214218_ s at AV699347 -0.4726 0.4109 -0.0243 0.5823 0.3901 -0.3468 0.3034 -0.809 0.1131 -0.528

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score mitogen- activated protein kinase

214219_ kinase kinase x_at kinase 1 B BEE66446666118Σ 0.2837 0.0364 0.1315 0.5178 0.0337 -0.03 0.1387 -0.3698 0.108 -0.5039 nuclear mitotic

214251_ apparatus s_at protein 1 AI337584 0.4164 -0.0571 0.1372 0.4116 -0.0532 0.0473 0.0949 -0.2531 0.0846 -0.3948 heterogeneous nuclear

214280_ ribonucleoprot x at eui Al X79536 0.4609 -0.079 0.0747 0.3391 -0.0703 0.0625 0.0653 -0.174 0.0668 -0.3116

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score homogentisate

U- dioxygenase

214308_ (homogentisate -8.00E- 6.00E- s_at oxidase) A AII447788117722 0.3692 04 -0.2296 0.1598 04 0.0404 -0.1078 0.032 -0.1494

Tumor necrosis factor (ligand) superfamily, member 10 ///

Tumor necrosis

214329_ factor (ligand) AW47443 x_at superfamily, 4 -0.6403 0.3286 0.0221 0.2334 0.3023 -0.2687 0.151 -0.4025 0.0434 -0.2024

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), HA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score member 10 w 214351_ ribosomal x_at protein L13 AA789278 0.5223 -0.1122 0.1194 0.3575 -0.1 0.0889 0.062 -0.1653 0.0701 -0.327 heat shock

214359_ 9OkDa protein s_at l. beta AI218219 0.4208 0.0072 -0.0026 0.4531 0.0064 -0.0057 0.1179 -0.3145 0.0912 -0.4257 hemoglobin, alpha 2 ///

214414_ hemoglobin, - x_at alpha 2 T50399 0.5818 -0.15 -0.1693 0.0402 -0.1367 0.1215 -0.0278 0.074 0.0078 -0.0364

214437_ serine NM_0054 - s_at hydroxymethyl 12 0.4245 -0.0238 0.0652 0.4395 -0.0218 0.0193 0.1035 -0.2759 0.0896 -0.4183

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG- Set ID Gene Title ID score score score score score 3 score score score score score transferase 2

(mitochondrial)

'Jl

214439_ bridging x at integrator 1 AF043899 0.3832 -0.0392 0.092 0.3815 -0.035 0.0311 0.0865 -0.2306 0.0763 -0.3563 v-ets erythroblastosi s virus E26 oncogene

214447_ homolog 1 NM_0052 at (avian) 38 0.2088 0.0913 -0.0176 0.4431 0.0845 -0.0751 0.1512 -0.4033 0.0917 -0.4278

214450_ cathepsin W NM 0013 at (lymphopain) 35 0.4811 -0.05 0.1745 0.5337 -0.0441 0.0392 0.1191 -0.3175 0.1071 -0.4996

Table 6: Group of 1645 genes that are differentially expressed in healthy donors', SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

/// cathepsin W _w (lymphopain) interferon-

214453_ induced protein NM_0064 s_at 44 17 -0.7088 0.6951 -0.3435 0.7876 0.662 -0.5885 0.379 -1.0107 0.1347 -0.6288

214469_ NM_0210 at histone 1, H2ae 52 0.6045 -0.109 -0.3066 -0.041 -0.0993 0.0882 -0.0176 0.0469 0.008 -0.0374 killer cell lectin-like receptor

214470_ subfamily B, NM_0022 - at member 1 /// 58 0.6369 -0.1002 0.1685 0.5555 -0.0868 0.0771 0.1115 -0.2974 0.1086 -0.5067

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score killer cell

U( lectin-like receptor subfamily B, member 1 zinc finger

214482_ protein 46 NM_0069 at (KUP) 77 0.4043 0.0064 0.0126 0.4484 0.0056 -0.005 0.1151 -0.3069 0.0898 -0.4191

214505_ four and a half s_at LIM domains 1 AF220153 0.5309 -0.1229 -0.0117 0.2115 -0.1144 0.1017 0.0222 -0.0591 0.0424 -0.1979

214511_ x at L03419 -0.5691 0.2343 -0.0189 0.0163 0.2173 -0.1931 0.0639 -0.1705 0.0032 -0.0147

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

214522 NM 0210

£ x at histone 1, Mid 65 -0.3663 0.2255 -0.0868 0.1379 0.218 -0.1938 0.098 -0.2613 0.0279 -0.1303 214551_ CD7 antigen NM_0061 s_at (p41) 37 0.3007 0.009 0.1893 -0.518 0.0081 -0.0072 0.1314 -0.3505 0.1065 -0.4969 chemokine (C motif) ligand 1

/// chemokine

214567_ (C motif) NMJ)(Bl s_at ligand 2 75 0.4796 -0.1479 0.2436 0.3374 -0.138 0.1227 0.0462 -0.1231 0.0681 -0.3179 azurocidin 1

214575_ (cationic NMJ)Ol 7 s at antimicrobial 00 -0.3801 -0.0523 -0.2428 0.7676 -0.0461 0.041 -0.2025 0.5401 -0.1591 0.7423

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein 37) ubiquitin-

VO conjugating enzyme E2D 1

(UBC4/5

214590_ homolog, s_at yeast) A ALL5544557766(0 -0.4768 0.173 0.0597 0.0243 0.1605 -0.1427 0.0518 -0.1381 0.0048 -0.0222 perforin 1

(pore forming protein) ///

214617_ perform 1 at (pore forming AI445650 0.5001 -0.066 0.2016 0.5368 -0.058 0.0516 0.1178 -0.314 0.1071 -0.4997

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein) w K) 214637 -

© at oncostatin M BG437034 -0.4588 0.0464 0.1218 0.2349 0.0437 -0.0388 -0.0498 0.1327 -0.0481 0.2243 tumor protein 214667_ p53 inducible s_at protein 11 AK026607 -0.6272 0.1399 0.08 0.2004 0.1277 -0.1135 -0.0161 0.0428 -0.0393 0.1833

Immunoglobuli 214669_ n kappa x_at constant BG485135 0.1946 0.1592 -0.191 0.4422 0.1491 -0.1325 0.1528 -0.4074 0.091 -0.4246

MADS box

214684_ transcription at enhancer factor X63381 -0.4733 0.0997 -0.0179 0.2424 0.0897 -0.0797 -0.036 0.0961 -0.0475 0.2218

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ED Gene Title ID score score score score score 3 score score score score score

2, polypeptide

U( A (myocyte enhancer factor

2A)

Anti-fflV-1 gpl20 V3 loop antibody

DO142-10

214777_ light chain at variable region BG482805 0.3292 0.1713 -0.3121 0.4977 0.1588 -0.1412 0.1697 -0.4525 0.1015 -0.4735

214836_ HRV Fab N8- x at VL BG536224 0.1701 0.1164 -0.0639 0.4253 0.1089 -0.0968 0.1375 -0.3666 0.0881 -0.4113

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score upstream binding

K) transcription 214881_ factor, RNA s_at polymerase I X56687 0.2561 0.0279 0.0331 -0.372 0.0261 -0.0232 0.1023 -0.2729 0.0771 -0.36 transformation/ transcription domain-

214908_ associated s_at protein AC004893 0.4451 -0.1114 0.0516 0.2143 -0.1031 0.0917 0.0258 -0.0688 0.0429 -0.2002

214916_ immunoglobuli x_at n heavy locus BG340548 0.3071 0.0675 -0.2903 0.2189 0.0627 -0.0557 0.0731 -0.195 0.0442 -0.2064

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA ρatients_} and WG patients,

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

III

K) immunoglobuli n heavy constant alpha 1 11/ immunoglobuli n heavy constant alpha 2 (A2m marker) /// immunoglobuli n heavy

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score constant gamma 1 (GIm

4- marker) /// immunoglobuli n heavy constant gamma 2 (G2m marker) /// immunoglobuli n heavy constant gamma 3 (G3m

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score marker) /// immunoglobuli

1» rji n heavy constant mu /// hypothetical protein

MGC27165 /// similar to Ig heavy chain V- III region VH26 precursor

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

214945_ AW51426 w at — 7 0.4207 -0.1625 0.1929 0.1887 -0.1518 0.1349 0.0066 -0.0175 0.0376 -0.1756

214962_ nucleoporin s_at 16OkDa AK026236 0.2206 0.0877 -0.0452 0.4192 0.0815 -0.0725 0.1358 -0.362 0.0867 -0.4047 chemokine (C- 214974_ X-C motif) x_at Iigand 5 AK026546 0.4792 -0.0141 -0.1403 0.3243 -0.0128 0.0114 0.0831 -0.2215 0.065 -0.3034

PI-3-kinase- related kinase

SMG-1-like ///

215002_ pps22-l at protein /// BE000837 0.3984 -0.1648 -0.2146 0.2331 -0.1559 0.1386 -0.107 0.2852 -0.0472 0.2202

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score similar to PI-3- kinase-related

-4 kinase SMG-I isoform 1; lambda/iota protein kinase C-interacting protein; phosphatidylin ositol 3-kinase- related protein kinase ///

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score similar to

MGC9515 protein /// similar to

MGC9515 protein sodium channel,

215026_ nonvoltage- x_at gated 1 alpha U81961 -0.486 -0.0104 0.1347 0.4021 -0.0094 0.0083 -0.1099 0.2931 -0.0804 0.3753 215049_ x at CD 163 antigen Z22969 -0.36 -0.0258 -0.1009 0.5393 -0.0231 0.0206 -0.1395 0.3721 -0.1105 0.5155

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

215111 TSC22 domain s at family 1 AK027071 0.4907 -0.0159 -0.1763 0.2966 -0.0141 0.0125 0.0735 -0.1961 0.0579 -0.2701 immunoglobuli n lambda locus /// immunoglobuli n lambda constant 1 (Meg marker) ///

215121_, immunoglobuli x at n lambda AA680302 0.1744 0.1353 -0.211 0.3385 0.1284 -0.1142 0.1211 -0.323 0.0699 -0.3261

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score constant 2

(Kern-Oz-

O marker) /// immunoglobuli n lambda variable 2-14

215176_ HRV Fab 027- AW40489 x_at VL 4 0.1914 0.1636 -0.228 0.4153 0.1535 -0.1365 0.1468 -0.3915 0.0852 -0.3974

215177_ integrin, alpha s_at 6 AV733308 0.4323 -0.0849 0.0156 -0.237 -0.0785 0.0697 0.0381 -0.1015 0.0477 -0.2225

215182_ MRNA; cDNA x at DKFZp586E12 AL050122 0.3436 -0.0946 -0.2777 0.1634 -0.088 0.0782 -0.0718 0.1914 -0.0328 0.1532

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

1 (from clone DKFZp586E12

1) major histocompatibil ity complex,

215193_ class II, DR x_at beta l AJ297586 0.4062 0.0429 -0.0131 0.5229 0.0377 -0.0335 0.1411 -0.3762 0.1055 -0.4926

215221_ Forkhead box at Pl AK025064 0.4725 -0.2422 -0.1245 0.2758 -0.2237 0.1989 -0.1377 0.3671 -0.0534 0.2492

215236_ phosphatidylin s at ositol binding AV721177 -0.343 0.1441 0.0556 0.0822 0.1364 -0.1212 0.0587 -0.1566 0.0166 -0.0774

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score clathrin assembly protein growth factor

215248_ receptor-bound at protein 10 AU145002 -0.1507 -0.1701 0.7783 -0.1359 0.1208 -0.2382 0.6351 -0.1635 0.7629

Clone 24629

215262_ mRNA at sequence AF052160 0.3788 -0.0362 0.1298 0.4212 -0.0336 0.0298 0.0958 -0.2555 0.0866 -0.4041

TRAF3-

215275_ interacting Jun AW96313 at N-terminal 8 0.402 0.003 -0.0462 0.3805 0.0027 -0.0024 0.1014 -0.2703 0.0763 -0.3559

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score kinase (JNK)- activating modulator CD8 antigen, beta

215332_ polypeptide 1 AW29630 s at (p37) 9 0.2716 0.0345 -0.0066 0.3672 0.0321 -0.0285 0.1064 -0.2837 0.0758 -0.3537 natural killer- tumor

215338_ recognition s_at sequence AI688640 0.5279 -0.155 -0.0256 0.1095 -0.1448 0.1287 -0.0117 0.0312 0.0218 -0.1017

215342 RAB GTPase AB019490 0.3456 -0.0521 0.0225 - -0.0486 0.0432 0.0499 -0.133 0.0491 -0.2291

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s at activating 0.2411 protein 1-like PoIy(A)

215374_ polymerase at alpha AK024849 0.4385 -0.1843 -0.0586 0.0932 -0.1749 0.1555 -0.0709 0.1889 -0.0187 0.0873 immunoglobuli n lambda locus III immunoglobuli n lambda

215379_ constant 1 x at (Meg marker) AV698647 0.0984 0.1367 -0.2739 0.2029 0.1307 -0.1162 0.0847 -0.2258 0.0417 -0.1944

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

III immunoglobuli

'Jl n lambda constant 2 (Kern-Oz- marker) /// immunoglobuli n lambda variable 2-14 /// immunoglobuli n lambda

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score joining3 w 215561_ interleukin 1 s_at receptor, type I AK026803 -0.3489 0.0488 -0.1182 0.3453 0.0458 -0.0407 -0.0795 0.212 -0.0711 0.3319

215706_ x_at zyxin BC002323 -0.4609 0.0503 0.0461 0.2996 0.0448 -0.0398 -0.0644 0.1716 -0.059 0.2753

N-

215743_ myristoyltransf at erase 2 AL134489 0.4348 -0.0642 0.0452 0.3234 -0.0586 0.0521 0.0644 -0.1717 0.065 -0.3034 alkaline phosphatase,

215783_ liver/bone/kidn s at ey X14174 -0.3599 0.0116 0.0311 0.3124 0.0108 -0.0096 -0.0773 0.2061 -0.064 0.2987

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

T cell receptor gamma

-4 constant 2 /// T cell receptor gamma variable 9 /// similar to T- cell receptor gamma chain C region PT-

215806_ gamma-1/2 /// 9.00E- x at TCR gamma M13231 0.4028 -0.0522 04 0.2793 -0.048 0.0427 0.0584 -0.1557 0.0564 -0.2631

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score alternate w reading frame

90 protein prostaglandin 215894_ D2 receptor at (DP) AI460323 0.408 -0.1353 0.0869 0.1461 -0.1263 0.1123 0.0028 -0.0074 0.0292 -0.1364

215925_ s_at CD72 antigen AF283777 0.3805 0.0443 -0.1621 0.3565 0.0414 -0.0368 0.101 -0.2693 0.0733 -0.3422

215967_ lymphocyte s — at antigen 9 AL582804 0.4677 -0.0187 0.1255 -0.556 -0.0168 0.0149 0.1339 -0.3571 0.1134 -0.529

215984_ ADP- s_at ribosylation AL121845 0.3515 -0.0155 -0.0782 -0.248 -0.0145 0.0129 0.0613 -0.1634 0.0509 -0.2373

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score factor related w protein 1

B-cell

CLL/lymphom 215990_ a 6 (zinc finger s_at protein 51) S67779 -0.3298 0.0516 -0.0784 0.2801 0.0477 -0.0424 -0.0577 0.1539 -0.0569 0.2656

FYN oncogene 216033_ related to SRC₅ s_at FGR₅ YES S74774 0.4252 -0.0215 0.1029 0.4827 -0.0187 0.0166 0.1164 -0.3105 0.0961 -0.4484

CDNA:

216050_ FLJ20931 fis, at clone AK024584 0.4484 -0.1549 0.1474 0.1939 -0.1459 0.1297 0.0103 -0.0275 0.0391 -0.1823

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

ADSEO 1282 reversion-

O inducing- cysteine-rich

216153 protein with x at kazal motifs AK022897 0.4316 -0.1473 -0.199 0.1369 -0.1346 0.1196 -0.0775 0.2066 -0.0267 0.1246 similar to 60S ribosomal protein L29 (Cell surface

216177_ heparin AW58226 at binding protein 7 0.411 -0.0404 0.0088 0.3271 -0.0368 0.0327 0.0701 -0.1869 0.0659 -0.3077

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set H) Gene Title ID score score score score score 3 score score score score score

HIP)

4- T cell receptor alpha locus /// 216191_ T cell receptor s_at delta locus X72501 0.6445 -0.0307 0.1015 0.6843 -0.0263 0.0234 0.1617 -0.4312 0.136 -0.6344 mitogen- activated

216199_ protein kinase s_at kinase kinase 4 AL109942 0.3309 -0.0614 0.155 0.3286 -0.057 0.0507 0.0645 -0.172 0.0671 -0.3131 serine

216202_ palmitoyltransf s_at erase, long U15555 -0.4673 0.1426 -0.124 0.2238 0.1308 -0.1162 -0.0205 0.0547 -0.0442 0.2061

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (hipus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score chain base

4- subunit 2

216233_ at CD 163 antigen Z22970 -0.3038 -0.0041 0.0025 0.3235 -0.0039 0.0034 -0.0841 0.2243 -0.0668 0.3119 solute carrier family 2

(facilitated glucose transporter), member 3 ///

216236_ solute carrier s at family 2 ALl 10298 -0.4709 0.1207 -0.0101 0.1761 0.1108 -0.0985 -0.0145 0.0387 -0.0348 0.1625

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(facilitated glucose transporter), member 14 glycerol kinase /// glycerol

216316_ kinase x at pseudogene 3 X78713 -0.3351 0.1955 0.0042 -0.178 0.1847 -0.1642 0.0963 -0.2568 0.0355 -0.1655 similar to dJ753D5.2

216348_ (novel protein at similar to AL049693 0.3527 0.0141 0.0333 0.4354 0.0127 -0.0113 0.1173 -0.3128 0.0886 -0.4135

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

RPS 17 (40S

<_*> ribosomal protein S 17)) CD24 antigen (small cell lung carcinoma

216379_ cluster 4 x at antigen) AK000168 -0.2333 -0.102 -0.29 0.7932 -0.0888 0.0789 -0.2197 0.5859 -0.1646 0.7682 ribosomal protein Ll 8a ///

216383_ similar to at ribosomal U52111 0.1962 0.0496 0.107 0.4388 0.0457 -0.0407 0.1279 -0.3412 0.0909 -0.424

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein L 18a; w 60S ribosomal protein Ll 8a similar to

216384_ prothymosin x_at alpha AF257099 0.3756 -0.0339 -0.0256 0.2745 -0.0312 0.0278 0.0631 -0.1682 0.0556 -0.2595 tumor rejection 216449_ antigen (gp96) x at 1 AK025862 0.3231 0.1011 -0.0728 0.5344 0.0936 -0.0832 0.1651 -0.4403 0.111 -0.518

- immunoglobuli

216510_ n heavy x at constant AB035175 0.2751 0.1591 -0.1864 0.5301 0.1473 -0.1309 0.1726 -0.4604 0.1091 -0.5092

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score gamma 1 (GIm

4- marker) /// immunoglobuli n heavy constant mu /// similar to Ig heavy chain V- III region VH26 precursor

216565_ similar to x at Interferon- AL121994 -0.4728 0.3158 -0.2005 0.1587 0.2962 -0.2633 0.1184 -0.3158 0.0297 -0.1385

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score induced transmembrane

-4 protein 3 (Interferon- inducible protein 1-8U)

216570_ x_at AL096829 0.5045 -0.0896 0.0279 -0.311 -0.079 0.0702 0.0565 -0.1506 0.0604 -0.2817

216576_ HRV Fab 027- x_at VL AF103529 0.1822 0.1728 -0.3017 0.3592 0.1637 -0.1455 0.1375 -0.3667 0.0736 -0.3433

216598_ chemokine (C- s at C motif) ligand S69738 -0.2637 0.3032 -0.3053 -0.241 0.2945 -0.2618 0.1342 -0.3579 0.048 -0.2242

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients.. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

2 w 216705 adenosine J HH itH nHilH iHt iif- ae s at deaminase X02189 0.2881 0.1215 # 0.6219 0.1078 -0.0958 0.1813 -0.4834 0.1278 -0.5962

RRN3 RNA polymerase I transcription

216902_ factor homolog s at (yeast) AF001549 0.4636 0.0202 0.002 0.5365 0.0179 -0.0159 0.1381 -0.3682 0.1084 -0.506

T cell receptor gamma

216920_ constant 2 /// T s at cell receptor M27331 0.4352 -0.0819 0.0102 0.2427 -0.0755 0.0671 0.0416 -0.111 0.0487 -0.2274

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score gamma variable 9 /// similar to T- cell receptor gamma chain C region PT- gamma-1/2 /// TCR gamma alternate reading frame protein

216925 T-cell acute X51990 0.559 -0.1672 -0.1206 -0.1541 0.1369 -0.0387 0.1032 0.0034 -0.016

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at lymphocytic 0.0176

Ul leukemia 1

O

PAS domain containing

216945_ serine/threonin x_at e kinase U79240 0.4655 -0.0651 0.0048 0.3137 -0.0589 0.0524 0.0629 -0.1678 0.0625 -0.2917

Fc fragment of

IgG, high affinity Ia,

216950_ receptor s_at (CD64) X14355 -0.552 0.2097 -0.0414 0.0532 0.1938 -0.1723 0.0397 -0.1059 -0.0103 0.0481

216956 inteεrin. alpha -0.0818 -0.2959 -0.013 -0.0766 0.0681 -0.0181 0.0482 0.0026 -0.0122

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at 2b (platelet

U( glycoprotein lib of Ifb/IIIa complex, antigen

CD41B) plectin 1, intermediate filament

216971_ binding protein s_at 50OkDa Z54367 0.4235 -0.1281 -0.0809 0.0198 -0.1216 0.1081 -0.0273 0.0727 0.004 -0.0187

216984_ Immunoglobuli D84143 0.1892 0.1215 -0.1689 0.1156 -0.1027 0.1193 -0.3182 0.0742 -0.3464

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x at n lambda 0.3574

U(

Ά variable 3-21

K> immunoglobuli n heavy constant alpha Mil immunoglobuli n heavy constant alpha 2 (A2m

217022_ marker) /// s at hypothetical S55735 0.196 0.1463 -0.2755 0.3281 0.1405 -0.1249 0.128 -0.3414 0.0681 -0.3178

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein

Ul MGC27165

T cell receptor alpha locus ///

217143_ T cell receptor s_at delta locus X06557 0.6383 -0.0435 0.1177 0.6594 -0.0369 0.0328 0.1535 -0.4094 0.1296 -0.6046

T cell receptor

217147_ interacting s_at molecule AJ240085 0.2106 0.1361 0.1731 0.7481 0.1207 -0.1073 0.2181 -0.5815 0.1559 -0.7275 immunoglobuli

217148_ n lambda x at variable 2-14 AJ249377 0.2545 0.1246 -0.2578 0.3479 0.1169 -0.1039 0.1199 -0.3196 0.0712 -0.3324

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Nuclear <jj 217152_ receptor co-

4- at repressor 1 AK024136 0.4905 -0.1242 -0.2548 0.068 -0.1152 0.1024 -0.0505 0.1347 -0.0135 0.063

217 '165 _ metallothionein x_at IF (functional) M10943 -0.1636 0.3735 -0.1886 0.6448 0.3525 -0.3133 0.2833 -0.7555 0.128 -0.5972

217185_ zinc finger s_at protein 259 Z95118 0.3859 -0.0127 0.0492 0.4137 -0.0117 0.0104 0.1013 -0.2702 0.0846 -0.3948 signal transducer and activator of

217199_ transcription 2, s at 113kDa S81491 -0.3586 0.2715 -0.2506 -0.111 0.2612 -0.2321 0.1011 -0.2696 0.022 -0.1024

Table 6: Group of 1645 genes that are differentially expressed in healthy donors_* SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

217232 hemoglobin,

U( x at beta AF059180 0.5788 -0.1621 -0.1986 0.0233 -0.1479 0.1315 -0.0469 0.125 -0.0045 0.021

'Jl

IgM rheumatoid factor RF-TT9,

217281_ variable heavy x_at chain AJ239383 0.3325 0.101 -0.1373 -0.482 0.094 -0.0836 0.1461 -0.3895 0.0997 -0.4655

217379_ at AL121934 0.3731 -0.0262 0.1313 0.4436 -0.0233 0.0207 0.1064 -0.2838 0.0894 -0.417

217414_ hemoglobin, x_at alpha 2 V00489 0.7024 -0.1728 -0.2031 0.0721 -0.1551 0.1378 -0.0255 0.068 0.0137 -0.0641

217418 membrane- X12530 0.4345 -0.0384 -0.0624 - -0.0358 0.0318 0.0623 -0.1662 0.0586 -0.2737

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set E) Gene Title ID score score score score score 3 score score score score score x at spanning 4- 0.2879

'Jl domains,

Os subfamily A, member 1

217466_ ribosomal x at protein S2 L48784 0.3511 -0.0159 0.1062 -0.424 -0.0145 0.0129 0.1046 -0.279 0.0866 -0.4043 interferon- induced protein with

217502_ tetratricopeptid at e repeats 2 BE888744 -0.5484 0.5553 -0.234 0.6868 0.5263 -0.4679 0.3076 -0.8203 0.1242 -0.5798

217506 Hypothetical H49382 0.4791 -0.1077 0.0102 -0.0987 0.0878 0.0277 -0.074 0.0436 -0.2034

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at gene supported 0.2195

'Jl by BC041875; -4

BX648984

MyoD family inhibitor

217599_ domain s_at containing B BEE9911006600(0 0.1762 0.0328 0.2092 0.4716 0.0303 -0.027 0.1246 -0.3324 0.098 -0.4575

Secβl alpha 1

217716_ subunit (S. NM_0133 s_at cerevisiae) 36 0.405 -0.0591 0.1059 0.3644 -0.0544 0.0484 0.076 -0.2025 0.0741 -0.3457

217729_ amino-terminal NMJ)OIl s at enhancer of 30 0.3815 -0.009 0.0956 0.4638 -0.008 0.0071 0.1147 -0.3059 0.0937 -0.4372

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score split

U(

Ά retinol

06 dehydrogenase

217775_ 11 (all-trans NMJ) 160 s_at and 9-cis) 26 0.2489 0.0516 0.1938 0.5822 0.0457 -0.0406 0.155 -0.4134 0.1197 -0.5585 butyrate-

217777 '_ induced NMJ)163 s_at transcript 1 95 0.1886 0.1027 -0.0413 0.4297 0.0954 -0.0848 0.1374 -0.3665 0.0889 -0.4149 nuclear ubiquitous

217802_ casein kinase NM_0227 s at and cvclin- 31 0.4449 -0.0938 0.0821 0.2905 -0.0848 0.0754 0.0499 -0.1329 0.0576 -0.2687

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score)., RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score dependent kinase

VO substrate glioma tumor suppressor

217807_ candidate NM_0157 s at region gene 2 10 0.4292 -0.0932 0.0948 0.2879 -0.0845 0.0751 0.0489 -0.1304 0.0572 -0.2668 ubiquitin- conjugating enzyme E2, Jl

217823_ (UBC6 s at homolog, AL562528 -0.5265 0.1401 -0.1763 0.3422 0.1225 -0.1089 -0.0511 0.1364 -0.0654 0.3054

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score yeast) ubiquitin- o conjugating enzyme E2, Jl

(UBC6

217826 homolog, NM_0160 s_at yeast) 21 -0.4232 0.1472 -0.0956 0.1383 0.1364 -0.1212 0.0022 -0.0059 -0.0274 0.1277

217838 NM 0163 s_at Enah/Vasp-like 37 0.3195 0.0421 0.1286 0.5674 0.0372 -0.033 0.1525 -0.4067 0.116 -0.5415

217848_ pyrophosphatas NM_0211 s_at e (inorganic) 29 0.3631 -0.0016 0.0156 0.3872 -0.0015 0.0013 0.0983 -0.2621 0.0785 -0.3666

217895 FLJ20758 NM 0179 0.4194 -0.0478 0.0283 -0.0431 0.0383 0.0709 -0.1891 0.0669 -0.3124

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients. ^!

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at protein 52 0.3347

217929_ KIAA0319- NM_0248

^ s_at like 74 -0.5045 0.1401 -0.0298 0.1783 0.1318 -0.1171 -0.0097 0.0259 -0.0359 0.1676 leucine

217933_ aminopeptidase NMJ) 159 s_at 3 07 -0.342 0.4342 -0.1532 0.6558 0.4079 -0.3626 0.2741 -0.731 0.1252 -0.5842 translocase of outer mitochondrial membrane 22

217960_ homolog NMJ)202 s at (yeast) 43 0.4272 -0.0432 0.0244 0.3514 -0.0395 0.0351 0.0784 -0.209 0.071 -0.3315

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score nerve growth w factor receptor

K)

(TNFRSF 16)

217963_ associated NM_0143 s_at protein 1 80 0.4953 -0.1103 -0.0376 0.1832 -0.1 0.0889 0.0185 -0.0493 0.0359 -0.1673

217979_ NM_0143 at tetraspanin 13 99 0.3938 -0.0344 -0.0506 0.2679 -0.0317 0.0282 0.0587 -0.1566 0.0541 -0.2525

218012_ NM_0221 at TSPY-like 2 17 0.3908 0.0181 0.0919 -0.542 0.0159 -0.0142 0.141 -0.3759 0.1098 -0.5122 chromatin

218085 modifying NM 0159 - at protein 5 61 -0.6325 0.424 -0.1568 0.3237 0.3922 -0.3486 0.1883 -0.5021 0.0572 -0.2667

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

218092_ HIV-I Rev NM_0045

$ s_at binding protein 04 -0.3764 0.0101 -0.0328 0.395 0.009 -0.008 -0.0961 0.2563 -0.0794 0.3707

Ui

218152_ high-mobility NM_0182 at group 20A 00 0.3142 -0.0053 0.0863 0.3948 -0.0048 0.0043 0.097 -0.2586 0.0805 -0.3758 molybdenum

218212_ cofactor NM_0045 s_at synthesis 2 31 0.2455 0.0589 0.1014 0.5092 0.0536 -0.0477 0.1407 -0.3752 0.1053 -0.4914 solute carrier

218237_ family 38, NM_0306 - s_at member 1 74 0.4908 -0.1182 0.1332 0.3221 -0.1066 0.0948 0.0504 -0.1344 0.0635 -0.2964

218244_ nucleolar NM_0179 - at protein 8 48 0.2659 0.0236 0.0578 0.3944 0.0217 -0.0193 0.1045 -0.2787 0.0811 -0.3784

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hypothetical w 218272 protein NMJ)179 at FLJ20699 31 0.3002 0.0393 0.1575 0.5678 0.0354 -0.0314 0.1638 -0.4367 0.1172 -0.5468 hepatocellular carcinoma-

218345_ associated NMJ)184 at antigen 112 87 0.1845 0.0556 0.1637 0.4972 0.0517 -0.046 0.1458 -0.3887 0.1039 -0.4848 2 '-5'- oligoadenylate

218400_ synthetase 3, NM_0061 at 10OkDa 87 -0.6704 0.6652 -0.2723 0.8163 0.6279 -0.5582 0.3755 -1.0014 0.1416 -0.6607

218429 hypothetical NM 0183 -0.2394 0.3064 -0.1104 0.2861 -0.2543 0.1933 -0.5154 0.0897 -0.4187

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at protein 81 0.4624 w FLJl 1286 hypothetical

218449_ protein NMJ) 183 at FLJ11200 59 0.2481 0.0264 0.0363 0.3628 0.0246 -0.0218 0.0944 -0.2516 0.0749 -0.3496 hypothetical

218454_ protein NM_0248 at FLJ22662 29 -0.3252 -0.1417 0.1108 0.6084 -0.1224 0.1088 -0.1906 0.5083 -0.1222 0.5703

218477 — transmembrane NM — 0140 - at protein 14A 51 0.3364 0.048 0.082 0.5559 0.0434 -0.0386 0.1515 -0.4041 0.1146 -0.5349

218543_ zinc finger NM_0227 - s_at CCCH type 50 -0.3582 0.4571 -0.2493 0.6075 0.4301 -0.3823 0.2692 -0.7179 0.1123 -0.5238

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score domain containing 1

Os

218545_ GGA binding NM_0183 at partner 18 0.2002 0.0502 0.1197 0.4566 0.0459 -0.0408 0.126 -0.3361 0.0944 -0.4404 melanoma

218573_ antigen family NM_0140 at H, l 61 0.3021 -0.0425 0.1701 0.3637 -0.0391 0.0348 0.0792 -0.2111 0.0743 -0.3466 progressive external

218590_ ophthalmoplegi NM_0218 at a l 30 0.4208 -0.0019 -0.0421 0.3908 -0.0017 0.0015 0.0968 -0.258 0.0785 -0.3663

218660 dysferlin, limb NM 0034 -0.4292 -0.0206 0.1606 0.3454 -0.0185 0.0165 -0.0938 0.2501 -0.0689 0.3217

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at girdle muscular 94 dystrophy 2B

-4

(autosomal recessive)

218670_ pseudouridylat NM_0252 at e synthase 1 15 0.4068 0.0313 -0.1003 0.4088 0.0287 -0.0255 0.1143 -0.3048 0.0834 -0.389 eukaryotic translation initiation factor

218696_ 2-alpha kinase NM_0048 at 3 36 0.2096 0.0314 0.0969 0.3944 0.0292 -0.0259 0.1035 -0.2761 0.0817 -0.3814

218711 serum NM 0046 0.6739 -0.1172 -0.1431 -0.1023 0.0909 0.0334 -0.0891 0.047 -0.2194

Table 6: Group of 1645 genes that are differentially expressed hi healthy donors, SLE patients (ktpϊts score), RA patients, and. WG patients_*

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at deprivation 57 0.2485

Q^y response OC

(phosphatidyls erine binding protein)

218764_ protein kinase NM_0240 at C, eta 64 0.3764 -0.02 0.093 0.4266 -0.0177 0.0158 0.1012 -0.2699 0.0856 -0.3994 sex comb on

218793_ midleg-like 1 NM_0067 s_at (Drosophila) 46 0.4485 -0.0099 0.0578 0.4943 -0.009 0.008 0.1256 -0.3349 0.1009 -0.4708

218805_ GTPase, IMAP NMJ)183 at family member 84 0.3581 -0.0135 0.1547 0.4843 -0.0119 0.0106 0.1179 -0.3145 0.0977 -0.4561

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

5 /// GTPase,

IMAP family

VO member 5 hypothetical

218865_ protein NM_0227 at FLJ22390 46 -0.3568 -0.0513 0.1183 0.3929 -0.0476 0.0423 -0.1141 0.3042 -0.0807 0.3767 chondroitin

218871_, sulfate NMJ)185 x_at GalNAcT-2 90 -0.3649 0.0471 -0.0235 0.2755 0.0432 -0.0384 -0.0577 0.154 -0.0556 0.2596

218880_ FOS-like at antigen 2 N36408 -0.4704 0.0828 0.0892 0.1811 0.0749 -0.0666 -0.0264 0.0704 -0.0356 0.166

218918 mannosidase, NM 0203 0.3722 0.0063 0.1748 - 0.0056 -0.0049 0.1446 -0.3856 0.1162 -0.5421

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at alpha, class 1C, 79 0.5711 member 1

O zinc finger,

218919_ ANl -type NM_0246 at domain 1 99 0.2173 0.0547 0.1658 0.5307 0.0498 -0.0443 0.1423 -0.3795 0.11 -0.5134 carbohydrate

(chondroitin 4)

218927 sulfotransferas NMJ)186 s_at e l2 41 0.2639 0.0338 0.0551 -0.417 0.0314 -0.0279 0.1149 -0.3063 0.0864 -0.4033

218935 EH-domain NM_0146 at containing 3 00 0.4568 -0.1681 -0.1003 0.0712 -0.1585 0.1409 -0.0601 0.1603 -0.0142 0.0665

218943_ DEAD (Asp- NM_0143 -0.715 0.5825 -0.2224 0.544 -0.4835 0.2991 -0.7977 0.102 -0.4762

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at Glu-Ala-Asp) 14 0.5978

-4 box polypeptide 58 hypothetical

218957_ protein NM_0251 s_at FLJl 1848 55 0.2525 0.0051 0.0914 0.3635 0.0048 -0.0042 0.0933 -0.2488 0.0755 -0.3524

218967_ phosphotriester NMJB06 s_at ase related 64 0.2835 -0.0442 0.153 0.3235 -0.0412 0.0366 0.0685 -0.1828 0.0664 -0.3099 hypothetical

218986_ protein NM__0176 s_at FLJ20035 31 -0.6112 0.6606 -0.2735 0.8645 0.6214 -0.5524 0.3798 -1.0128 0.1512 -0.7055

219013_ UDP-N-acetyl- NM_0220 0.3473 0.0387 0.0216 0.0346 -0.0308 0.1289 -0.3438 0.0985 -0.4598

patients.

gaiactosamine: polypeptide N- acetylgalactosa minyltransferas e ll (GaINAc- TIl) zinc finger,

219062_^ CCHC domain NM_0177 s_at containing 2 42 -0.5819 0.5722 -0.251 0.6808 0.536 -0.4764 0.3233 -0.8621 0.1184 -0.5524

219093_ hypothetical NMJH79 at protein 33 03078 0.0164 0.2713 0.6242 0.0145 -0.0129 0.1571 -0.4189 0.1281 -0.598

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patieats (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

FLJ20701 /// hypothetical protein

FLJ20701 hypothetical

219130_ protein NM_0190 at FLJ10287 83 0.3273 0.022 0.049 0.4453 0.0198 -0.0176 0.1155 -0.3079 0.0907 -0.4235 kelch-like 2,

219157_ Mayven NM_0072 at (Drosophila) 46 -0.4065 0.0076 -0.0339 0.4339 0.0068 -0.0061 -0.1071 0.2856 -0.0876 0.4086

219158_ NMDA NM_0250 s at receptor 85 0.4598 -0.1035 0.1412 0.3368 -0.0956 0.085 0.0581 -0.155 0.068 -0.3174

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus- score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score regulated 1 interferon

-4 induced with

219209_ helicase C NM_0221 at domain 1 68 -0.4637 0.5039 -0.1814 0.6883 0.4731 -0.4205 0.2949 -0.7864 0.1267 -0.5911 ubiquitin

219211_ specific NM_0174 at protease 18 14 -0.7075 0.6368 -0.3162 0.6599 0.6096 -0.5418 0.3326 -0.887 0.1154 -0.5383 5', 3'-

219214_ nucleotidase, NM_0211 s_at cytosolic 63 0.4002 0.0097 -0.0445 -0.398 0.0087 -0.0077 0.1012 -0.2698 0.0802 -0.374

219271 UDP-N-acetyl- NM 0245 -0.5046 0.1119 -0.1758 0.3941 0.1019 -0.0905 -0.0773 0.2062 -0.0788 0.3679

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at alpha-D- 72

-J galactosamine: Ui polypeptide N- acetylgalactosa minyltransferas e 14 (GaINAc-

T14)

219279_ dedicator of NM_0177 at cytokinesis 10 18 0.3551 0.0539 0.1082 0.6162 0.0483 -0.0429 0.1655 -0.4414 0.1271 -0.593 enoyl

219298_ Coenzyme A NM_0246 at hydratase 93 -0.0796 -0.1582 -0.0432 0.5461 -0.1473 0.131 -0.1718 0.4582 -0.1138 0.5312

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score domain containing 3 chromosome 6

219307_ open reading NM_0203 at frame 210 81 0.3899 -0.0731 0.1208 0.3257 -0.0683 0.0607 0.0639 -0.1705 0.0666 -0.3108 chromosome

16 open

219315_ reading frame NM_0246 s_at 30 00 0.41 -0.0301 0.0701 0.4123 -0.0265 0.0235 0.0975 -0.2599 0.0819 -0.3821

219352_ hect domain NMJ)179 at and RLD 6 12 -0.4576 0.5463 -0.2776 -0.715 0.5172 -0.4598 0.3203 -0.8543 0.1302 -0.6074

219356 chromatin NM 0164 -0.678 0.4524 -0.1638 0.4164 -0.3701 0.2009 -0.5357 0.0599 -0.2795

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s at modifying 10 0.3456 protein 5

-4 likely ortholog

219364_ of mouse NM_0241 at Dl llgp2 19 -0.5315 0.47 -0.1849 0.5241 0.4503 -0.4003 0.2562 -0.6832 0.0985 -0.4595 phosphatidyl

219394_ ycerophosphate NM_0244 at synthase 19 -0.5257 0.1094 -0.1248 0.3736 0.0975 -0.0866 -0.0669 0.1784 -0.0733 0.3422 tumor necrosis factor receptor

219423_ superfamily, NM_0037 x at member 25 90 0.3589 0.0289 0.1181 0.5629 0.0257 -0.0229 0.1441 -0.3843 0.1152 -0.5378

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score chromosome 3 20 open

219443_ reading frame NM_0177 at 13 14 0.2624 0.0591 -0.0591 0.3727 0.0549 -0.0488 0.1117 -0.2978 0.0768 -0.3585

219519_ sialoadhesin /// NM_0230 s_at sialoadhesin 68 -0.633 0.608 -0.3923 0.5872 0.5941 -0.5281 0.2979 -0.7943 0.1069 -0.499

B-cell

CLL/lymphom

219528_ a HB (zinc NM_0228 - s_at finger protein) 98 0.47 -0.0028 0.1374 0.6122 -0.0024 0.0022 0.152 -0.4054 0.1231 -0.5745

219529 chloride NM 0046 - at intracellular 69 0.7159 -0.1258 0.1574 0.5585 -0.1106 0.0983 0.1054 -0.2811 0.1096 -0.5113

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score channel 3 hypothetical

219541_ protein NM_0178 at FLJ20406 06 0.3587 -0.0479 0.0718 0.3134 -0.0443 0.0394 0.0667 -0.1778 0.0639 -0.298

PDZKl

219630_ interacting NM_0057 at protein 1 64 0.6768 -0.1278 -0.015 0.3467 -0.1128 0.1003 0.0586 -0.1563 0.0668 -0.3116

B-cell scaffold protein with

219667_ ankyrin repeats NM_0179 s_at 1 35 0.3546 0.0141 -0.0035 0.4018 0.0131 -0.0116 0.1021 -0.2724 0.0829 -0.3869

219669 polycythemia NM 0204 -0.4238 -0.0314 -0.1927 0.7089 -0.028 0.0249 -0.1812 0.4831 -0.1464 0.6834

₈₀₃

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at rubra vera 1 06

/8KJJ interferon

219684_ responsive NM_0221 at protein 47 -0.3264 0.4651 -0.1732 0.7349 0.4394 -0.3905 0.2955 -0.7881 0.1419 -0.6621 sterile alpha

219691_ motif domain NM_0176 at containing 9 54 -0.5955 0.5586 -0.1637 0.7144 0.5165 -0.4591 0.3176 -0.8468 0.1249 -0.5828

SIDl transmembrane

219734_ family, NM_0176 at member 1 99 0.3647 -0.0134 0.0224 -0.364 -0.0121 0.0108 0.0881 -0.2348 0.0735 -0.3432

Table 6: Group of 1645 genes that are differentia] Iy expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

219762_ ribosomal NM_0154

& s_at protein L36 14 0.365 -0.0051 0.0908 0.4523 -0.0045 0.004 0.1129 -0.3011 0.0915 -0.4268

GTPase, IMAP

219777 '_ family member NM_0247 at 6 11 0.26 0.031 0.1537 0.5003 0.0278 -0.0247 0.1338 -0.3569 0.1025 -0.4782 dehydrogenase/ reductase

219799_ (SDR family) NM_0057 s_at member 9 71 -0.5054 0.2771 -0.1599 0.0608 0.2603 -0.2314 0.0863 -0.2302 0.0117 -0.0544 mitochondrial

219819 ribosomal NM 0140 - s at protein S28 18 0.2449 0.0893 0.1187 0.6062 0.0803 -0.0714 0.1691 -0.451 0.1257 -0.5866

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

219863 hect domain NM_0163

OO at and RLD 5 23 -0.8171 0.7281 -0.3047 0.8008 0.6835 -0.6076 0.3899 -1.0397 0.1319 -0.6155 latent transforming growth factor

219922_ beta binding NM_0210 s_at protein 3 70 0.5929 -0.1332 0.245 0.4955 -0.1193 0.106 0.0908 -0.2422 0.0982 -0.4584

219971_ interleukin 21 NM_0217 at receptor 98 0.4133 -0.0356 -0.0153 0.3189 -0.0329 0.0292 0.0725 -0.1933 0.0648 -0.3022 thioesterase

219975_ domain NMJ)183 x at containing 1 24 -0.4173 -0.1067 -0.1396 0.8516 -0.0931 0.0827 -0.2378 0.6343 -0.1769 0.8256

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score mannosidase, g 219999 alpha, class NM_0186 at 2A, member 2 21 -0.1892 -0.078 -0.0848 0.4859 -0.0706 0.0627 -0.1403 0.3741 -0.1001 0.4672 peptidyl arginine

220001_. deiminase, type NM_0123 at IV 87 -0.2843 -0.0837 0.1159 0.4064 -0.0773 0.0687 -0.1231 0.3282 -0.0834 0.3892 interleukin-1 receptor-

220034_ associated NM_0071 at kinase 3 99 -0.4411 -0.0091 -0.0644 0.5437 -0.0081 0.0072 -0.141 0.3761 -0.1104 0.5151

220054_ interleukin 23, NM_0165 0.3461 0.0323 -0.0239 0.0293 -0.026 0.1128 -0.3007 0.0859 -0.401

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at alpha subunit 84 0.4222

OO pl9 caspase recruitment

220066_ domain family, NM_0221 at member 15 62 -0.3817 0.1635 -0.1298 0.0847 0.1538 -0.1367 0.02 -0.0535 -0.0169 0.0789 chromosome 6

220094_ open reading NM_0221 s_at frame 79 02 0.4565 -0.0359 -0.0838 -0.297 -0.0328 0.0291 0.0639 -0.1703 0.0596 -0.2781

C-type lectin

220132_ superfamily 2, NM_0132 s at member D 69 0.2972 0.0936 -0.0703 0.4902 0.0845 -0.0751 0.1516 -0.4043 0.1001 -0.4671

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score tumor necrosis w factor, alpha-

220187_ induced protein NM_0246 at 9 36 -0.3967 0.1764 0.0802 0.1363 0.1665 -0.148 0.08 -0.2132 0.0273 -0.1272

220232_ stearoyl-CoA NM_0249 at desaturase 4 06 0.5713 -0.1536 -0.3036 0.1094 -0.1369 0.1217 -0.072 0.1919 -0.0208 0.097 male germ cell- 220302 associated NM 0059 at kinase 06 -0.3805 0.0554 -0.0223 0.2682 0.0517 -0.0459 -0.0571 0.1524 -0.0547 0.2551 hypothetical 220326_ protein NM_0180 s_at FLJ10357 71 -0.3409 0.0039 0.0259 0.3182 0.0036 -0.0032 -0.0785 0.2095 -0.0647 0.3021

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

SAM domain, & SH3 domain and nuclear

220330_ localisation NM_0221 s_at signals, 1 36 -0.4124 0.0671 0.07 0.1813 0.0622 -0.0553 -0.0289 0.077 -0.0365 0.1704

220368_ NM_0179 s_at KIAA2010 36 0.3423 -0.015 0.0633 -0.376 -0.0136 0.0121 0.095 -0.2534 0.0763 -0.3559 ubiquitin

220370_ specific NM_0250 - s_at protease 36 90 0.2897 0.0153 0.1507 0.4864 0.0141 -0.0125 0.1337 -0.3565 0.1006 -0.4696

220418_ ubiquitin NMJ)189 - at associated and 61 0.455 0.0287 0.2001 0.7412 0.0253 -0.0225 0.1904 -0.5078 0.1525 -0.7119

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

SH3 domain containing, A

220421_ butyrophilin- NM_0248 at like δ 50 -0.2315 0.1733 -0.0227 0.2002 0.1681 -0.1495 0.0977 -0.2604 0.0414 -0.1931 signal-

220485_ regulatory NMJ)185 s_at protein beta 2 56 0.382 0.0349 0.018 0.5066 0.0314 -0.0279 0.1324 -0.353 0.1035 -0.4828

220492_ NM_0048 s_at otoferlin 02 -0.3659 0.4234 -0.3387 0.4236 0.4121 -0.3663 0.2032 -0.5418 0.0819 -0.3824

220528_ NM_0183 at vanin 3 99 -0.4988 0.1785 -0.0788 0.1172 0.1641 -0.1459 0.0155 -0.0414 -0.0228 0.1064

220532 LR8 protein NM 0140 0.2471 0.0268 0.2337 0.025 -0.0222 0.1518 -0.4049 0.1159 -0.5409

$ 220570 NM_0204 at resistm 1 155 -0.2349 -0.0959 -0.1856 0.6781 -0.0864 0.0768 -0.1904 0.5076 -0.1415 0.6601 multiple C2- domains with two

220603_ transmembrane NMJ)183 s_at regions 2 49 -0.4482 0.0636 0.043 0.2538 0.0575 -0.0511 -0.0477 0.1273 -0.0502 0.2345 male sterility

220615_ domain NMJ)180 s_at containing 1 99 -0.5065 0.0841 -0.1605 0.4556 0.0738 -0.0656 -0.0977 0.2606 -0.0897 0.4186

220646 killer cell NM 0165 0.6055 -0.1832 0.3216 -0.1629 0.1448 0.065 -0.1733 0.0872 -0.4069

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

3 4 5 10 11 12 13

Representa Healthy tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score s_at lectin-like 23 0.4493

OO receptor

VO subfamily F, member 1

220684_ NMJ)133 at T-box 21 51 0.3911 -0.0975 0.1609 0.3007 -0.0884 0.0786 0.0518 -0.1382 0.0598 -0.2791 chromosome

21 open

220918_ reading frame NM_0251 at 96 43 0.6199 -0.2886 -0.1038 0.2266 -0.266 0.2365 -0.1341 0.3576 -0.043 0.2008

220925_ MAKlO NM_0219 at homolog, 29 0.2594 0.0922 0.1023 0.6133 0.084 -0.0746 0.1782 -0.4753 0.1278 -0.5964

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score amino-acid N- e subunit, (S. cerevisiae)

220940_ NM_0251 at KIAA1641 90 0.6251 -0.1886 -0.0476 0.0994 -0.1726 0.1534 -0.0224 0.0599 0.0192 -0.0897

220960_ ribosomal NM_0009 x_at protein L22 83 0.4247 -0.0754 0.1101 0.3454 -0.0672 0.0597 0.0677 -0.1807 0.0683 -0.3188 unc-93 homolog Bl

220998_ (C. elegans) /// NMJB09 s at unc-93 30 -0.4147 0.3385 -0.127 0.3502 0.3218 -0.2861 0.1867 -0.4979 0.0674 -0.3147

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score homolog Bl (C. elegans) likely ortholog of mouse limb- bud and heart gene /// likely ortholog of mouse limb-

221011_ bud and heart NM 0309 s_at gene 15 0.4954 -0.0261 0.0899 0.5309 -0.0224 0.02 0.127 -0.3388 0.1051 -0.4904

221060_ toll-like NM 0032 s at receptor 4 /// 66 -0.3543 0.1403 -0.0161 0.0088 0.1319 -0.1173 0.0333 -0.0889 -0.0018 0.0082

₂₃₉

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score toll-like receptor 4 chromosome X

221196_ open reading NM_0243 - x_at frame 53 32 0.2343 0.1084 -0.071 0.4637 0.1003 -0.0891 0.1449 -0.3864 0.0958 -0.447

221205_ NM_0180 at — 41 0.0572 -0.1039 -0.2034 0.4135 -0.096 0.0853 -0.1341 0.3577 -0.0851 0.3972 chromosome

21 open

221211_ reading frame NM_0201 - s_at 7 52 0.7095 -0.0608 -0.2023 0.3789 -0.052 0.0462 0.0833 -0.2222 0.0717 -0.3347

221221 kelch-like 3 NM 0174 0.4459 -0.0864 0.0496 _ -0.0793 0.0705 0.0487 -0.1299 0.056 -0.2615

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score s_at (Drosophila) 15 0.2797

BTB and CNC homology 1, basic leucine zipper transcription factor 2 ///

BTB and CNC homology 1, basic leucine

221234_ zipper NM_0218 s at transcription 13 0.598 -0.0642 -0.0244 0.4254 -0.0563 0.05 0.0908 -0.242 0.0831 -0.3879

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score factor 2 u proτem-

221345_ coupled NM_0053 - at receptor 43 06 -0.4125 0.3231 -0 .0935 0 .3438 0.3072 -0.2731 0.169 -0.4508 0.0667 -0.3114

UDP-

Gal:betaGlcNA c beta 1 ,4- galactosyltrans

221485_ ferase, at polypeptide 5 AL035683 -0.523 0.1172 -0 .0387 0 .2671 0.1056 -0.0939 -0.038 0.1014 -0.0523 0.2441

221548_ integrin-linked - s at kinase- AY024365 0.4118 -0.0594 0. 0236 0 .2916 -0.0543 0.0483 0.058 -0.1547 0.0586 -0.2736

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score associated

VO serine/threonin e phosphatase 2C lymphoid enhancer-

221558_ binding factor s at 1 AF288571 0.4589 0.0272 0.0858 0.6309 0.0236 -0.021 0.1641 -0.4377 0.1276 -0.5954

Fas apoptotic inhibitory

221601_. molecule /// s at Fas apoptotic AI084226 0.3768 -0.0124 0.0698 0.4249 -0.0111 0.0098 0.1037 -0.2765 0.0857 -0.4

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score inhibitory molecule Fas apoptotic inhibitory molecule /// Fas apoptotic

221602_ inhibitory s at molecule AF057557 0.4428 -0.0205 0.0396 0.4425 -0.0184 0.0164 0.1044 -0.2784 0.0891 -0.416 zinc ringer

221645_ protein 83 s at ((HHPPFFll)) M27877 0.4535 -0.0271 0.0806 0.4757 -0.0245 0.0218 0.1084 -0.2891 0.0966 -0.4508

221657_ ankyrinrepeat BC001719 0.4237 -0.1393 0.1008 -0.165 -0.1311 0.1165 0.0066 -0.0177 0.0333 -0.1552

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at and SOCS box-

VO containing 6 -4

221658_ interleukin 21 s_at receptor A AFF226699113333 00..33119999 0.0881 -0.0116 0.5554 0.0804 -0.0715 0.1649 -0.4396 0.1149 -0.5362 immunoglobuli n kappa constant /// immunoglobuli

221671_ n kappa x_at variable 1-5 M63438 0.2496 0.0756 -0.1498 0.3162 0.0709 -0.063 0.1009 -0.269 0.0651 -0.3036

221691_ nucleophosmin x at (nucleolar AB042278 0.4248 -0.0057 0.0178 0.4424 -0.0051 0.0045 0.1103 -0.294 0.0886 -0.4133

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score phosphoprotein

B23, numatrin)

00

/// nucleophosmin

(nucleolar phosphoprotein

B23, numatrin)

221728_ x_at AA628440 -0.4585 0.3758 -0.0671 0.4622 0.3598 -0.3198 0.2604 -0.6943 0.0903 -0.4212

221756_ HGFL gene /// at HGFL gene AL540260 0.5044 -0.1183 0.1233 0.3263 -0.1058 0.094 0.0547 -0.146 0.0639 -0.298

221757 HGFL gene /// BE042976 0.5923 -0.077 -0.003 -0.0671 0.0596 0.0881 -0.2349 0.0788 -0.3677

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at HGFL gene 0.4061

Ul

^o DEAD (Asp- ^o

Glu-Ala-Asp)

221780_ box s at polypeptide 27 AF336851 0.3754 -0.0204 0.1534 0.4825 -0.0184 0.0164 0.1123 -0.2996 0.0983 -0.4586

DnaJ (Hsp40) homolog,

221781_ subfamily C, s_at member 10 BG168666 0.1614 0.1257 -0.0021 0.5007 0.1176 -0.1045 0.158 -0.4214 0.1045 -0.4877 low density

221790_ lipoprotein s at receptor AL545035 0.505 -0.0016 0.0803 0.5969 -0.0014 0.0012 0.1491 -0.3975 0.12 -0.5599

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score adaptor protein

4- 1 j.

O O hypothetical gene supported

221823_ by AF038182; at BC009203 A ALL5566557744Ϊ1 -0.1161 -0.0895 -0.2304 0.581 -0.0809 0.0719 -0.1696 0.4524 -0.1205 0.5622

CDNA clone

IMAGE:52170

21, with

221973_ apparent at retained intron AI983904 0.3204 0.069 -0.027 0.4902 0.063 -0.056 0.1468 -0.3916 0.1009 -0.4709

221988_ Hypothetical A AAA4466338855:3 0.4076 -0.1171 0.0855 -0.1096 0.0974 0.0185 -0.0493 0.0389 -0.1815

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set E) Gene Title ID score score score score score 3 score score score score score at protein 0.1928

4-

© MGC2747 nascent- polypeptide- associated

222018_ complex alpha at polypeptide AI992187 0.4356 -0.1087 0.01 0.1714 -0.102 0.0907 0.016 -0.0425 0.0347 -0.1617

222062_ interleukin 27 at receptor, alpha AI983115 0.3104 -0.0532 0.2028 0.3753 -0.0483 0.043 0.0789 -0.2105 0.076 -0.3544 solute carrier

222088_ family 2 s at (facilitated AA778684 -0.4773 0.0729 0.0562 0.2466 0.0659 -0.0586 -0.0443 0.118 -0.0487 0.2274

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score glucose

O transporter), member 3 /// solute carrier family 2 (facilitated glucose transporter), member 14 Zinc finger

222136_ protein 43 x at (HTF6) AK022905 0.2055 0.0588 -0.0032 -0.367 0.0552 -0.049 0.1097 -0.2927 0.0761 -0.3553

Table 6: Group of 1645 genes that are differential y expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

222146_ transcription

4-

O s at factor 4 AK026674 0.2092 0.1158 -0.1651 0.3667 0.1098 -0.0976 0.1284 -0.3424 0.0761 -0.3551

DNA polymerase-

222154_ transactivated s_at protein 6 AK002064 -0.5106 0.5957 -0.3732 0.6996 0.5749 -0.511 0.3405 -0.908 0.1273 -0.5943

G protein- 222155_ coupled s_at receptor 172A AK021918 0.4488 -0.0537 -0.0821 0.2432 -0.0496 0.0441 0.0494 -0.1317 0.049 -0.2287

RRN3 RNA

222204_ polymerase I s_at transcription ALl 10238 0.2551 0.0268 0.1297 0.4608 0.0245 -0.0217 0.1192 -0.3178 0.095 -0.4435

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score factor homolog

(yeast) hypothetical

222228_ protein s_at FLJ20013 A AKK00226600997'. 0.3708 -0.041 -0.0237 0.2525 -0.038 0.0338 0.0536 -0.1429 0.0513 -0.2393 chondroitin

222235_ sulfate s_at GalNAcT-2 AL139812 0.0462 -0.0797 0.3841 0.0416 -0.037 -0.0849 0.2263 -0.0772 0.3601

Chromosome

19 open

222266_ reading frame at 2 BF796940 0.5119 -0.0701 0.0397 -0.382 -0.0637 0.0566 0.0767 -0.2045 0.0766 -0.3576

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

222303 έ at — AV700891 -0.2503 -0.0491 0.0034 0.3873 -0.0456 0.0406 -0.1116 0.2976 -0.08 0.3735

222306_ 5-azacytidine at induced 2 AA521034 0.49 -0.18 -0.0744 0.0435 -0.1684 0.1497 -0.0611 0.1629 -0.0086 0.0401

CCR4-NOT transcription

222313_ complex, AW97235 at subunit 2 9 0.5871 -0.2266 -0.0416 0.0356 -0.2142 0.1904 -0.0724 0.1929 -0.007 0.0328

Phosphodiester

222330_ ase 3B, cGMP- AW97499 - at inhibited 5 0.4984 -0.0949 -0.2213 0.0507 -0.0892 0.0793 -0.0119 0.0318 0.0102 -0.0478

222357 zinc fineer and AW97482 0.51 -0.227 -0.1256 0.1973 -0.2092 0.186 -0.113 0.3013 -0.0381 0.1777

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at BTB domain 3

O containing 20 butyrate-

222404_ induced x at transcript 1 AI984229 0.3737 -0.0086 0.0562 0.4187 -0.0078 0.0069 0.104 -0.2774 0.085 -0.3968 aldehyde dehydrogenase

222416_ 18 family, at member Al U76542 0.1617 0.0765 0.1016 0.4695 0.0712 -0.0633 0.1384 -0.369 0.0979 -0.4569 ubiquitin-

222435_ conjugating s at enzyme E2, Jl AF161502 -0.4774 0.1187 -0.0394 0.2165 0.1071 -0.0952 -0.0247 0.0658 -0.0423 0.1972

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(UBC6 g homolog,

-4 yeast)

222453_ cytochrome b at reductase 1 AL136693 -0.2703 -0.0747 0.1296 0.3548 -0.0695 0.0618 -0.1093 0.2915 -0.0728 0.3399

222496_ RNA-binding AW24174 s_at protein 2 -0.5578 0.1733 0.0213 0.0958 0.156 -0.1387 0.0194 -0.0516 -0.0183 0.0852

222498_ 5-azacytidine at induced 2 AI809206 -0.4961 0.2353 -0.0977 0.0189 0.2187 -0.1944 0.0703 -0.1875 0.0036 -0.0169 hypothetical

222551_ protein - s — at FLJ20989 AI197841 0.2655 0.0215 -0.014 0.3192 0.0202 -0.0179 0.0904 -0.2411 0.066 -0.3078

Table 6: Group of 1645 g enes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hypothetical

§ 222662 protein oe at LOC286044 W60806 -0.5195 0.1296 -0.0353 0.2271 0.1167 -0.1038 -0.0243 0.0649 -0.0442 0.2062 fibronectin

222692_ type III domain s_at containing 3B BF444916 -0.4883 0.214 0.002 0.0661 0.1987 -0.1766 0.0717 -0.1912 0.0128 -0.0598 fibronectin

222693_ type III domain at containing 3B BF444916 -0.5046 0.2635 -0.0596 -0.122 0.2485 -0.2209 0.0988 -0.2634 0.0237 -0.1107 serum

222717_ deprivation at response BF982174 0.5418 -0.0113 -0.2647 0.2767 -0.0101 0.009 0.0687 -0.1833 0.0542 -0.2531

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(phosphatidyls

O erine binding protein) trimethyllysine 222744_ hydroxylase, s_at epsilon AI635160 -0.6302 0.1088 0.0183 0.3458 0.0956 -0.0849 -0.0703 0.1875 -0.0667 0.3111 chromosome

15 open

222745_ reading frame s_at 29 AI924685 -0.5763 0.2402 -0.0223 0.0215 0.2216 -0.197 0.0671 -0.179 0.0041 -0.0191

222787_ hypothetical s_at protein AV705186 0.3402 -0.1319 0.0042 0.0052 -0.1259 0.1119 -0.033 0.088 0.0011 -0.0049

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

FLJl 1273

DEAD (Asp-

Glu-Ala-Asp)

222793_ box - at polypeptide 58 AK023661 -0.417 0.37 -0.1171 0.4416 0.3481 -0.3094 0.2022 -0.5392 0.0834 -0.3891 zinc finger,

222816_ CCHC domain - s_at containing 2 BE676543 -0.1824 0.3638 - -00..221133 00..55775588 0.348 -0.3093 0.2366 -0.6309 0.1149 -0.5363 hypothetical

222833_ protein at FLJ20481 AUl 54202 -0.6465 0.2205 0.0395 0.0442 0.1991 -0.-177 0.0459 0.1225 -0.0083 0.0389

222841 translocase of AI762874 0.2457 -0.0125 0.1829 -0.0115 0.0103 0.0973 0.2595 0.0819 -0.382

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score s_at inner 0.3976 mitochondrial membrane 22 homolog

(yeast) leucine zipper

222848_ protein - at FKSG14 BC005400 0.257 0.0394 -0.0473 0.3261 0.0371 -0.033 0.1033 -0.2755 0.0676 -0.3155 dual adaptor of phosphotyrosin

222859_ e and 3- - s_at phosphoinositi AA150186 -0.4842 0.2963 -0.0681 0.2223 0.2748 -0.2443 0.1328 -0.3542 0.0416 -0.194

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score des

B-cell

CLL/lymphom 222895_ a HB (zinc s_at finger protein) AA918317 0.4842 -0.0111 0.1476 0.6146 -0.0097 0.0086 0.1501 -0.4004 0.1242 -0.5796

222920_ KIAA0748 s_at gene product BG231515 0.3459 0.0536 0.1192 0.6163 0.0486 -0.0432 0.1671 -0.4455 0.1279 -0.597

C-type lectin

222934_ domain family s_at 4, member E BC000715 -0.4534 0.0979 -0.0201 0.2283 0.0905 -0.0805 -0.0326 0.087 -0.0458 0.2136

222945_ thioesterase x at domain AI125696 -0.2866 -0.0386 -0.144 0.5389 -0.035 0.0311 -0.143 0.3813 -0.1112 0.5192

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score containing 1

£ 222986_ s at scotm BC001463 -0.5814 0.321 -0.1189 0.1385 0.2954 -0.2625 0.1158 -0.3088 0.0253 -0.1183 ubiquitin-

223014_ conjugating at enzyme E2R 2 BC004862 -0.4989 0.048 0.1213 0.2725 0.0421 -0.0374 -0.0572 0.1525 -0.0527 0.246

223027_ at sorting nexin 9 BF972871 0.2384 0.0286 0.1152 0.4346 0.0264 -0.0235 0.1133 -0.3021 0.0899 -0.4196 solute carrier family 40

223044_ (iron-regulated at transporter), AL136944 -0.5593 0.0651 0.0617 0.347 0.0567 -0.0504 -0.0707 0.1886 -0.067 0.3129

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score member 1 egl nine

223046_ homolog 1 (C. at elegans) ALl 17352 -0.5815 0.1417 0.0487 0.1781 0.1255 -0.1115 -0.0094 0.025 -0.0338 0.1579 ankylosis, progressive 223092_ homolog at (mouse) AA854943 0.399 -0.0212 0.254 0.6019 -0.0186 0.0165 0.1411 -0.3763 0.122 -0.5691

DEAH (Asp-

Glu-Ala-His) 223138_ box s_at polypeptide 36 AI937206 0.3278 0.002 -0.0323 0.3142 0.0018 -0.0016 0.0821 -0.2189 0.0644 -0.3004

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Hypothetical

4- 223144_ protein 8.00E- Ul s at PRO2266 BC000764 -0.6202 0.1791 -0.0106 0.1758 0.1585 -0.1409 04 -0.0022 -0.0331 0.1543 poly (ADP- ribose) polymerase

223220_ family, s at member 9 AF307338 -0.8747 0.4601 -0.1171 0.2072 0.4098 -0.3642 0.1737 -0.4633 0.0349 -0.1627 serologically defined colon

223282_ cancer antigen at 33 W60810 0.1538 0.0798 0.1873 0.5528 0.0719 -0.0639 0.1578 -0.4209 0.1143 -0.5333

Table 6: Group of 1645 genes that are differentially expressed in healthy donors ₅ SLE patients (lupus score), RA patients j, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

223298_ 5 -nucleotidase, s at cytosolic III AF312735 -0.4523 0.3977 -0.2748 0.3269 0.377 -0.3351 0.1811 -0.483 0.0599 -0.2797 solute carrier family 37 (glycerol-3- phosphate

223304_ transporter), at member 3 AL136583 -0.6505 0.0021 0.0866 0.5857 0.0018 -0.0016 -0.1489 0.397 -0.1141 0.5327 hypothetical protein

223418_ DKFZp566Dl x at 346 AL136717 0.1617 0.0928 0.1094 0.5207 0.0854 -0.0759 0.1532 -0.4087 0.1084 -0.5057

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score guanylate ^ 223434_ binding protein at 3 AL136680 -0.2648 0.251 -0.0563 0.3405 0.2395 -0.2129 0.1501 -0.4002 0.0684 -0.3192

223451_ chemokine-like s_at factor AF096895 -0.5824 0.1928 -0.0693 0.1567 0.1722 -0.1531 0.0092 -0.0246 -0.0295 0.1378 chemokine (C- 223454_ X-C motif) at ligand lδ AF275260 -0.4488 0.1057 -0.016 0.199 0.0962 -0.0855 -0.0241 0.0643 -0.0392 0.1831 tumor necrosis factor (ligand)

223501_ superfamily, AW15136 - at member 13b 0 -0.7307 0.4155 -0.066 0.2867 0.3772 -0.3353 0.1802 -0.4805 0.0502 -0.2344

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients,, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score tumor necrosis factor (ligand)

QO 223502_ superfamily, s_at member 13b AF134715 -0.7348 0.4171 -0.1257 0.2294 0.3797 -0.3375 0.1655 -0.4415 0.04 -0.1869

Notch homolog

1, translocation- 223508_ associated at (Drosophila) AF308602 -0.3588 0.0158 0.0402 0.2912 0.0149 -0.0133 -0.0718 0.1914 -0.0601 0.2804 caspase

223514_ recruitment at domain family, AF322641 0.3832 -0.0167 0.1408 0.4886 -0.0153 0.0136 0.124 -0.3308 0.1004 -0.4687

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score member 11 leucine rich 223552_ repeat at containing 4 AF196976 -0.6619 -0.0028 0.0767 0.6199 -0.0024 0.0021 -0.161 0.4293 -0.123 0.5739

223553_ docking s_at protein 3 BC004564 -0.5511 0.0753 0.0481 0.3245 0.0659 -0.0586 -0.0633 0.1689 -0.0627 0.2928

223592_ ring finger s_at protein 135 BC005084 -0.2785 -0.0555 0.0027 0.4341 -0.0503 0.0447 -0.123 0.328 -0.0888 0.4145 solute carrier family 12

223596_ (potassium/chl at oride AF 105366 -0.5194 0.121 0.0263 0.1905 0.1096 -0.0974 -0.0176 0.047 -0.0372 0.1736

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score transporters),

4- member 6

O

223599_ tripartite motif- at containing 6 AF220030 -0.5306 0.4268 -0.2548 0.3426 0.4092 -0.3638 0.2043 -0.5448 0.0641 -0.2991

223609_ at ropporin 1-like AF239723 -0.4932 0.0448 0.1267 0.27 0.0398 -0.0354 -0.0563 0.1502 -0.0528 0.2464

223649_ s at CGI-69 protein AF317711 0.5512 -0.1427 0.0405 0.2301 -0.127 0.1129 0.0235 -0.0626 0.0441 -0.206 nuclear receptor

223650_ binding factor s at 2 AF267866 -0.5311 0.1485 0.039 0.1172 0.1338 -0.1189 0.0079 -0.0211 -0.0225 0.105

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

223660_ at AD026 protein AF226731 -0.3855 -0.0216 0.0674 0.3924 -0.0202 0.0179 -0.1064 0.2838 -0.081 0.3779 ubiquitin

223701_ specific s_at protease 47 AF059318 0.2873 0.0194 0.0093 0.3587 0.0181 -0.0161 0.0976 -0.2603 0.0739 -0.3451

223717_ acrosin binding s_at protein AB051833 0.5574 -0.1191 -0.174 -0.093 -0.1064 0.0946 -0.0069 0.0183 0.0178 -0.0833

223733_ s_at — AFl 19843 -0.628 0.0805 0.0508 0.3877 0.0708 -0.0629 -0.0809 0.2157 -0.0754 0.3517

223750 toll-like AW66525 s at receptor 10 -0.5496 0.2325 -0.1951 0.1378 0.2134 -0.1897 0.0268 -0.0716 -0.0264 0.1231

223754_ hypothetical BC005083 0.6378 -0.1156 -0.1973 -0.163 -0.1022 0.0908 0.012 -0.0321 0.0311 -0.1449

Table 6: Group of 1645 genes that are differentially expressed ill healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at protein MGC13057

K) general transcription factor HH,

223758_ polypeptide 2, s_at 44IcDa BC005345 -0.3997 0.2549 -0.1309 0.1391 0.2423 -0.2154 0.1031 -0.2749 0.0273 -0.1273 G protein-

223161 _ coupled at receptor 84 AF237762 -0.4207 0.0211 -0.1269 0.5023 0.0192 -0.0171 -0.1308 0.3488 -0.1029 0.4802

223777_ hypothetical at protein BC005070 0.4694 -0.1903 -0.0781 0.0959 -0.1785 0.1587 -0.0755 0.2012 -0.019 0.0886

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

MGCl 3005

4- contactin associated protein-like 3 /// similar to cell recognition

223796_ molecule at CASPR3 AF333769 -0.353 -0.0018 -0.0292 0.399 -0.0017 0.0015 -0.104 0.2773 -0.0823 0.3839 lectin, galactoside-

223828_ binding, s at soluble, 12 AF222694 0.4792 -0.1593 0.0996 0.1681 -0.1485 0.132 0.0022 -0.0059 0.0335 -0.1561

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(galectin 12)

223836 at Ksp37 protein AB021123 0.3698 -0.0947 0.3368 0.4553 -0.0862 0.0766 0.0885 -0.2361 0.092 -0.4295

MovlO,

Moloney leukemia virus

223849_ 10, homolog s at (mouse) BC002548 -0.59 0.5251 -0.1421 0.6514 0.4972 -0.442 0.3072 -0.8193 0.1199 -0.5597 G protein-

223887_ coupled at receptor 132 BC004555 -0.3132 -0.0749 0.2272 0.3059 -0.0695 0.0618 -0.1019 0.2716 -0.0622 0.2903

223952_ dehydrogenase/ AF240698 -0.5042 0.2788 -0.1254 0.2626 -0.2334 0.0974 -0.2597 0.0192 -0.0896

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus scored RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x at reductase 0.0997

(SDR family) member 9 dehydrogenase/ reductase

224009_ (SDR family) x_at member 9 AF240697 -0.5206 0.2709 -0.0905 0.0954 0.2545 -0.2262 0.0938 -0.2503 0.0184 -0.0857 224148_ at AFl 16653 -0.3049 0.2254 -0.0449 0.2416 0.2147 -0.1908 0.1178 -0.3141 0.0483 -0.2256 mitochondrial

224173_ ribosomal s at protein L30 BC000217 0.3058 -0.0221 0.199 0.4499 -0.0201 0.0179 0.1045 -0.2787 0.092 -0.4295

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupws score), RA patients, and WG patients-

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score tripartite motif-

4- containing 34 /// tripartite motif- containing 6 and tripartite

224175_ motif- s_at containing 34 AB039904 -0.4021 0.2023 -0.0023 0.1204 0.1927 -0.1713 0.0876 -0.2335 0.0241 -0.1126 ets variant gene

224225_ 7 (TEL2 s_at oncogene) AF218365 -0.4291 0.3441 -0 .1897 0 .2898 0.3303 -0 .2936 0 .172 -0.4587 0.0561 -0.2619

224314 egl nine AF277174 -0.707 0.2066 0. 0036 0 .1789 0.1853 -0 .1647 0. 0081 -0.0215 -0.0339 0.1582

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ED Gene Title ID score score score score score 3 score score score score score s at homolog 1 (C.

4- elegans) -4 transmembrane protein with EGF-like and two follistatin- like domains 2 /// transmembrane protein with

224321_ EGF-like and at two follistatin- AB004064 -0.3881 0.1218 -0.1862 0.257 0.1135 -0.1009 -0.0343 0.0916 -0.0518 0.2419

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients-, and WG patients- „,

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score like domains 2 toll-like

OO receptor 4 /// 224341_ toll-like x_at receptor 4 U93091 -0.6125 0.275 -0.0646 -0.036 0.2512 -0.2233 0.0786 -0.2097 0.0067 -0.0313 brain expressed

X-linked 2 ///

224367_ brain expressed at X-linked 2 AF251053 0.2685 0.035 0.0777 0.4465 0.0322 -0.0286 0.1213 -0.3234 0.0922 -0.4304 cat eye

224393_ syndrome s at chromosome AF307451 -0.7063 0.1365 0.1388 0.2348 0.1219 -0.1083 -0.0265 0.0707 -0.0452 0.2109

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score region,

4- candidate 6 /// cat eye syndrome chromosome region, candidate 6 caspase recruitment domain family,

224414_ member 6 /// s at caspase AF356193 -0.5865 0.1113 0.044 0.2691 0.0969 -0.0862 -0.0406 0.1083 -0.0511 0.2385

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score recruitment domain family,

O member 6 hypothetical protein

MGCl 1324 /// hypothetical

224480_ protein s_at MGCl 1324 BC006236 -0.5626 0.018 0.0898 0.449 0.0156 -0.0139 -0.108 0.2881 -0.0879 0.4101 hypothetical

224489_. protein at LOC284058 /// BC006271 0.4671 -0.2349 0.1044 0.0414 -0.2236 0.1988 -0.0724 0.1931 -0.0082 0.0383

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupos score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hypothetical

4- protein

LOC284058 hypothetical protein

LOC284058 /// hypothetical

224490_ protein s_at LOC284058 BC006271 0.5381 -0.2754 0.0699 0.109 -0.2644 0.235 -0.1043 0.2782 -0.0216 0.1009

224549_ x_at AF194537 0.3102 -0.088 -0.2314 0.1357 -0.0826 0.0734 -0.0579 0.1544 -0.0275 0.1283

224560 tissue inhibitor BF107565 -0.6935 0.1963 0.0487 0.1488 0.17 -0.1511 0.012 -0.032 -0.0272 0.1269

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at of

4- metalloproteina se 2 metastasis associated lung adenocarcinom a transcript 1

224567_ (non-coding x_at RNA) BG534952 0.2382 -0.0141 -0.178 -0.038 -0.0135 0.012 0.0061 -0.0162 0.0079 -0.0367 endoplasmic

224576_ reticulum-golgi at intermediate AK000752 -0.3575 -0.0797 0.0694 0.5165 -0.0715 0.0636 -0.1488 0.3968 -0.1052 0.4911

Table 6: Group of 1645 genes that are differeiitially expressed in healthy donors , SLE patients (lupus score), RA patients, arid WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score compartment

4- 32 kDa protein endoplasmic reticulum-golgi intermediate

224577_ compartment at 32 kDa protein AB033007 -0.3261 -0.0368 -0.0068 0.4428 -0.0335 0.0298 -0.1185 0.316 -0.0907 0.4235

224588_ at AA167449 -0.7412 0.5348 -0.0146 0.6433 0.5091 -0.4525 0.3977 -1.0605 0.1205 -0.5625

224589_ at BF223193 -0.5591 0.4522 -0.0482 0.5798 0.4312 -0.3833 0.3261 -0.8695 0.1111 -0.5186

224590 BE644917 -0.8555 0.5298 -0.0166 - 0.501 -0.4454 0.3733 -0.9954 0.0936 -0.4366

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at 0.5095

224595_ CDW92 at antigen AK022549 -0.473 0.038 0.1489 0.2458 0.0351 -0.0312 -0.0538 0.1434 -0.0495 0.2311

HCV F-

224605_ transactivated at protein 1 AV727336 -0.4856 0.194 -0.1031 0.0855 0.1779 -0.1581 0.0279 -0.0744 -0.0165 0.0768

Lectin,

224629_ mannose- at binding, 1 BF217539 0.3443 -0.0056 0.0604 0.4003 -0.0051 0.0045 0.0983 -0.2622 0.0817 -0.3811

Cl 14 SLIT-

224686_ like testicular x_at protein /// AA045233 0.5001 -0.2235 0.0887 0.0079 -0.2088 0.1856 -0.0548 0.1461 0.0015 -0.0072

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and. WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Hypothetical

4- W LOC388397 Ul poly (ADP- ribose) polymerase

224701 _ family, at member 14 A AAA0055665544S8 -0.5652 0.4383 -0.1528 0.4355 0.4114 -0.3657 0.2248 -0.5996 0.0791 -0.3691 putative

224707_ nuclear protein at ORF1-FL49 AL522667 0.0882 -0.0933 0.5295 0.0756 -0.0672 -0.1124 0.2997 -0.1025 0.4784

224736_ cell division at cycle and BE617899 0.3748 -0.0345 -0.015 0.2821 -0.0321 0.0285 0.0625 -0.1666 0.0575 -0.2681

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set DD Gene Title ID score score score score score 3 score score score score score apoptosis regulator 1 hypothetical

224759_ protein s_at MGC17943 A AKK000011773311 00..334422 00..11119933 0.0288 0.7006 0.1054 -0.0937 0.2057 -0.5486 0.1445 -0.6744 development and differentiation

224790_ enhancing at factor 1 AI023398 -0.5778 0.1542 0.0612 0.1292 0.1378 -0.1224 0.0065 -0.0172 -0.0246 0.1148

224796_ development at and W03103 -0.5749 0.0973 0.0842 0.2557 0.0842 -0.0749 -0.0413 0.11 -0.0484 0.2257

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score differentiation enhancing

-4 factor 1

224818_ at sortilin 1 BE622952 -0.4626 0.037 -0.0721 0.4505 0.032 -0.0284 -0.1063 0.2834 -0.0886 0.4134 cytoplasmic polyadenylatio n element

224831_ binding protein at 4 BE620832 -0.5498 0.2302 -0.1342 0.0855 0.2102 -0.1869 0.0367 -0.0979 -0.0162 0.0756

224833_ v-ets at erythroblastosi BE218980 0.2318 0.0891 0.1315 0.6046 0.0786 -0.0698 0.1752 -0.4673 0.1244 -0.5807

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s virus E26 oncogene

OO homolog 1

(avian)

224840_ FK506 binding at protein 5 AI753747 -0.1991 -0.0354 -0.1051 0.4021 -0.0332 0.0295 -0.1085 0.2892 -0.0837 0.3906

SH3KBP1

224846_ binding protein at 1 AI348000 -0.5065 0.0183 0.0794 0.4 0.0162 -0.0144 -0.0959 0.2557 -0.079 0.3688

224856_ FK506 binding at protein 5 W86302 -0.1696 -0.0534 -0.0696 0.3852 -0.0503 0.0447 -0.1073 0.2861 -0.0804 0.375

224889 forkhead box BE888885 -0.2235 -0.0631 0.0613 0.341 -0.0583 0.0518 -0.1034 0.2757 -0.0699 0.3261

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at O3A cirrhosis, autosomal

224903_ recessive IA at (cirhin) AL519818 0.1779 0.0799 0.0647 0.4599 0.0748 -0.0665 0.1422 -0.3791 0.096 -0.4481

UDP-glucose ceramide

224967_ glucosyltransfe at rase W72338 -0.3774 0.0346 -0.1693 0.4621 0.0307 -0.0273 -0.1044 0.2784 -0.0929 0.4334

Hypothetical

224996_ protein at MGC34646 N30209 -0.5327 0.1025 -0.1929 0.465 0.0912 -0.0811 -0.0918 0.2448 -0.0922 0.4301

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

RAB3D,

4- 4- member RAS

O

225001_ oncogene at family AI744658 -0.4299 -0.0064 0.1352 0.3326 -0.0057 0.0051 -0.0865 0.2306 -0.0659 0.3076 Hypothetical

225008_ protein AW46935 at MGC34646 1 -0.283 -0.0182 -0.131 0.468 -0.0164 0.0146 -0.1214 0.3238 -0.0958 0.4472 signal-induced proliferation-

225056_ associated 1 at like 2 AB037810 -0.7242 0.2383 -0.1598 0.2694 0.2133 -0.1896 -0.0078 0.0209 -0.0509 0.2374

225076 KLAA1404 AA150460 -0.539 0.2181 -0.0419 0.0177 0.1975 -0.1756 0.0516 -0.1377 -0.0033 0.0155

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at protein

225098_ AbI interactor at 2 BF245400 0.3651 0.0102 -0.0064 0.3996 0.0093 -0.0082 0.1042 -0.278 0.0814 -0.3799

225129_ AWl 7057 at copine ll 1 -0.1784 -0.1485 0.0284 0.5538 -0.1336 0.1188 -0.1786 0.4764 -0.1136 0.5302

225142_ KIAA1718 AW29402 at protein 2 -0.5924 0.1681 0.0162 0.1504 0.1491 -0.1325 0.0046 -0.0123 -0.0283 0.1323 hypothetical

225149_ protein at FLJl 1305 AU144029 0.2146 0.1106 0.0526 0.5681 0.1011 -0.0899 0.177 -0.472 0.1181 -0.5511

225155_ chromosome 6 at open reading BG339050 0.3738 -0.1951 0.1926 0.0529 -0.1847 0.1642 -0.0375 0.0999 0.0105 -0.0492

frame 160 tetratricopeptid 225178_ e repeat at domain 14 W73788 0.3732 -0.0049 -0.0476 0.3281 -0.0044 0.0039 0.0831 -0.2215 0.0665 -0.3101 musashi

225237_ homolog 2 s_at (Drosophila) BF435123 0.2565 0.0209 0.1532 0.4692 0.0189 -0.0168 0.1208 -0.3221 0.0963 -0.4496

225262_ FOS-like at antigen 2 AI670862 -0.5187 0.0917 0.0487 0.2465 0.0811 -0.0721 -0.0395 0.1054 -0.0476 0.2221 polyribonucleo

225291_ tide at nucleotidyltran AI967971 -0.2791 0.415 -0.212 0.6131 0.387 -0.344 0.2578 -0.6874 0.1153 -0.5379

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score sferase 1

4- ADP-

225347_ ribosylation at factor-like 1OB AL520984 -0.7875 0.1311 0.073 0.3969 0.1113 -0.0989 -0.0743 0.1981 -0.074 0.3454 heterogeneous nuclear

225385_ ribonucleoprot AW27381 s_at ein L-like 1 - -00..44112255 0.2502 -0.0049 0.2346 0.2368 -0.2105 0.1393 -0.3715 0.0463 -0.2159

RNA pseudouridylat

225398_ e synthase 5.00E- -4.00E- at domain AL580514 0.2729 04 0.0864 0.3675 04 0.0904 -0.241 0.0755 -0.3526

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set BD Gene Title ID score score score score score 3 score score score score score containing 4 * 225415_ deltex 3-like

J- at (Drosophila) AA577672 -0.5874 0.3782 -0.0947 0.3082 0.3465 -0.308 0.176 -0.4694 0.0548 -0.2557

225457_ DKFZP564I11 s_at 71 protein BF528646 0.331 0.0297 -0.0349 0.3889 0.0276 -0.0245 0.109 -0.2905 0.0801 -0.3737

225458_ DKFZP564I11 at 71 protein BF528646 0.1882 0.0545 0.1035 0.4403 0.0503 -0.0448 0.1272 -0.3391 0.0913 -0.4259 hypothetical

225466_ protein at FLJ36874 BG291961 -0.5321 0.2394 0.0452 -0.13 0.2168 -0.1927 0.095 -0.2534 0.0243 -0.1132

225468_ hypothetical at protein AI761804 -0.4313 0.2527 -0.0454 0.1829 0.2358 -0.2096 0.1092 -0.2913 0.0351 -0.1637

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

3 4 10 11 12 13

Representa Healthy tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score

FLJ36874

225496_ synaptotagmin-

'Jl s_at Iike 2 N21426 0.5084 -0.1309 0.0902 -0.265 -0.1176 0.1046 0.0349 -0.0932 0.0516 -0.2409 dehydrogenase/ reductase

225503_ (SDR family) at X-linked AL547782 -0.4413 -0.0239 0.3127 0.2204 -0.0219 0.0195 -0.0614 0.1636 -0.044 0.2052 protein phosphatase 4,

225519_ regulatory at subunit 2 AA206408 -0.5497 0.1287 -0.0118 0.2383 0.1142 -0.1015 -0.0275 0.0733 -0.0457 0.2134

225525 KIAA1671 AB051458 0.1104 0.1191 0.1753 0.1064 -0.0946 0.1814 -0.4837 0.1242 -0.5797

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients_*

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at protein 0.6009

£ 225557_ AXINl up- at regulated 1 AI091372 -0.6935 0.2913 0.0054 0.0628 0.2626 -0.2334 0.0932 -0.2485 0.0115 -0.0537 Hypothetical

225599_ protein AW30330 s_at LOC286144 0 -0.3441 0.0305 -0.098 0.3698 0.0276 -0.0246 -0.0864 0.2303 -0.0749 0.3493 Hypothetical

225603_ protein s__at LOC286144 BE962119 -0.4162 -0.01 -0.0317 0.4888 -0.0087 0.0078 -0.1324 0.3531 -0.0979 0.4567 UDP-

225612_ GlcNAc:betaG -9.00E- s at al beta-l,3-N- BE672260 -0.7299 0.2231 -0.0671 0.2267 0.1958 -0.174 04 0.0025 -0.0419 0.1958

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score acetylglucosam myitransrerase

5 hypothetical

225615_ protein - at LOC126917 AK024480 0.2896 0. 0072 0 .1102 0.4258 0.0067 -0.0059 0.1084 -0.289 0.0876 -0.409 zinc finger and

225629_ BTB domain s_at containing 4 AI669498 0.3195 -0 .0094 0 .1491 -0.45 -0.0084 0.0074 0.1112 -0.2964 0.0914 -0.4263

RAB43,

225632_ member RAS s at oncogene BE736242 -0.6056 0. 1461 0 .0308 0.2088 0.1287 -0.1144 -0.0167 0.0445 -0.0395 0.1845

Table 6: Group of 1645 g enes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score family

4- signal

90 transducer and activator of

225636_ transcription 2, at 113kDa H98105 -0.4254 0.3567 -0.1175 0.3969 0.3368 -0.2994 0.1928 -0.5142 0.0754 -0.3518 ubiquitrn-like, containing PHD and

225655_ RING finger at domains, 1 AK025578 -0.3642 0.0911 -0.1343 0.2641 0.0858 -0.0763 -0.0458 0.122 -0.0541 0.2523

225661 interferon AA811138 -0.6664 0.1926 0.0272 0.1512 0.1703 -0.1514 0.0105 -0.0281 -0.0283 0.1319

Table 6: Group of 1645 genes that are differentially expressed in healthy ^"donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set BD Gene Title ID score score score score score 3 score score score score score at (alpha, beta and omega) receptor 1 CDC42 effector protein

225685_ (Rho GTPase at binding) 3 AI801777 -0.6313 0.1464 0.0749 0.1921 0.1266 -0.1125 -0.0117 0.0312 -0.0356 0.1663 CDNA FLJ34013 fis, clone

225710_ FCBBF200211 at 1 H99792 -0.5588 0.2743 -0.0949 0.0606 0.249 -0.2213 0.0854 -0.2277 0.0111 -0.0518

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

225712_ AW02456 at 3 0.1982 0.0214 0.125 0.3828 0.02 -0.0177 0.1053 -0.2809 0.0795 -0.371

O nuclear receptor subfamily 1,

225768_ group D, at member 2 AI761621 0.2271 0.0772 0.0343 0.4746 0.0709 -0.063 0.1387 -0.3698 0.0982 -0.4581

225782_ AW02733 at — 3 -0.207 -0.0081 -0.2154 0.4437 -0.0075 0.0067 -0.119 0.3174 -0.0922 0.4301

225792_ Hook homolog at 1 (Drosophila) AA618420 0.2798 -0.0112 0.1713 0.4252 -0.0102 0.0091 0.103 -0.2747 0.0871 -0.4066

225796 PX domain AI684747 -0.4713 0.0613 -0.0203 0.3448 0.0541 -0.0481 -0.0727 0.1939 -0.0676 0.3155

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at containing serine/threonin e kinase thyrotrophic

225840_ embryonic at factor AA779795 0.4806 -0.1285 0.0461 0.2002 -0.1185 0.1054 0.0182 -0.0486 0.0398 -0.1856 breast cancer

225864 membrane at protein 101 AL039862 0.1515 0.1063 0.0839 0.5213 0.0968 -0.086 0.157 -0.4186 0.1079 -0.5037

225866 brix domain at containing 1 AA976536 0.1692 0.0753 0.1994 0.5683 0.0683 -0.0607 0.1612 -0.4299 0.118 -0.5507

225897_ Myristoylated AI709406 -0.68 0.3998 -0.0445 -0.318 0.3626 -0.3223 0.184 -0.4906 0.056 -0.2613

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at alanine-rich protein kinase C substrate chromosome 17 open

225929_. reading frame s at 27 AA233374 -0.3999 0.3359 -0.2209 0.2681 0.3181 -0.2827 0.1591 -0.4243 0.0505 -0.2355 chromosome 17 open

225931_ reading frame s_at 27 AI954660 -0.3605 0.3752 -0.2808 0.3562 0.3558 -0.3163 0.1872 -0.4991 0.0662 -0.3088

225935 FP6778 AI350995 -0.3123 -0.129 0.1575 0.5163 -0.1128 0.1002 -0.1713 0.4567 -0.1031 0.481

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at

4- Ul eukaryotic

(*) translation

225940_ initiation factor at 4E member 3 BE465037 -0 .6522 0 .186 0.0126 0.1681 0.1625 -0.1445 0.0046 -0.0123 -0.0311 0.1452

225954_ -8 .00E- 7.00E- s_at midnolin AL512725 -0 .2783 04 -0.0103 0.3008 04 -0.0768 0.2047 -0.0616 0.2873 transporter 2,

ATP-binding cassette, sub¬

225973_ family B at (MDR/TAP) AA573502 -0 .3496 0. 2589 -0.0471 0.2824 0.2441 -0.217 0.1349 -0.3596 0.0552 -0.2578

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

226003_ kinesin family £ at member 21A AB051495 0.2757 0.0074 0.1353 0.4361 0.0069 -0.0061 0.1104 -0.2944 0.0901 -0.4205 disrupted in 226026_ renal at carcinoma 2 AI147467 -0.3665 -0.0534 0.1635 0.3652 -0.0475 0.0422 -0.1066 0.2844 -0.0726 0.339

Murine retrovirus

226047_ integration site at l homolog N66571 -0.4595 0.0511 0.0194 0.3215 0.0461 -0.041 -0.0699 0.1863 -0.0641 0.2989 slingshot

226080_ homolog 2 at (Drosophila) BE676214 -0.4658 0.0371 0.0162 0.3686 0.0325 -0.0289 -0.0837 0.2233 -0.0724 0.3378

Table 6: Group of 1645 genes that are differentially expressed in healthy donors_* SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set E) Gene Title ID score score score score score 3 score score score score score

Chromobox homolog 5

(HPl alpha 226085_ homolog, at Drosophila) AA181060 0.4775 -0.168 0.0891 0.1329 -0.1552 0.1379 -0.009 0.0241 0.0261 -0.1217 elongation factor, RNA

226099_ polymerase II, at 2 AI924426 -0.3232 0.1742 -0.1574 0.0222 0.1646 -0.1463 0.0399 -0.1065 -0.0044 0.0207

TRAF-

226117_ interacting at protein with a AA195074 -0.4283 0.2729 -0.0467 0.2385 0.2548 -0.2265 0.131 -0.3493 0.0456 -0.2126

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients .(lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score forkhead-

4- associated domain hypothetical

226121_ protein at MGC23280 AI076793 -0.552 0.1492 -0.0456 0.2185 0.1347 -0.1198 -0.0176 0.0469 -0.0424 0.1979

226155_ at KIAA1600 AB046820 -0.4905 0.0645 -0.0015 0.3381 0.0564 -0.0501 -0.0696 0.1856 -0.0657 0.3066

226169_ SET binding AW27657 at factor 2 2 -0.5246 0.1936 -0.0366 0.0629 0.1759 -0.1564 0.0332 -0.0885 -0.012 0.0559

226179_ at FP15737 N63920 -0.4683 0.0557 0.0472 0.2919 0.0499 -0.0444 -0.0609 0.1623 -0.0577 0.2691

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Homo sapiens, clone

-4

226203_ IMAGE:52998 at 88, mRNA AA868896 0.2988 -0.0157 -0.0444 0.2252 -0.0149 0.0132 0.0541 -0.1444 0.0465 -0.2171

226218_ Interleukin 7 at receptor BE217880 0.3437 0.022 0.1687 0.5777 0.0196 -0.0174 0.1498 -0.3995 0.1182 -0.5516 pleckstrin homology domain containing,

226247_ family A at (phosphoinositi AI346026 0.3505 -0.0343 0.1361 0.4031 -0.0309 0.0274 0.0946 -0.2523 0.0815 -0.3802

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score de binding

Ul specific) member 1 226254_ s_at KIAA1430 AI912523 0.2786 0.0228 0.1393 0.4839 0.0206 -0.0183 0.126 -0.336 0.0993 -0.4632

226259_ SEC15-like 1 at (S. cerevisiae) AL137438 -0.6454 0.1566 -0.0815 0.3302 0.136 -0.1209 -0.0438 0.1167 -0.0623 0.2906 jun

226267 dimerization at protein 2 AA716425 -0.3388 0.0239 -0.0177 0.3046 0.0219 -0.0194 -0.0709 0.1891 -0.0616 0.2877

226272_ Full length - at insert cDNA N25986 0.3775 -0.0246 0.1605 0.4804 -0.0222 0.0197 0.1149 -0.3063 0.0977 -0.4559

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score clone ZD79H10 likely ortholog of mouse TORC2- specific protein

226310_ AVO3 (S. at cerevisiae) AI743511 -0.4465 0.2702 -0.1401 0.1226 0.2535 -0.2254 0.097 -0.2586 0.0234 -0.1093 Full-length cDNA clone

226311_ CS0DI014YH2 at 1 of Placenta BF058422 -0.2581 -0.0214 -0.3069 0.6202 -0.0194 0.0173 -0.1535 0.4093 -0.1289 0.6014

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Cot 25- normalized of o Homo sapiens (human) transcription elongation

226388_ factor A (SII), at 3 AI675780 0.287 -0.012 0.0499 0.3137 -0.0112 0.01 0.0767 -0.2045 0.0647 -0.3019 ankyrin repeat and BTB

226442_ (POZ) domain at containing 1 H06267 -0.2152 -0.0275 0.0516 0.2467 -0.0259 0.0231 -0.068 0.1814 -0.051 0.238

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Solute carrier family 39 (zinc

226444_ transporter), - at member 10 A AII770000447766 00..44339977 - -00..00661144 00..00772288 00..33662233 -0.057 0.0506 0.0775 -0.2067 0.0739 -0.345 phosphoinositi de-3 -kinase

226459_ adaptor protein AW57575 at 1 4 - -00..553344 00..22663366 --00..00559955 00..00991188 0.2402 -0.2135 0.0903 -0.2408 0.017 -0.0792 transmembrane

226489_ and coiled-coil at domains 3 BG177562 -0.4622 0.1115 0.0171 0.1656 0.1021 -0.0907 -0.0138 0.0369 -0.0327 0.1526

226497 Fms-related AA149648 -0.2556 0.0385 -0.0365 0.1975 0.0362 -0.0321 -0.0413 0.11 -0.0405 0.1888

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at tyrosine kinase

1 (vascular endothelial growth factor/vascular permeability factor receptor) branched chain

226517_ aminotransfera at se 1 , cytosolic AL390172 -0.1531 -0.1045 -0.046 0.4818 -0.0964 0.0857 -0.1537 0.4098 -0.1 0.4666

226542_ Full-length at cDNA clone AI300571 -0.6162 0.0861 0.0477 0.3634 0.0745 -0.0662 -0.07 0.1866 -0.0696 0.3246

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

CS0DJ002YF0

2 of T cells

(Jurkat cell line) Cot 10- normalized of

Homo sapiens

(human) hypothetical

226548_ protein at LOCI 12868 AI935915 0.3654 0.0143 0.198 0.6078 0.0129 -0.0115 0.1526 -0.4069 0.1254 -0.5851

226576_ Rho GTPase at activating AI768563 -0.561 0.1161 0.0023 0.2699 0.1013 -0.0901 -0.0388 0.1034 -0.0514 0.2396

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients., and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein 26

Prader-

226587_ Willi/Angelma at n region-1 BE783065 0.4144 -0.0909 0.0438 0.2294 -0.0847 0.0753 0.0367 -0.098 0.0464 -0.2165 chromosome 7 226603_ open reading at frame 6 BE966604 -0.6921 0.4861 -0.1438 -0.44 0.4509 -0.4008 0.2373 -0.6328 0.0771 -0.3599

Transforming growth factor, - beta receptor 226625_ III (betaglycan, AWl 9369 at 30OkDa) 0.3586 -0.0484 0.2193 -0.454 -0.0433 0.0385 0.1031 -0.2748 0.0915 -0.4272

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hypothetical

*j 226682 protein AW00618 at LOC283666 5 0.3003 0.0105 0.1816 0.5141 0.0094 -0.0083 0.1302 -0.3471 0.1052 -0.4909 hypothetical

226702_ protein at LOC129607 AI742057 -0.897 0.7298 -0.2344 0.7901 0.6819 -0.6061 0.3956 -1.0549 0.1309 -0.6107

O- acyltransferase

(membrane

226726_ bound) domain at containing 2 W63676 -0.464 0.0504 0.0074 0.3399 0.0446 -0.0396 -0.073 0.1947 -0.0669 0.3122

226733 6- AA587884 -0.3815 -0.0363 -0.0508 0.5413 -0.033 0.0293 -0.1434 0.3823 -0.1115 0.5202

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at phosphofructo-

2- kinase/fructose

-2,6- biphosphatase

2 interferon- induced protein with

226757_ tetratricopeptid at e repeats 2 AA131041 -0.8553 0.6201 -0.2297 0.5456 0.5733 -0.5096 0.299 -0.7974 0.09 -0.42

226771 ATPase, Class AB032963 0.1451 0.01 0.322 0.009 -0.008 0.1245 -0.3319 0.0998 -0.4658

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at I, type 8B, 0.4871 member 2

-4 syntaxin

226794_ binding protein at 5 (tomosyn) AI825998 -0.434 0.1053 -0.0346 0.2026 0.0961 -0.0854 -0.0243 0.0649 -0.0401 0.187

226830_ x at LOC440309 BG339245 -0.303 0.2328 -0.1087 0.2019 0.2246 -0.1996 0.1178 -0.3143 0.0408 -0.1903 regulatory factor X, 2 (influences

226872_ HLA class II at expression) AK024288 -0.3785 -0.073 0.0736 0.5163 -0.0655 0.0582 -0.1505 0.4012 -0.1051 0.4905

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score nuclear g. ubiquitous casein kinase and cyclin- dependent 226880_ kinase at substrate AL035851 0.289 0.013 0.0905 0.4215 0.0118 -0.0105 0.1102 -0.2939 0.0863 -0.4027 leucine rich

226884_ repeat neuronal at 1 N71874 -0.6045 0.1138 0.0624 0.2634 0.1048 -0.0932 -0.0389 0.1038 -0.0525 0.2451

226905_ hypothetical at protein BG036514 -0.0214 -0.2823 0.286 0.4995 -0.2606 0.2316 -0.1979 0.5276 -0.0982 0.4582

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

MGC45871 acid

226925_ phosphatase- AW06972 at Iike 2 9 -0.1771 -0.0735 -0.0406 0.4187 -0.0673 0.0598 -0.1216 0.3243 -0.0862 0.4024

226968_ kinesin family at member IB AK023184 -0.3786 -0.0151 -0.0671 0.4976 -0.0133 0.0118 -0.1289 0.3437 -0.1004 0.4685

Nuclear factor of activated T- cells, cytoplasmic,

226991_ calcineurin- - at dependent 2 AA489681 0.1765 0.073 0.1199 0.4931 0.0688 -0.0612 0.1492 -0.398 0.1037 -0.484

Table 6: Group of 1645 genes that are differentially expressed ήi healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

227030_ Putative 0RB3 at gene, 5' BG231773 0.2648 0.026 0.1564 0.4946 0.0242 -0.0215 0.1312 -0.3498 0.1031 -0.4813

O

227077_ zinc finger at protein 286 BF432238 0.389 -0.0756 0.1452 0.3417 -0.069 0.0614 0.0656 -0.1748 0.0688 -0.3213

227088_ at — BF221547 0.368 0.0355 -0.3024 -0.185 0.0331 -0.0294 0.0572 -0.1524 0.0375 -0.1748

Inhibin, beta A

(activin A, activin AB

227140_ alpha at polypeptide) AI343467 -0.3073 0.0338 -0.2707 0.4891 0.0312 -0.0277 -0.1205 0.3214 -0.1009 0.4709

227198_ Lymphoid AW08550 0.4613 -0.062 -0.0237 - -0.0579 0.0515 0.0568 -0.1516 0.0592 -0.2761

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupps score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at nuclear protein 0.2902 related to AF4 Scm-like with

227210_ four mbt at domains 2 T65020 0.3349 0.0661 0.0629 0.5841 0.0588 -0.0522 0.1621 -0.4324 0.1198 -0.5593 RNA-binding region (RNPl,

227223_ RRM) at containing 2 BE466173 0.4417 -0.1767 -0.1004 0.1098 -0.1658 0.1474 -0.0766 0.2043 -0.0218 0.1019

227232_ at Enah/Vasp-like T58044 0.6305 -0.0958 0.0785 0.4739 -0.0846 0.0752 0.0958 -0.2553 0.0932 -0.435

227233 tetraspanin 2 AU147132 -0.4384 0.0814 -0.1082 0.3417 0.0744 -0.0661 -0.0648 0.1729 -0.0687 0.3206

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at

$ 227236_ at tetraspanin 2 AI743596 -0.4389 0.0461 -0.0858 0.4147 0.0414 -0.0368 -0.0926 0.247 -0.0832 0.3884

Kringle containing

227250_ transmembrane at protein 1 BF221745 -0.4226 -0.0206 0.1548 0.3442 -0.0188 0.0167 -0.0937 0.2498 -0.0693 0.3235

227261_ Kruppel-like at factor 12 AA020010 0.3228 -0.0078 0.1451 0.4535 -0.0071 0.0063 0.1096 -0.2924 0.0924 -0.4314 hypothetical

227270_ protein at LOC285550 BF593037 -0.4865 0.0966 -0.0282 0.2741 0.0863 -0.0767 -0.0457 0.1217 -0.0536 0.25

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

227297'_ Integrin,alpha

5 at 9 AI479176 -0.1731 -0.0353 -0.2904 0.5533 -0.0324 0.0288 -0.1547 0.4125 -0.1151 0.5369 hairy and enhancer of

227347_ split 4 NM_0211 - x_at (Drosophila) 70 -0.4035 0.5114 -0.265 0.6901 0.4892 -0.4349 0.3205 -0.8547 0.1302 -0.6075 chromosome

16 open

227351_ reading frame - at 52 H06491 0.2518 0.0362 0.0167 0.3738 0.0338 -0.0301 0.1069 -0.2852 0.0774 -0.3612

227356_ CDNA: at FLJ22198 fis, BG499974 -0.4624 0.0751 0.0904 0.1924 0.0677 -0.0602 -0.0298 0.0795 -0.0377 0.1762

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score clone

HRC01218 U 227404_ Early growth s_at response 1 AI459194 -0.6076 0.1134 0.1913 0.1436 0.104 -0.0924 -0.0086 0.023 -0.0283 0.1321

CDNA

FLJ40165 fis, 227425_ clone at TESTI2015962 AI984607 -0.2451 -0.0701 0.0527 0.3902 -0.0644 0.0573 -0.115 0.3067 -0.0801 0.3737

227438_ at alpha-Mnase 1 AI760166 -0.5655 0.1598 -0.1074 0.2638 0.1419 -0.1261 -0.0262 0.07 -0.0504 0.2353

227458 — ^: - at CD274 antigen AI608902 -0.5357 0.3102 -0.1261 0.1501 0.2899 -0.2577 0.1182 -0.3151 0.0282 -0.1317

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Leukocyte-

-4 derived Ul

227462_ arginine at aminopeptidase BE889628 0.0158 0.1524 -0.0251 0.3984 0.1449 -0.1288 0.1465 -0.3907 0.0829 -0.3867 hypothetical

227466_ protein at LOC285550 BF108695 -0.4347 0.0276 -0.0034 0.3805 0.0241 -0.0214 -0.0907 0.2419 -0.0748 0.3491

227552_ at septin 1 AI003777 0.2515 0.0563 0.0336 0.4433 0.0513 -0.0456 0.1294 -0.345 0.0911 -0.4252 epithelial

227609_ stromal at interaction 1 AA633203 -0.7528 0.6536 -0.2625 0.7094 0.6179 -0.5492 0.3514 -0.9371 0.1218 -0.5683

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(breast)

$ threonyl-tRNA

227611_ synthetase-like at 2 AA442856 0.3237 -0.0151 0.0419 0.3356 -0.014 0.0124 0.0795 -0.2121 0.0687 -0.3205 hypothetical 227686_ protein at BC008322 BE465433 0.4902 0.0015 0.0529 0.5633 0.0013 -0.0011 0.1452 -0.3873 0.1115 -0.5202 suppressor of

227697_ cytokine at signaling 3 AI244908 -0.7263 0.1898 0.0537 0.1953 0.1683 -0.1496 -0.0015 0.0039 -0.0368 0.1718

221169 _ G protein- 3.00E- at coupled AI703476 -0.6681 0.2089 04 0.1355 0.1869 -0.1661 0.0183 -0.0489 -0.0255 0.119

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score receptor 27

4- -4 Poly (ADP- -4 ribose) polymerase 227807_ family, at member 9 AI738416 -0.5875 0.3388 -0.0887 -0.209 0.3104 -0.2759 0.1424 -0.3798 0.0378 -0.1762

Phosphatidylgl 227851_ ycerophosphate s_at synthase AI084056 -0.2705 -0.0208 -0.0815 0.4143 -0.0191 0.017 -0.1138 0.3035 -0.0854 0.3984 hypothetical 227867_ protein at LOC129293 AA005361 0.4163 -0.0388 0.1116 0.4357 -0.0347 0.0309 0.1023 -0.2729 0.0876 -0.4089

Table 6: Group of 1645 genes that are differentially expressed iii healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Cas-Br-M

-4 (murine)

OO ecotropic retroviral

227900_ transforming at sequence b AV70175< 0.0306 0.0192 0.4235 0.0284 -0.0252 0.1118 -0.2982 0.0875 -0.4083

Homo sapiens, clone

227929_ IMAGE:52779 at 45, mRNA AUl 5134 0.0976 0.0317 0.3006 0.0859 -0.0764 -0.0518 0.1381 -0.058 0.2706

227952_ Hypothetical at protein AI580142 0.6298 -0.1245 -0.1617 0.1656 -0.1145 0.1018 0.0112 -0.0297 0.0327 -0.1527

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

FLJ90036 Homo sapiens, clone

IMAGE:52426

227984_ 23, mRNA, at partial cds BE464483 0.3766 -0.013 0.1102 0.4619 -0.0119 0.0106 0.1125 -0.3001 0.0948 -0.4422 Ras protein- specific guanine nucleotide-

228109_ releasing factor at 2 AI912976 0.4473 -0.1117 0.1364 0.2973 -0.1006 0.0894 0.046 -0.1228 0.0585 -0.2731

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hypothetical

228152_ protein

O s_at FLJ31033 AK023743 -0.9335 0.495 -0.1977 0.1614 0.4412 -0.3922 0.1681 -0.4481 0.0268 -0.1251

228153_ IBR domain at containing 2 AI953847 -0.4229 0.0404 0.0202 0.3115 0.0361 -0.0321 -0.0682 0.1819 -0.0617 0.2881 Golgi autoantigen,

228174_ golgin at subfamily a, 1 AI832363 0.2159 0.0256 0.1687 0.4545 0.0234 -0.0208 0.1188 -0.3167 0.0938 -0.4379 CDNA

228191_ FLJ33420 fis, at clone AA206016 0.3787 -0.0205 0.023 0.3603 -0.0185 0.0164 0.0875 -0.2334 0.0726 -0.3387

Table 6: Group of 1645 genes that are differentially expressed hi healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

BRACE20200

²⁸ ^ Hypothetical

228195_ protein at MGC13057 BE645119 0.6278 -0.1288 -0.1585 0.1549 -0.114 0.1013 0.0067 -0.0179 0.0294 -0.1374

CDNA

FLJ38931 fis, clone

228209_ NT2NE201318 at 9 AI147033 -0.1282 -0.0504 -0.1647 0.4259 -0.0474 0.0421 -0.1307 0.3484 -0.089 0.4154

228230_ peroxisomal - at proliferator- AL121829 -0.709 0.4306 -0.1029 0.3138 0.3963 -0.3523 0.1901 -0.5068 0.0556 -0.2595

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score activated

4-

OO receptor A interacting complex 285

228245_ AW59432 s_at ovostatin 2 0 0.3838 -0.073 -0.0328 0.1719 -0.069 0.0613 0.0256 -0.0683 0.0352 -0.1641 hypothetical

228298_ protein at MGC 16044 BF056901 0.2147 0.0454 0.1417 0.4801 0.0411 -0.0365 0.1338 -0.3567 0.0989 -0.4614

228304_ Transcribed at locus BE674118 -0.0493 0.2375 -0.0574 0.5269 0.2201 -0.1956 0.1913 -0.5102 0.1069 -0.499

228325 KIAA0146 AI363213 -0.4082 -0.0083 0.1253 0.3247 -0.0075 0.0067 -0.0837 0.2231 -0.0654 0.3051

Table 6: Group of 1645 genes that are differentially expressed in. healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at protein

4-

OO Nudix

(nucleoside diphosphate linked moiety

228341_ X)-type motif at 16 AI809108 -0.3056 0.0128 -0.1363 0.414 0.0116 -0.0103 -0.1011 0.2696 -0.0842 0.393

SNRPN

228370_ upstream at reading frame BFl 14870 0.42 -0.0578 0.146 0.4221 -0.0525 0.0467 0.0932 -0.2486 0.0854 -0.3988

228390_ Homo sapiens, at clone AA489100 0.2753 0.0515 0.006 0.4287 0.0483 -0.043 0.1216 -0.3243 0.0893 -0.4167

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

IMAGE:52592 * 72, HiRNA

228408_ SDAl domain s_at containing 1 AI738666 0.2671 0.0297 0.089 0.4419 0.027 -0.024 0.118 -0.3146 0.0907 -0.423

228409_ at KIAA1881 T62068 -0.3711 -0.0237 -0.0011 0.4493 -0.0218 0.0194 -0.1243 0.3314 -0.0924 0.4312 hypothetical

228439_ protein AW08382 at BC012330 0 -0.6302 0.3828 -0.0154 0.3524 0.3567 -0.317 0.1907 -0.5085 0.0656 -0.3059

Nuclear factor

228442 of activated T- - at cells, AI770171 0.3316 0.0132 0.2431 0.6131 0.0117 -0.0104 0.1525 -0.4066 0.1257 -0.5868

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score cytoplasmic,

OO calcineurin- Ul dependent 2 solute carrier family 22

(organic cation

228497_ transporter), at member 15 AI279062 -0.453 0.0659 -0.0066 0.3003 0.0589 -0.0524 -0.0587 0.1564 -0.0592 0.2763

6- phosphofructo-

228499_ 2- at kinase/fructose AL038787 -0.4614 0.0537 -0.0483 0.3819 0.0478 -0.0425 -0.0825 0.2201 -0.0759 0.354

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set BD Gene Title ID score score score score score 3 score score score score score

-2,6- biphosphatase

4 sterile alpha

228531_. motif domain at containing 9 AA741307 -0.6291 0.4843 -0.2175 0.4297 0.454 -0.4035 0.2361 -0.6295 0.0756 -0.3529

Metastasis associated lung adenocarcinom a transcript 1

228582_ (non-coding x at RNA) AI475544 -0.3761 0.2342 0.022 0.2556 0.2234 -0.1986 0.1267 -0.3379 0.0513 -0.2392

Table 6: Group of 1645 genes that are differential^] y expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Weakly similar

S 228585 to zinc finger at protein 195 AI301948 -0.3656 0.0033 -0.0676 0.4354 0.003 -0.0026 -0.1085 0.2893 -0.0883 0.4122 Membrane- spanning 4- domains,

228592_ subfamily A, AW47485 at member 1 2 0.2693 0.0372 -0.0685 0.3124 0.0351 -0.0312 0.0865 -0.2307 0.0648 -0.3024 T-S'- oligoadenylate

228607_ synthetase 2, at 69/7IkDa AI651594 -0.3464 0.4273 -0.2092 0.5788 0.4041 -0.3592 0.2556 -0.6816 0.1095 -0.5109

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

RABI l family

*± interacting

00

228613_ protein 3 (class at II) BF183535 0.4531 -0.0941 0.0406 0.2579 -0.0861 0.0766 0.0409 -0.1091 0.0514 -0.2401

XIAP

228617_ associated at factor-1 AA142842 -0.7218 0.6379 -0.2372 0.7241 0.6019 -0.535 0.35 -0.9334 0.1255 -0.5858 leucine-rich

228648_ alpha-2- at glycoprotein 1 AA622495 -0.4747 0.0962 -0.0246 0.2593 0.0875 -0.0777 -0.041 0.1093 -0.0514 0.2398

228674 echinoderm - s at microtubule AA524507 0.4006 -0.1171 -0.042 0.0628 -0.1104 0.0981 -0.0141 0.0377 0.0127 -0.0592

—

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score associated

OO protein like 4

VO

Serine (or cysteine) proteinase inhibitor, clade

228726_ B (ovalbumin), AW51219 at member 1 6 -0.4535 0.0539 -0.0496 0.3741 0.0474 -0.0422 -0.0807 0.2151 -0.0736 0.3436

228758_ Hypothetical AW26403 at LOC389185 6 -0.5864 0.0549 -0.0167 0.478 0.0478 -0.0425 -0.1076 0.2869 -0.0937 0.4375

228818_ Tumor protein at D52 BFl 10792 0.5007 -0.0231 -0.0113 0.4468 -0.0209 0.0185 0.1076 -0.287 0.0901 -0.4206

Tab] Ie 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Homo sapiens, clone

O

228828_ IMAGE:52159 at 17, mRNA AI761658 0.3745 0.025 0.0148 0.4693 0.0221 -0.0197 0.1278 -0.3409 0.0946 -0.4417

228855_ at — AI927964 0.1797 0.0555 0.1302 0.4596 0.0512 -0.0455 0.1317 -0.3512 0.0954 -0.4453

228866_ Ankyrin repeat at domain 11 BF514864 0.3418 -0.2407 -0.0478 0.3333 -0.2306 0.205 -0.1531 0.4084 -0.0676 0.3153 dachshund

228915_ homolog 1 at (Drosophila) AI650353 -0.4688 0.0073 0.069 0.4002 0.0066 -0.0058 -0.1022 0.2726 -0.0801 0.374

229007_ hypothetical N50864 0.3013 -0.0317 0.1449 - -0.0299 0.0266 0.0883 -0.2354 0.0765 -0.357

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at protein 0.3676 LOC283788 Transcribed locus, weakly similar to XP_499236.1 LOC442377

229029_. [Homo at sapiens] AI745230 0.411 0.0181 -0.0011 0.4734 0.0161 -0.0143 0.1293 -0.3448 0.0956 -0.4464 chromosome 6

229070_ open reading at frame 105 AA470369 0.1552 0.0324 0.2859 0.5228 0.0296 -0.0263 0.1424 -0.3797 0.1083 -0.5052

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (tapus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Homo sapiens, clone

229072_ IMAGE:52592 at 72, mRNA BF968097 0.3524 0.0342 0.0502 -0.505 0.0315 -0.028 0.1332 -0.3551 0.1046 -0.4883

Hypothetical 229101_ protein at LOC150166 AI963142 -0.6171 0.0599 0.0969 0.387 0.0509 -0.0453 -0.0836 0.223 -0.0735 0.3428

CDNA

FLJ44441 fis, clone

229121_ UTERU20202 - at 42 BE857553 0.4209 -0.0946 0.2474 0.4226 -0.086 0.0764 0.082 -0.2187 0.0851 -0.3973

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

229141 WD repeat AW27537

£ at domain 33 9 0.4056 -0.0656 0.11 0.3518 -0.059 0.0524 0.0722 -0.1925 0.0702 -0.3277 polycomb

229194_ group ring at finger 5 AL045882 -0.2369 0.3825 -0.2541 0.5297 0.36 -0.32 0.2328 -0.6209 0.1007 -0.4701

229202_ Pecanex-like 2 at (Drosophila) AI768826 0.247 0.0432 0.177 0.5417 0.039 -0.0347 0.144 -0.384 0.1119 -0.522 cAMP responsive element

229228_ binding protein at 5 AI819043 -0.6048 0.1753 -0.0517 0.2096 0.1574 -0.1399 -0.0087 0.0231 -0.0402 0.1874

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Karyopherin alpha 5

229317_ (importin alpha at 6) BG231980 0.3189 -0.0097 0.0493 0.3522 -0.0089 0.0079 0.0862 -0.2298 0.0717 -0.3344 nuclear ubiquitous casein kinase and cyclin- dependent

229353_ kinase AW51544 s_at substrate 3 0.4543 -0.052 -0.0067 -0.326 -0.0479 0.0426 0.0694 -0.185 0.066 -0.3081

229373 Transcribed AW13971 -0.3201 0.011 -0.0923 0.3915 0.01 -0.0089 -0.095 0.2533 -0.0796 0.3715

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients-

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at locus 9 hypothetical

229382_ protein AW14927 at LOC284465 0 - -00..66777744 00..00660011 0.1972 0.3523 0.0535 -0.0476 -0.0779 0.2078 -0.0689 0.3213

Staufen, RNA binding protein,

229417_ homolog 2 at (Drosophila) W46994 -0.495 0.1167 0.0119 0.1906 0.1067 -0.0948 -0.0236 0.063 -0.0376 0.1754 interferon-

229450_ induced protein at with AI075407 -0.9219 0.6475 -0.1471 0.6289 0.5898 -0.5243 0.3334 -0.889 0.1027 -0.4792

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score tetratricopeptid

4- e repeats 3 similar to

229452_ RIKEN cDNA at 2600017H02 AL544576 -0.5196 0.0246 0.1571 0.3218 0.0222 -0.0197 -0.0783 0.2089 -0.0638 0.2977

CDNA

FLJ37917 fis, clone

229460_ CTONGl 0001 at 37 A AII992277660055 --00..559988 00..11552244 -0.0518 0.2637 0.1356 -0.1205 -0.028 0.0746 -0.0506 0.236

229521_ hypothetical at protein BE466274 -0.6999 0.2639 0.0597 0.0354 0.2358 -0.2096 0.0759 -0.2025 0.0065 -0.0304

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

FLJ36031

Unc-84

-4

229548_ homolog B (C. at elegans) BG231709 -0.5835 0.1634 -0.0846 0.2508 0.1473 -0.131 -0.0228 0.0607 -0.0485 0.2265

229584_ leucine-rich at repeat kinase 2 AK026776 -0.6031 0.2066 0.0889 0.0112 0.184 -0.1636 0.0561 -0.1496 0.0021 -0.0097

Guanylate

229625_ binding protein at 5 BG545653 -0.3745 0.3586 -0.0813 0.4895 0.3382 -0.3007 0.2168 -0.5782 0.0945 -0.4412

229629_ Transcribed at locus AI923633 0.2222 0.0393 0.1495 0.4792 0.0357 -0.0318 0.1303 -0.3475 0.0989 -0.4613

229694_ WD repeat BF062828 0.4205 -0.1803 0.0639 -0.017 -0.1695 0.1507 -0.042 0.112 0.0034 -0.0157

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at domain 11

VO hypothetical 229770_ protein at FLJ31978 AI041543 -0.5144 0.0408 0.0821 0.3456 0.0363 -0.0322 -0.0775 0.2068 -0.0681 0.3177

Hypothetical 229778_ protein at MGC10946 BE326710 0.4602 -0.104 -0.0254 0.1755 -0.0978 0.087 0.0185 -0.0494 0.0356 -0.1661

COBW domain containing 1 ///

COBW domain

229804_ containing 2 /// AWl 6933 x_at dopamine 3 -0.3897 0.3065 -0.0883 0.3282 0.2898 -0.2576 0.1694 -0.4518 0.0634 -0.296

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score responsive g protein

229817_ zinc finger at protein 608 AI452715 -0.4602 0.0129 -0.1656 0.6023 0.0114 -0.0102 -0.1519 0.405 -0.1225 0.5717 hypothetical

229873_ protein at LOC283219 AI391633 -0.6988 0.1103 0.1234 0.3117 0.0971 -0.0863 -0.0539 0.1437 -0.0598 0.2791

229881_ Kruppel-like at factor 12 R41200 0.5632 -0.0966 0.0582 0.3825 -0.0884 0.0786 0.0747 -0.1991 0.0769 -0.3586

229899_ similar to RPE- s_at spondin AI625235 -0.3491 -0.0774 0.1326 0.4408 -0.0703 0.0625 -0.1295 0.3454 -0.0896 0.418

229934 — Transcribed N39230 -0.4777 0.0055 0.035 0.447 0.0049 -0.0043 -0.1127 0.3006 -0.0893 0.4166

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at locus g chromosome 7

O

230036_ open reading at frame 6 BE669858 -0.6582 0.4969 -0.2067 0.4436 0.4672 -0.4153 0.2407 -0.6419 0.0786 -0.3667

230048_ Transcribed at locus BF061555 -0.4961 0.1562 0.1409 0.0378 0.1432 -0.1273 0.0497 -0.1326 0.0074 -0.0344

230141_ at — AI640594 -0.5631 0.2147 0.044 0.0309 0.196 -0.1742 0.0684 -0.1824 0.0059 -0.0274

230170_ at oncostatin M AI079327 -0.6043 0.1585 0.0752 0.1315 0.1446 -0.1286 0.0078 -0.0208 -0.0256 0.1194

230245_ hypothetical - s — at p ^rrotein AI926479 0.3673 -0.0415 -0.099 0.1751 -0.0391 0.0347 0.0343 -0.0915 0.0358 -0.1672

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ED Gene Title ID score score score score score 3 score score score score score

LOC283663

O u pro lem- h-i

230252_ coupled AWl 8308 - at receptor 92 0 0. .3502 -0.0468 0.0528 0. 2893 -0.0435 0.0386 0.06 -0.1601 0.059 -0.2755

ST8 alpha-N- acetyl- neuraminide alpha-2,8-

230261_ sialyltransferas - at e 4 AA552969 -0 .5774 0.2574 -0.0087 0. 0791 0.234 -0.208 0.0855 -0.2281 0.0147 -0.0687

230314_ Similar to AW01455 - at hypothetical 7 -0 .1722 0.4046 -0.28 0. 6308 0.3759 -0.3341 0.2582 -0.6884 0.1197 -0.5584

Table 6: Group of 1645 genes that are differential y expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein 628

Ul

O NFAT KJ activating

230322_ protein with at ITAM motif 1 AI492017 -0.4428 0.0336 0.1012 0.2722 0.0302 -0.0269 -0.061 0.1627 -0.054 0.2518

230323_ transmembrane AW24283 s_at protein 45B 6 -0.4232 0.108 0.1689 0.0119 0.1007 -0.0895 0.0334 -0.089 0.0024 -0.0111

230332_ at PRO1550 AA872187 0.4721 -0.242 -0.1074 0.2591 -0.2244 0.1994 -0.1331 0.355 -0.0503 0.2347

230354_ Transcribed at locus BG236273 -0.3735 -0.1584 0.0693 0.743 -0.1426 0.1268 -0.2227 0.5939 -0.1541 0.7192

230416 Solute carrier AI709335 -0.3036 0.0351 -0.1223 0.339 0.0322 -0.0286 -0.0776 0.207 -0.069 0.3218

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at family 18

O (vesicular monoamine), member 2 endothelial differentiation, sphingolipid

G-protein-

230464_ coupled at receptor, 8 AI814092 0.511 -0.0961 0.2597 0.5236 -0.0862 0.0766 0.1041 -0.2776 0.1051 -0.4906

230480_ piwi-like 4 at (Drosophila) AI808955 -0.3971 0.0871 -0.1269 0.3019 0.0804 -0.0715 -0.0564 0.1504 -0.061 0.2847

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

230494

'M at — AI671885 0.2461 -0.018 0.0928 0.2967 -0.0171 0.0152 0.0715 -0.1906 0.0619 -0.2891

Similar to

Chloride intracellular channel protein

4 (Intracellular chloride ion

230543_ channel protein at p64Hl) AI761675 -0.424 0.0402 0.0389 0.2951 0.0376 -0.0334 -0.068 0.1814 -0.0604 0.282

230559_ FYVE, x at RhoGEF and AI277617 -0.3998 0.078 -0.1437 0.3449 0.0713 -0.0634 -0.07 0.1866 -0.0695 0.3242

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

PH domain

O containing 4 Ul

RasGEF

230563_ domain family, at member IA BF446578 -0.4298 0.0795 -0.1334 0.3623 0.0717 -0.0637 -0.0708 0.1888 -0.0723 0.3376

Slingshot

230590_ homolog 2 at (Drosophila) BE675486 0.1145 -0.1983 -0.1249 0.5303 -0.1851 0.1646 -0.1942 0.5179 -0.1094 0.5105

230653_ Transcribed at locus AI469960 0.4582 -0.1175 0.064 0.2236 -0.107 0.0951 0.0281 -0.0751 0.0441 -0.2058

230656_ cirrhosis, 5.00E- s at autosomal AL578336 0.2852 0.0609 04 0.4587 0.0567 -0.0504 0.1325 -0.3533 0.0953 -0.4447

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score recessive IA g (cirhin)

230690_ at tubulin, beta 1 N63244 0.568 -0.107 -0.1412 0.1678 -0.097 0.0862 0.0156 -0.0416 0.0328 -0.1532

Zinc finger

230760_ protein, Y- at linked BF592062 0.4676 -0.2896 0.0839 0.2066 -0.2794 0.2483 -0.1401 0.3735 -0.0411 0.1919

Rho GTPase

230803_ activating s_at protein 24 AI761947 -0.1816 -0.1461 0.0482 0.5315 -0.1352 0.1202 -0.174 0.464 -0.1102 0.5144

230833_ acrosin binding - at protein AI141116 0.6958 -0.071 -0.3406 0.2044 -0.0638 0.0568 0.0351 -0.0937 0.0398 -0.1857

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, arid WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

230860 Transcribed AW66574

Ui

O at locus 8 -0.5259 0.1886 -0.0841 0.1236 0.1725 -0.1533 0.0167 -0.0446 -0.0239 0.1113 -4

230866_ at BE549540 -0.3927 0.3358 0.0458 0.5323 0.3094 -0.275 0.2194 -0.585 0.1024 -0.4776

Slingshot

230970_ homolog 2 at (Drosophila) AA975530 0.1612 -0.2137 -0.0876 0.4871 -0.2028 0.1803 -0.1834 0.4891 -0.1006 0.4696 CCR4-NOT transcription

231005_ complex, at subunit 1 T91195 0.3926 -0.2324 0.0856 0.1301 -0.2213 0.1967 -0.0916 0.2442 -0.0258 0.1204

231093 Fc receptor- BF514552 0.2576 0.0552 0.1007 - 0.0502 -0.0446 0.1401 -0.3736 0.1057 -0.4931

₈₅₀

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at like protein 3 0.5113

repeat, RNA

231109_ binding protein at 2 R44974 0. 2501 -0.1745 -0 .1234 0 .325 -0.1662 0.1478 -0.1371 0.3656 -0.0667 0.3111

231124_ Lymphocyte - x_at antigen 9 AI524095 0. 3533 -0.0077 0. 2415 0. 5784 -0.007 0.0062 0.138 -0.3681 0.1191 -0.5557

Wiskott-

Aldrich syndrome

231182_ protein - at interacting BF446719 -0 .5517 0.1903 0. 1343 0. 0646 0.1709 -0.1519 0.0673 -0.1794 0.0122 -0.0569

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score protein

O natural killer- tumor

231235_ recognition at sequence AA732581 0.4841 -0.1065 -0.2103 0.0154 -0.0986 0.0876 -0.0242 0.0645 0.0031 -0.0143 similar to mouse

231292_ 1700027M21R at ik gene AI964053 0.3759 -0.1145 0.2553 0.3303 -0.1062 0.0944 0.0515 -0.1374 0.0668 -0.3118

231455_ FLJ42418 at protein AA768888 -0.3217 0.4111 -0.123 0.6442 0.3915 -0.348 0.2866 -0.7641 0.1268 -0.5917

231470 BE138486 -0.2843 0.0138 -0.0383 0.2948 0.0131 -0.0117 -0.0749 0.1996 -0.0612 0.2856

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at « 231472 F-box protein

O at 15 BE464323 0.2452 0.0271 0.0368 0.3619 0.0252 -0.0224 0.1024 -0.2729 0.0748 -0.3491 chromosome 11 open

231530_ reading frame s at 1 BG150085 0.2241 0.0744 0.1233 0.5496 0.0669 -0.0594 0.1571 -0.4189 0.1134 -0.5294 guanylate binding protein 1, interferon-

231577_ inducible, AW01459 s at 67kDa 3 -0.4544 0.4695 -0.1317 0.6539 0.4412 -0.3921 0.2897 -0.7725 0.1224 -0.5712

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

X (inactive)-

« 231592_ specific at transcript AV646335 -0.4446 0.2666 -0.007 0.2432 0.2528 -0.2247 0.1566 -0.4175 0.0478 -0.2232

231597_ x_at AI371550 0.8218 -0.3195 -0.2971 0.2858 -0.2882 0.2561 -0.1617 0.4311 -0.0532 0.2484 231662_ at Argmase, liver AV652232 -0.3335 0.0019 -0.1199 0.4563 0.0017 -0.0015 -0.1193 0.3182 -0.0946 0.4414

231688_ Transcribed AW33783 at locus 3 -0.6812 0.0631 -0.409 0.9321 0.0521 -0.0463 -0.2155 0.5748 -0.1846 0.8614 cysteinyl

231747_ leukotriene NM_0066 at receptor 1 39 -0.3836 0.3556 -0.0111 0.5397 0.3293 -0.2927 0.2236 -0.5962 0.1032 -0.4817

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set E) Gene Title ID score score score score score 3 score score score score score

231769 at F-box protein 6 AF129536 -0.6374 0.3262 -0.0108 0.1984 0.3015 -0.268 0.1347 -0.3591 0.037 -0.1727 calcium/cahno dulin- dependent protein kinase

231793_ (CaM kinase) s_at IIdelta AA448956 0.3007 0.0203 0.0389 0.4034 0.0188 -0.0167 0.1055 -0.2814 0.0831 -0.388

231798_ at Noggin AL575177 0.6751 -0.1697 0.1076 0.3513 -0.1534 0.1363 0.0459 -0.1223 0.0686 -0.3203

231840_ x at AK000803 0.1806 0.1244 -0.0402 0.4804 0.1155 -0.1027 0.1544 -0.4116 0.0996 -0.4648

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

231886 Hypothetical

<2 at LOC388572 AL137655 -0.0518 -0.168 0.005 0.4969 -0.1574 0.1399 -0.1717 0.4579 -0.1032 0.4815

MRNA; cDNA

DKFZp586O0

clone

231929_ DKFZp586O0 at 724) AI458439 0.256 0.1023 0.0796 0.6149 0.0936 -0.0832 0.1787 -0.4765 0.1284 -0.5992

231956_ at KIAA1618 AA976354 -0.3284 0.2996 -0.2743 0.1942 0.2864 -0.2546 0.1233 -0.3288 0.0377 -0.1757

232014_ zinc ringer at protein 30 AI700188 0.4464 -0.1106 0.1323 0.2954 -0.1014 0.0902 0.0449 -0.1199 0.0591 -0.2756

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(KOX 28) hypothetical

232034_ protein at LOC203274 AL117607 -0.5864 0.1873 -0.0403 0.1474 0.1693 -0.1505 0.0102 -0.0272 -0.0282 0.1316

232058_ Actinin, alpha at 4 AU158358 0.4098 -0.2804 -0.098 0.4172 -0.2626 0.2334 -0.1828 0.4875 -0.0823 0.3839 phenylalanine- tRNA

232063_ synthetase-like, AW02461 x_at beta subunit 7 0.4525 -0.1299 0.157 0.2741 -0.1216 0.1081 0.0366 -0.0976 0.0555 -0.2589 232068_ toll-like s at receptor 4 AF177765 -0.7321 0.3226 -0.0277 0.0745 0.2925 -0.26 0.101 -0.2694 0.0136 -0.0635

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Chromosome 2

^« 232071 open reading

Ul at frame 3 BF670827 0.3947 -0.0356 -0.2257 0.0971 -0.0335 0.0298 0.0161 -0.043 0.0198 -0.0922 EST from

232081_. clone 208499, at full insert AL355688 -0.6311 0.194 -0.0211 0.1574 0.1786 -0.1588 0.01 -0.0265 -0.0307 0.1432 neutral sphingomyelin ase (N-SMase) activation

232149_. associated s at factor BF056507 -0.3975 0.1923 -0.1412 0.0354 0.1792 -0.1593 0.0395 -0.1054 -0.0069 0.0323

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

TNFAIP3 2 232160_ interacting s_at protein 2 AL137262 -0.5019 0.0855 0.1107 0.1861 0.0783 -0.0696 -0.027 0.072 -0.0369 0.1723

Pellino

232213_ homolog 1 at (Drosophila) AU147506 -0.4998 0.1507 -0.0144 0.1304 0.1374 -0.1221 0.0052 -0.014 -0.0254 0.1183 chromosome

18 open 232222_ reading frame - at 49 AK000229 -0.6397 0.506 -0.1619 0.5302 0.4737 -0.4211 0.2848 -0.7594 0.0942 -0.4395

232264_ E3 identified at by differential AK022204 0.4108 -0.2172 -0.205 0.3507 -0.2016 0.1792 -0.1538 0.4101 -0.0695 0.3244

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score display

CΛ Lymphoid

232286_ nuclear protein at related to AF4 AA572675 0.4844 -0.1428 -0.1066 0.0189 -0.1322 0.1175 -0.0325 0.0866 0.0037 -0.0174

232303_ zinc finger at protein 608 AB033107 -0.141 -0.0666 -0.1831 0.5002 -0.0619 0.0551 -0.1467 0.3913 -0.1045 0.4876

232315_ Zinc finger- at like AU149712 0.2541 0.0125 0.0086 0.3052 0.0118 -0.0105 0.0827 -0.2204 0.0631 -0.2947

START

232322_ domain x_at containing 10 D60944 -0.4323 0.0856 0.0609 0.1614 0.0798 -0.071 -0.0199 0.053 -0.0326 0.152

232375_ Signal AI539443 -0.4576 0.3182 -0.0668 - 0.2974 -0.2643 0.1621 -0.4322 0.0585 -0.2728

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at transducer and 0.3097 activator of

QO transcription 1,

9IkDa solute carrier family 5

(sodium/glucos e

232378_ cotransporter), at member 9 AI767388 -0.4688 0.0431 -0.1999 0.5639 0.0387 -0.0344 -0.1363 0.3635 -0.1147 0.5354

232392_ Splicing factor, at arginine/serine- BE927772 0.3158 0.0328 -0.1277 -0.292 0.0307 -0.0273 0.0873 -0.2328 0.06 -0.2798

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score rich 3 hypothetical

S 232489_ protein at FLJl 0287 AKOOl 149 0.5911 -0.1489 -0.0922 0.1272 -0.137 0.1218 -0.0056 0.0149 0.025 -0.1166

232563_ zinc finger AW27501 at protein 684 6 -0.5066 0.315 -0.1719 0.1491 0.3022 -0.2687 0.1265 -0.3372 0.0291 -0.1358

232599_ SEC15-like 1 at (S. cerevisiae) AF220217 -0.1872 -0.0329 -0.1786 0.4539 -0.0306 0.0272 -0.1316 0.351 -0.0945 0.4411 chromosome Y

232618_ open reading at frame 15A AF332224 0.5126 -0.3144 0.1254 0.1861 -0.3012 0.2677 -0.1318 0.3515 -0.0363 0.1695

232629 prokineticin 2 AF182069 -0.7021 0.1909 0.0688 0.1529 0.1711 -0.1521 0.0097 -0.0259 -0.0291 0.1356

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at

2'-5'- oligoadenylate

232666_ synthetase 3, at 10OkDa R13458 -0.4149 0.3893 -0.129 0.4835 0.3694 -0.3284 0.2249 -0.5997 0.0925 -0.4316

Homo sapiens, clone

232726_ IMAGE:51942 at 04, mRNA AK024956 0.2462 -0.2241 -0.0989 0.4375 -0.2099 0.1866 -0.1701 0.4535 -0.0885 0.4128

Spi-B

232739_ transcription at factor (Spi- AK025419 0.4207 -0.1176 -0.0122 -0.111 -0.1116 0.0992 -0.0017 0.0045 0.0226 -0.1054

Table 6: Group of 1645 genes that are differentially expressed in healthy donors j, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

1/PU.l related)

'Jl κ> cnromosome o

232777_ open reading s_at frame 118 AI206615 -0.353 0.049 -0.0066 0.2419 0.0458 -0.0407 -0.0516 0.1375 -0.0494 0.2306 peroxisomal proliferator- activated receptor A

232787_ interacting at complex 285 AK023724 -0.2015 0.2442 -0.0231 -0.42 0.2302 -0.2046 0.1684 -0.449 0.0845 -0.3943

232876_ CDNA: at FLJ21881 fis, AK025534 -0.3844 -0.019 -0.1469 0.5906 -0.0166 0.0148 -0.1554 0.4143 -0.1201 0.5603

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score clone 3 HEP02746 κ>

232914_ synaptotagmin- s_at like 2 AB046817 0.3536 -0.0199 0.0637 0.3749 -0.0179 0.0159 0.0904 -0.2411 0.0756 -0.3529

233072_ at netrin G2 AI348745 -0.7776 0.3097 -0.1671 0.1414 0.2743 -0.2438 0.0426 -0.1135 -0.0255 0.1189 thioesterase

233126_ domain s_at containing 1 AK001844 -0.3098 -0.0387 -0.3603 0.7715 -0.034 0.0303 -0.2137 0.5698 -0.1596 0.7447

Neural

233223_ precursor cell at expressed, AK000850 0.0228 -0.1431 -0.1059 0.4601 -0.1335 0.1187 -0.1598 0.4261 -0.0953 0.4447

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score developmentall y down- regulated 9 phosphatase and tensin homolog (mutated in multiple

233254_ advanced x_at cancers 1) AU144828 -0.3346 0.0383 -0.1143 0.355 0.035 -0.0311 -0.0824 0.2198 -0.0721 0.3364 233302_ B-cell at CLL/lymphom AU146285 0.6462 -0.1745 0.0308 0.2343 -0.156 0.1387 0.0154 -0.0411 0.0448 -0.209

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score a HB (zinc

K> finger protein) zinc finger,

233425_ CCHC domain at containing 2 AU147903 -0.6659 0.5438 -0.2601 -0.509 0.5203 -0.4625 0.3058 -0.8155 0.0917 -0.4277 signal-induced proliferation-

233587_ associated 1 s_at like 2 A AKK002222885522 --00..55009977 00..116677 -0.1152 0.1943 0.153 -0.136 -0.0068 0.0181 -0.038 0.1773

CDNA:

233591_ FLJ23098 fis, at clone AK026751 -0.4012 0.3244 -0.1839 0.2718 0.3106 -0.2761 0.1526 -0.4071 0.0527 -0.2461

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

LNG07440

^ 233819 zinc finger

'Jl s at protein 294 AK023499 0.4875 -0.144 -0.1545 0.0274 -0.1358 0.1207 -0.0451 0.1202 -0.0055 0.0256 Rho GTPase

233849_ activating s at protein 5 AK023014 0.1743 0.0611 0.0545 0.3961 0.0572 -0.0509 0.1144 -0.3052 0.0824 -0.3847 chromosome 17 open

233880_ reading frame at 27 AL161961 -0.4405 0.3304 -0.1022 0.3258 0.3095 -0.2751 0.166 -0.4426 0.0612 -0.2857

233955_ x at CXXC finger 5 AK001782 0.3946 -0.0705 0.0376 0.2574 -0.0652 0.058 0.0502 -0.134 0.052 -0.2428

Table 6: Group of 1645 genes that are differentially expressed in healthy donors^ SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Mitogen-

Ul K> activated protein kinase kinase kinase 7

233957_ interacting at protein 2 ALl 17426 0.36 -0.0185 -0.0338 0.2913 -0.0171 0.0152 0.0688 -0.1835 0.0593 -0.2767 butyrate-

234000_ induced s_at transcript 1 AJ271091 0.3455 -0.028 0.1093 0.3889 -0.0257 0.0228 0.089 -0.2372 0.0794 -0.3706

234032_ at PRO1550 AF119847 0.4554 -0.2139 -0.1124 0.2065 -0.1995 0.1773 -0.1142 0.3046 -0.0405 0.1892

234151 CUG triplet AK024629 0.3808 -0.1729 -0.0973 0.1599 -0.1659 0.1474 -0.0853 0.2276 -0.0326 0.1522

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

3 4 5 8 9 10 11 12 13

Representa Healthy tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score at repeat, RNA

Ui κ> binding protein

2

CDNA:

FLJ22748 fis,

234186_ clone at KAIA0249 AK026401 0.4368 -0.065 0.009 0.2882 -0.0596 0.053 0.0568 -0.1514 0.0579 -0.2702 glioma tumor suppressor

234339_ candidate s_at region gene 2 AF296124 0.44 -0.0662 0.0169 0.2961 -0.06 0.0533 0.0591 -0.1575 0.059 -0.2754

234344 RAP2C, AF093744 -0.3355 0.2402 -0.0706 0.228 -0.2027 0.1181 -0.315 0.0444 -0.2072

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at member of 0.2247

RAS oncogene family

TCRAVNl mRNA for T- cell receptor

234396_ alpha-chain V at region AE000660 0.216 0.0687 0.0114 0.4182 0.0637 -0.0566 0.1235 -0.3292 0.0866 -0.4041

Chemokine-

234562_ like factor -5.00E- x_at super family 8 AKOOOl 15 0.4115 -0.0697 -0.2526 0.0025 -0.0657 0.0584 -0.019 0.0506 04 0.0023

234644 CDNA: AK026079 -0.3992 0.0946 0.0034 0.1584 0.0879 -0.0781 -0.0159 0.0424 -0.0318 0.1484

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients,, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x at FLJ22426 fis, clone

VO

HRC08780

CDNA:

FLJ23566 fis,

234675_ clone x at LNG10880 AK027219 0.3946 -0.0367 -0.261 0.0601 -0.0336 0.0299 0.0065 -0.0172 0.0119 -0.0556

CDNA:

FLJ21228 fis,

234723_ clone x_at COL00739 AK024881 0.4848 -0.1077 -0.3361 0.108 -0.0972 0.0864 -0.0574 0.153 -0.021 0.0979

234744 KRMPl AB033338 0.2691 -0.0198 -0.2903 0.0532 -0.0186 0.0165 -0.0194 0.0517 -0.0108 0.0505

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score x at mRNA for mitotic

O kinesin-related protein, partial cds, alternative exon sequence. Ig lambda chain V-region (VL-AIG) /// Immunoglobuli

234764_ n lambda x at variable 3-21 U96394 0.1067 0.1522 -0.3201 0.2082 0.1458 -0.1296 0.0935 -0.2493 0.0427 -0.1994

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

T-cell antigen

Ul receptor beta chain /// T cell receptor V beta6-D-J /// T

234883_ cell receptor V- x_at beta 6 M97943 0.1182 0.0571 0.2757 0.5404 0.0517 -0.046 0.1492 -0.3977 0.1116 -0.521 chromosome 6

234897_ open reading s_at frame 21 AF129756 0.4228 - -00. .00777744 - -00. .11442222 0 0. .00995511 - -00..00772266 0 0. .00664466 0.0044 -0.0116 0.0192 -0.0897

234970_ membrane -1 .00E- - 1 .00E- at targeting AI741469 0.3294 04 0. 0584 0 .3975 04 0.0992 -0.2646 0.0817 -0.3815

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(tandem) C2 domain

Is) containing 1 chromosome

13 open

234993_ reading frame at 6 B BEE330011770022 --00..44119944 0.2021 0.032 0.1348 0.1908 -0.1696 0.093 -0.248 0.0268 -0.125

Mitogen- activated

235011_ protein kinase at kinase kinase 2 BG504375 -0.3623 0.1421 -0.046 0.0409 0.1344 -0.1195 0.0274 -0.0732 -0.0083 0.0385

235020 TAF4b RNA AI366784 0.1809 0.1384 -0.1293 0.129 -0.1147 0.154 -0.4106 0.089 -0.4154

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at polymerase II, 0.4322 TATA box binding protein (TBP)- associated factor, 105kDa CDNA FLJ42313 fϊs, clone

235028_ TRACH20194 at 25 BG288330 0.0824 -0.1253 -0.1756 0.4179 -0.116 0.1031 -0.1406 0.3749 -0.0859 0.4007

235046 Transcribed AA456099 0.1969 0.0612 0.2308 0.0556 -0.0494 0.1591 -0.4243 0.1226 -0.5721

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at locus 0.5896

% 235048_ KIAA0888 at protein AV720650 0.3019 0.0066 0.1447 -0.47 0.0061 -0.0054 0.1267 -0.3377 0.0976 -0.4555 protein phosphatase IK (PP2C

235061_ domain at containing) AV706522 0.004 0.2868 -0.2737 0.5053 0.2709 -0.2408 0.2049 -0.5465 0.1017 -0.4745 mastermind-

235106_ like 2 AW84731 - at (Drosophila) 8 -0.2526 0.2698 0 .0494 0 .5052 0.2497 -0.222 0.2089 -0.557 0.1003 -0.4683

235145 Zinc finger BE778059 -0.4454 0.0427 0 .1249 0 .2277 0.0389 -0.0346 -0.0481 0.1284 -0.0454 0.2118

Attorney Docket No. 037377-57021-PCT Express Mail Label No. ER 293 835 748 US

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at protein 67 homolog

(mouse)

Poly (ADP- ribose) polymerase

235157_ family, AW29773 at member 14 1 -0.3446 0.316 -0.1326 0.3576 0.3032 -0.2695 0.1742 -0.4645 0.0706 -0.3293 guanylate

235175_ binding protein at 4 BG260886 -0.2852 0.2694 -0.0869 0.3391 0.256 -0.2275 0.1528 -0.4074 0.0671 -0.3133

235213 CDNA clone AA348410 0.3476 -0.0891 -0.0353 -0.0846 0.0752 -1.00E- 1.00E- 0.0182 -0.0848

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at IMAGE:62017 0.0889 04 04

73 establishment of cohesion 1

235216_ homolog 1 (S. at cerevisiae) BG532121 0.1902 -0.0389 -0.2301 0.1282 -0.0371 0.033 -0.0438 0.1167 -0.0264 0.1234

CDNA clone

235227_ IMAGE.-52871 at 21, partial cds AI025829 -0.3675 0.0577 -0.1181 0.341 0.0527 -0.0468 -0.0751 0.2004 -0.0689 0.3216 galactose

235256_ mutarotase s at (aldose 1- BE788984 -0.3738 0.3642 -0.1209 0.4672 0.344 -0.3057 0.2092 -0.558 0.0895 -0.4176

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score). RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score epimerase)

235276

-^j at — AA781795 -0.8187 0.7067 -0.2885 0.7577 0.6701 -0.5956 0.3887 -1.0366 0.1284 -0.5992 polycomb

235331_ group ring x_at finger 5 AI341142 -0.345 0.3786 -0.206 0.4533 0.363 -0.3226 0.2235 -0.5961 0.0879 -0.41

EST from

235427_ clone 223524, at 5 'end AA418074 -0.5788 0.1172 0.0144 0.274 0.102 -0.0907 -0.0396 0.1056 -0.052 0.2426 hypothetical

235514_ protein at FLJ25084 AI739528 -0.492 0.1963 -0.0957 0.0789 0.1795 -0.1595 0.0295 -0.0787 -0.0151 0.0705

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score solute carrier family 8

(sodium/calciu 235518_ m exchanger), at member 1 AI741439 -0.4779 0.0457 -0.0247 0.3976 0.0406 -0.0361 -0.089 0.2372 -0.079 0.3685

235549_ IBR domain at containing 2 AL575512 -0.3723 0.0199 0.0816 0.2545 0.0186 -0.0166 -0.0617 0.1644 -0.0521 0.2434

CDNA

FLJ31407 fis, clone

235567_ NT2NE200013 - at 7 AA034012 0.416 -0.0334 0.004 0.3461 -0.0311 0.0276 0.0817 -0.218 0.0709 -0.3309

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hypothetical 235568_ protein

Ui at LOC199675 BF433657 -0.5489 -0.0318 -0.0834 0.7344 -0.0272 0.0242 -0.1906 0.5084 -0.1481 0.6911 guanylate

235574_ binding protein AW39295 at 4 2 -0.1996 0.2862 -0.105 0.4551 0.2719 -0.2417 0.1846 -0.4923 0.0912 -0.4258 chromosome 7 235643_ open reading at frame 6 BE886225 -0.2171 0.31 -0.2095 0.3998 0.3006 -0.2672 0.1828 -0.4876 0.0806 -0.3762

235670_ Transcribed at locus AI916948 -0.6516 0.2102 0.0156 0.1002 0.1855 -0.1649 0.0282 -0.0752 -0.0185 0.0864

235699_ hypothetical H19232 -0.5106 0.1279 -0.1102 0.2944 0.1146 -0.1018 -0.0421 0.1122 -0.0574 0.2677

Table 6: Group of ϊ 645 ge»es that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

2 3 4 5 6 7 8 9 10 11 12 13

Represenia Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score at protein FLJ38964

4-

O Multiple C2- cbmains with two

235740_. transmembrane at regions 1 BG250585 -0.4946 0.1101 -0.0668 0.2837 0.0984 -0.0875 -0.0476 0.1268 -0.0554 0.2585 Chromosome 10 open

235757_ reading frame at 18 AAS14006 0.4527 -0.1845 -0.0809 0.1006 -0.174 0.1546 -0.0764 0.2037 -0.02 0.0935

235764 Transcribed AA029888 -0.3786 0.0319 0.1672 0.1465 0.0297 -0.0264 -0.0289 0.0771 -0.0296 0.138

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at locus chromosome

14open

235802_ reading frame at 175 BE676703 0.3813 -0.0116 0.0652 0.4275 -0.0104 0.0093 0.1025 -0.2734 0.0867 -0.4045

RaI-GDS

235816_ related protein s_at Rgr AI867408 -0.4372 -0.0056 -0.025 0.4924 -0.005 0.0044 -0.1252 0.3337 -0.0994 0.464

235818_ at LAIRhlog AI498747 -0.3895 0.0357 0.2202 0.0966 0.0335 -0.0298 -0.0158 0.0421 -0.0196 0.0916

235925_ Transcription AW05752 at factor 12 0 0.6335 -0.2466 -0.1552 0.1501 -0.2274 0.2022 -0.1037 0.2765 -0.0289 0.1347

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (hipus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(HTF4, helix-

4- loop-helix transcription factors 4) Anaphase promoting

235926_ complex at subunit 5 AI312527 0.4985 -0.1847 0.0059 0.0302 -0.1723 0.1531 -0.0393 0.1047 0.0059 -0.0277 Transcribed locus, weakly

235949_ similar to 4.00E- -1.00E- 4.00E- at NP 775735.1 BF664545 -0.4074 0.1628 -0.0127 04 0.1547 -0.1375 0.0403 -0.1073 04 04

. O

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score transcriptional adaptor 2

(AD A2

236248_ homolog, x_at yeast)-beta AI859834 -0.4582 -0.0148 0.2141 0.3085 -0.0133 0.0118 -0.084 0.2239 -0.061 0.2848

CDNA

FLJ31407 fis, clone 236266_ NT2NE200013 - at 7 BG149557 0.2622 0.0389 0.0219 0.3968 0.0358 -0.0318 0.1199 -0.3196 0.0816 -0.3807

236280_ Transcribed - at locus AI225238 0.1254 0.174 0.1066 0.6966 0.1563 -0.1389 0.2164 -0.577 0.1448 -0.6757

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Hypothetical

« 236285 protein

'Jl at BC009980 AI631846 -0.2497 0.3075 -0.0961 0.4684 0.2897 -0.2575 0.1943 -0.5181 0.0922 -0.4303 Ras homolog

236293_ gene family, at member H BE676335 0.4823 -0.1481 0.0062 0.1113 -0.139 0.1235 -0.0098 0.026 0.0223 -0.104

236295_ s_at NOD3 protein AA694067 0.361 -0.0358 0.1666 0.4393 -0.0321 0.0286 0.0995 -0.2655 0.0888 -0.4143

236297_ Plexin domain at containing 2 AI420817 -0.5396 0.1473 0.0035 0.1635 0.1322 -0.1176 -0.0042 0.0111 -0.0314 0.1466

236301_ Full length at insert cDNA AA789123 0.2147 0.0193 0.1847 0.4519 0.0176 -0.0156 0.118 -0.3147 0.093 -0.4342

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score clone

YY82H04 cyclin- dependent kinase inhibitor

236313_ 2B (pl5, AW44476 at inhibits CDK4) 1 - -00..55007711 0.086 0.1418 0.1601 0.0791 -0.0703 -0.0206 0.0548 -0.0318 0.1486

Choline/ethano lamine

236327_ phosphotransfe at rase 1 AA767373 0.3309 -0.1112 -0.1624 0.1099 -0.1051 0.0934 -0.0579 0.1543 -0.0223 0.1041

236341 cytotoxic T- AI733018 0.062 0.131 0.1162 0.1219 -0.1083 0.1683 -0.4488 0.1097 -0.5118

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at lymphocyte- 0.5256

4- associated -4 protein 4 potassium voltage-gated channel, Isk-

236407_ related family, at member 1 R73518 -0.3019 -0.0564 -0.0649 0.5261 -0.0523 0.0465 -0.1523 0.406 -0.1097 0.5119

236423_ Transcribed at locus AI022821 -0.5721 0.1223 0.027 0.2411 0.1132 -0.1006 -0.0309 0.0824 -0.0482 0.2247

236524_ Beta-amyloid at binding protein AA737437 0.3802 -0.1534 -0.0407 0.0539 -0.1461 0.1298 -0.0547 0.1458 -0.0109 0.051

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score precursor

Ubiquitin-

J-

OO conjugating enzyme E2, Jl

(UBC6

236528_ homolog, at yeast) N64079 -0.383 0.0259 -0.0545 0.3806 0.0234 -0.0208 -0.0905 0.2414 -0.0769 0.3587

Muscleblind-

236558_ like at (Drosophila) AA699809 0.3153 -0.2035 -0.0746 0.2874 -0.1963 0.1745 -0.1305 0.3481 -0.059 0.2755

236571_ Solute carrier AWl 9743 at family 2 1 -0.2639 -0.0257 0.0103 0.3322 -0.0238 0.0212 -0.0918 0.2448 -0.0683 0.3189

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

(facilitated glucose

VO transporter), member 3 Similar to hepatocellular carcinoma- associated

236607_ antigen at HCA557b AI921882 0.5141 -0.2261 0.0342 0.0367 -0.2124 0.1888 -0.0687 0.1833 -0.0072 0.0336

236694_ Chromosome AW46888 at Y open reading 5 0.3971 -0.2182 0.0532 0.1189 -0.2062 0.1833 -0.0904 0.2411 -0.0235 0.1095

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score frame 15A

Ul Ul Muscleblind-

O

236699_ Iike 2 at (Drosophila) AL566294 0.6716 -0.2102 0.0454 0.1796 -0.1934 0.1719 -0.0077 0.0206 0.0349 -0.1629 sterile alpha

236782_ motif domain at containing 3 AI 129628 0.2615 0.0591 0.0713 0.4974 0.0533 -0.0474 0.139 -0.3707 0.1022 -0.4771

BTB and CNC homology 1, basic leucine

236796_ zipper at transcription AI052447 0.6025 -0.1253 0.001 0.2917 -0.1109 0.0986 0.0425 -0.1135 0.0562 -0.2621

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score factor 2

$ 236801_ at T61953 0.599 -0.0873 -0.2685 0.1299 -0.0793 0.0705 0.0119 -0.0319 0.0255 -0.1188

236802_ Homeobox at C14 AI732132 -0.024 -0.1411 -0.1701 0.5648 -0.1298 0.1154 -0.1932 0.5152 -0.1175 0.5481

236841_ CXYorfl- at related protein BE464132 0.4021 -0.1348 -0.0901 0.0292 -0.1277 0.1135 -0.0427 0.1138 -0.0059 0.0275 Golgi associated PDZ and coiled-coil

236862_ motif at containing AA279958 0.4265 -0.066 -0.0616 0.2071 -0.0619 0.055 0.0361 -0.0962 0.0422 -0.1967

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

A disintegrin- like and metalloproteas e (reprolysin type) with thrombospondi

236901_ n type 1 motif, at 2 AA035730 -0.3054 -0.0332 -0.3237 0.7169 -0.0297 0.0264 -0.1872 0.4991 -0.1488 0.6946

G protein-

236946_ coupled -6.00E- at receptor 75 AI220134 0.3748 -0.1087 -0.1053 0.0027 -0.1035 0.092 -0.0293 0.0782 04 0.0026

237018 A kinase AI051967 0.5076 -0.248 -0.1087 0.2397 -0.2344 0.2084 -0.1284 0.3424 -0.0475 0.2215

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set BD Gene Title ID score score score score score 3 score score score score score at (PRKA)

Ul Ul anchor protein

13

237076_ at — AI634534 -0.3238 0. 0927 -0.293 0.3707 0.0854 -0.0759 -0.0797 0.2126 -0 .0752 0. 3509

237156_ - at — BE676171 0.4722 -0 .0914 -0.2376 0.0173 -0.0852 0.0758 -0.0196 0.0523 0. 0035 -0 .0161

237179_ 1.00E- at — BF509219 0.4675 -0 .2401 04 0.1554 -0.2257 0.2006 -0.1033 0.2754 -0 .0304 0. 1417

GTPase

237216_ activating - at Rap/RanGAP AV739182 0.4014 -0 .1583 0.0272 0.0204 -0.1521 0.1352 -0.0375 0.1 0. 0042 -0 .0194

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score domain-like 1 8 237218_ at — BFl 10977 0.3942 -0.1061 -0.212 0.0783 -0.0985 0.0876 -0.0476 0.1269 -0.0156 0.0729

237310_ Exostoses at (multiple) 1 AI743607 0.0604 -0.128 -0.1215 0.3956 -0.1209 0.1075 -0.1372 0.3659 -0.0822 0.3836 solute carrier 237340_ family 26, at member 8 BE551631 -0.6616 0.2029 0.012 0.1334 0.1836 -0.1632 0.019 -0.0506 -0.0254 0.1187

Insulin-like

237377 growth factor 1

— at receptor AA069425 0.3682 -0.2456 -0.045 0.3164 -0.2341 0.2081 -0.1401 0.3735 -0.0636 0.2966

237514_ — AA778658 0.3738 -0.0393 -0.2727 - -0.0366 0.0326 -0.0052 0.0139 0.0041 -0.0189

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at 0.0201 hypothetical

237870_ protein at LOC285771 B BFF443344553399 -0.2952 -0.0262 -0.0297 0.4046 -0.024 0.0213 -0.1155 0.3079 -0.083 0.3872

Trinucleotide

237895_ repeat at containing 6B A AVV7700009933(0 0.3249 -0.252 -0.0977 0.4293 -0.2366 0.2103 -0.1858 0.4954 -0.0859 0.4011

237943_ at — AI820802 0.3179 -0.2253 -0.0469 0.3163 -0.2172 0.1931 -0.1435 0.3826 -0.0647 0.302

Source of

238303_ immunodomin AW07037 at ant MHC- 1 0.3268 -0.1635 -0.0032 0.1002 -0.1566 0.1392 -0.074 0.1972 -0.0204 0.0951

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score associated peptides

RNA binding motif, single stranded

238317_ interacting x at protein 1 BF439728 0.3685 -0.2301 -0.0918 0.3199 -0.2212 0.1966 -0.1428 0.3808 -0.0652 0.3043

GRB2- associated

238405_ binding protein at 2 AI792896 -0.374 0.0601 -0.3043 0.5207 0.0548 -0.0488 -0.1165 0.3106 -0.1066 0.4976

238420 CDNA clone AV721958 -0.3015 0.2039 0.0397 0.1963 -0.1745 0.1239 -0.3304 0.0551 -0.2571

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score at IMAGE:52635 0.2693

Ul Ul 31, partial cds -4 potassium inwardly- rectifying channel,

238428_ subfamily J, at member 15 BG542347 -0.5521 0.2636 -0.0152 0.1158 0.2435 -0.2165 0.0979 -0.261 0.0219 -0.1024

238439_ ankyrin repeat at domain 22 AI925518 -0.6423 0.1591 -0.059 0.2985 0.1431 -0.1272 -0.0364 0.0972 -0.0579 0.2702

238451_ membrane at protein, BF693302 -0.2657 0.0465 -0.0595 0.2088 0.0438 -0.0389 -0.0441 0.1176 -0.0428 0.1998

Table 6: Group of 1645 genes that are differentially expressed ήi healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score pahnitoylated 7

(MAGUK ρ55 subfamily member 7)

238455_ Plexin domain at containing 2 AA329676 -0.4709 0.1773 -0.008 0.0232 0.1636 -0.1454 0.039 -0.1039 -0.0045 0.0211 eukaryotic translation

238461_ initiation factor at 4E member 3 AA228031 -0.4397 0.1589 0.0229 0.0103 0.1477 -0.1312 0.0377 -0.1007 -0.002 0.0094

238469_ Chromosome 6 at open reading BE620374 -0.4239 0.2845 -0.0197 0.3002 0.2678 -0.238 0.149 -0.3975 0.0583 -0.272

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score frame 155

8 238488 at synleurin BF511602 -0.4629 0.0178 -0.0839 0.5134 0.0161 -0.0143 -0.1337 0.3566 -0.1047 0.4885

Proline rich

GIa (G- carboxyglutami c acid) 4

238513_ (transmembran at e) BF905445 -0.6472 0.2981 -0.1133 0.0148 0.2747 -0.2442 0.0816 -0.2177 0.0028 -0.0129 solute carrier

238546_ family 8 at (sodium/calciu BF344961 -0.5673 0.0947 0.0789 0.2599 0.0854 -0.0759 -0.0451 0.1203 -0.051 0.238

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score m exchanger),

Ui member 1

O

Muscleblind-

238558_ like at (Drosophila) AI445833 0.2532 -0.0979 -0.2771 0.2653 -0.091 0.0809 -0.0976 0.2603 -0.0537 0.2507

Guanylate

238581_ binding protein at 5 BG271923 -0.5041 0.4185 -0.1369 0.4613 0.3971 -0.353 0.2278 -0.6075 0.0867 -0.4048

238595_ Transcribed at locus AV702101 0.4847 -0.195 -0.0872 0.1013 -0.1827 0.1624 -0.0734 0.1957 -0.02 0.0933

238642_ AW36757 at 1 0.2627 -0.1748 -0.0152 0.2083 -0.1673 0.1487 -0.1009 0.2691 -0.0425 0.1982

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score)_;, RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Hypothetical u CS. 238743 - protein at FL J38348 BG251692 -0.4456 0.2805 -0.0377 0.2495 0.2656 -0.2361 0.1363 -0.3636 0.0487 -0.2273 Mediator of RNA polymerase II transcription, subunit 28

238761_ homolog at (yeast) BE645241 0.2589 0.0134 0.0692 0.3709 0.0125 -0.0111 0.0964 -0.2571 0.0768 -0.3583

238774_ Hypothetical AW96045 at protein 4 0.3169 -0.2741 -0.0271 0.4282 -0.2624 0.2332 -0.1961 0.5229 -0.0868 0.4049

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

LOC284058 hypothetical

238783_ protein at MGC33214 AA213701 0.439 -0.0733 0.0517 0.3096 -0.0659 0.0586 0.0595 -0.1586 0.0614 -0.2865

Hypothetical

238807_ protein AW97396 at LOC157567 4 0.6173 -0.1652 0.0636 0.2609 -0.1492 0.1326 0.0239 -0.0637 0.0506 -0.236

Thyroid hormone receptor

238883_ associated AW97505 at protein 2 1 0.1243 -0.1679 -0.1743 0.4868 -0.1551 0.1378 -0.1749 0.4663 -0.0998 0.4656

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients_*

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Splicing factor, g 238929 arginine/serine- at rich, 46kD N30132 0.2685 0.0269 0.0251 0.3743 0.0249 -0.0221 0.0998 -0.2662 0.0771 -0.36

Zinc finger

238970_ RNA binding at protein BF509781 0.5348 -0.2411 0.0416 0.0482 -0.23 0.2045 -0.0748 0.1995 -0.0096 0.0447 hypothetical

238983_ protein at FLJ14001 AI538394 -0.4361 0.0804 -0.0907 0.3252 0.0741 -0.0659 -0.0601 0.1602 -0.0657 0.3068

239067_ s_at pannexin 2 AI360417 -0.5394 0.0034 0.1853 0.3719 0.0031 -0.0028 -0.0972 0.2593 -0.0743 0.347

239093 chromosome BGl 65743 0.2423 0.0251 0.1268 - 0.0231 -0.0205 0.1165 -0.3106 0.091 -0.4248

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at 10 open 0.4403

Ul reading frame

65

Male sterility

239108_ domain at containing 1 H16791 -0.4142 0.0433 -0.1248 0.4342 0.0384 -0.0342 -0.0985 0.2627 -0.0868 0.4052

239171_ Adducin 3 at (gamma) AA766886 0.4038 -0.1758 -0.0642 0.1118 -0.1654 0.147 -0.0757 0.202 -0.0223 0.1039

Calciurn/calmo dulin-

239179_ dependent at protein kinase AU155612 0.0148 -0.1504 -0.1096 0.4912 -0.1395 0.124 -0.1727 0.4606 -0.1017 0.4745

Ul II gamma

Chromosome

14 open

239188_ reading frame at 24 AA838428 -0.27 -0.007 -0.0879 0.3833 -0.0065 0.0058 -0.1099 0.293 -0.0797 0.3718 hypothetical

239203_ protein AW01472 at FLJ39575 8 -0.342 0.0069 -0.1455 0.4764 0.0062 -0.0055 -0.1195 0.3186 -0.097 0.4527 chromosome 6

239212_ open reading AW23621 at frame 93 4 0.3462 -0.030? -0.0603 0.2187 -0.029 0.0257 0.0481 -0.1282 0.0448 -0.2089

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients. ,;

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

239237

Ui at LOC442534 AI798822 0.3435 -0.0675 0.2049 0.3736 -0.0611 0.0543 0.0806 -0.2149 0.0752 -0.351

Os

239250_ zinc finger at protein 542 BE966038 0.4138 0.0268 -0.2612 -0.249 0.0242 -0.0215 0.0708 -0.1888 0.0494 -0.2304

239266_ Transcribed - at locus A AII773344225588 0 0..33993377 - -00..00990088 0 0..00224477 0 0..11990011 -0.0849 0.0755 0.0258 -0.0687 0.0385 -0.1796

Likely ortholog of mouse acyl-

Coenzyme A

239277_ thioesterase 2, - at mitochondrial AI559696 -0.3882 0.2668 -0.1082 0.2048 0.2512 -0.2233 0.1183 -0.3155 0.0394 -0.1841

239296 Zinc finger AI623184 0.3231 -0.1694 -0.1192 0.2316 -0.1601 0.1423 -0.104 0.2773 -0.0468 0.2183

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at homeobox Ib

RAS p21

-4 protein activator

(GTPase

239301_ activating at protein) 1 BE551451 0.3552 -0.185 -0.0717 0.1941 -0.1773 0.1576 -0.0978 0.2608 -0.0395 0.1844

239364_ AWl 9547 at 5 -0.3947 0.1931 -0.0634 0.0444 0.1844 -0.1639 0.0639 -0.1705 0.0089 -0.0417

239448_ at AI475033 0.4983 -0.165 -0.0299 0.0479 -0.1567 0.1393 -0.0311 0.0831 0.0097 -0.0451

239449 Ankylosis, AV693734 0.4487 -0.0626 -0.02 - -0.0581 0.0517 0.0569 -0.1516 0.0566 -0.2641

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG

Set ID Gene Title ID score score score score score 3 score score score score score at progressive 0.2791

Ul homolog

OO

(mouse)

Tumor rejection

239451_ antigen (gp96) at 1 AI684643 0.4642 -0.064 -0.0341 0.2779 -0.0579 0.0515 0.0555 -0.1479 0.0552 -0.2576

239479_ Transcribed x_at locus AI718964 0.332 -0.0828 0.1638 0.2812 -0.0774 0.0688 0.0501 -0.1336 0.0574 -0.2677

239487_ DKFZP564F05 at 22 protein AI743261 0.42 -0.0893 -0.0991 0.1019 -0.0846 0.0752 0.0032 -0.0087 0.0208 -0.097

239545 O- AI335004 0.4615 -0.1216 -0.0631 -0.1126 0.1001 -0.0071 0.0189 0.0186 -0.0867

Table 6: Group of 1645 genes fhat are differential y expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at acetyltransferas 0.0936 e

PABPl- dependent poly A-specific

239597_ ribonuclease at subunit PAN3 AA993566 0.3697 -0.1564 -0.0986 0.1286 -0.1493 0.1327 -0.0741 0.1976 -0.0262 0.1221 Transforming growth factor, beta receptor I

239605_ (activin A x at receptor type AI743727 0.3535 -0.1185 -0.2372 0.1778 -0.1128 0.1003 -0.0782 0.2085 -0.0364 0.1698

Table 6: Group of 1645 genes that are differentially expressed in healthy donors^ SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

II-like kinase, 53kDa)

O General

239649_ transcription at factor II, i AI817960 0.3882 -0.0189 -0.0697 -0.285 -0.0176 0.0156 0.0684 -0.1824 0.0582 -0.2714

239660_ KIAA1272 at protein BF110518 -0.2948 -0.0278 -0.0371 0.4157 -0.0255 0.0226 -0.112 0.2986 -0.0853 0.3979 Hypothetical protein FLJl 0770 ///

239695_ Janus kinase 1 at (a protein AI280194 0.2999 -0.1776 -0.1238 0.2818 -0.1699 0.1511 -0.1188 0.3168 -0.0578 0.2695

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set E) Gene Title ID score score score score score 3 score score score score score tyrosine

-4 Kinase;

239704_ IBR domain at containing 2 BE274992 -0.2644 -0.0655 -0.1191 0.5634 -0.0603 0.0536 -0.1646 0.4389 -0.1176 0.5488

239744_ AWl 5166 at — 0 0.4464 -0.0675 0.2437 0.5176 -0.0609 0.0542 0.1118 -0.2982 0.105 -0.4898

Zinc finger,

239757_ A20 domain at containing 3 AA741493 0.1585 -0.1582 -0.0498 0.3054 -0.1521 0.1352 -0.1309 0.3491 -0.0633 0.2956

Nuclear

239815_ receptor at coactivator 5 Rl6784 0.4099 -0.2033 -0.1278 0.2402 -0.1915 0.1702 -0.116 0.3093 -0.048 0.2238

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Activating

239825_ transcription

Ul -4 at factor 6 Rl 7746 -0.5048 0.1885 -0.1939 0.2075 0.1726 -0.1534 -0.005 0.0134 -0.0403 0.1883 Multiple C2- domains with two

239893_ transmembrane at regions 2 AA702409 -0.3232 0.0164 -0.0608 0.3501 0.015 -0.0133 -0.0844 0.2249 -0.0713 0.3328 Hypothetical

239901_ protein at FLJ43663 BF642798 0.4909 -0.2612 -0.0702 0.255 -0.2452 0.2179 -0.1339 0.357 -0.0498 0.2326

239979 Epithelial BE645480 -0.5588 0.5148 -0.2819 0.4947 -0.4397 0.2615 -0.6972 0.0957 -0.4466

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at stromal 0.5219 interaction 1

'Jl

-J (breast)

239988_ Hect domain at and RLD 6 AA708470 -0.4103 0.4091 -0.1418 0.5289 0.3822 -0.3397 0.2451 -0.6535 0.098 -0.4575

240027_ lin-7 homolog at A (C. elegans) BF062244 -0.499 0.1663 -0.0417 0.1141 0.1541 -0.137 0.0133 -0.0354 -0.0225 0.1048

240036_ SEC14-like 1 at (S. cerevisiae) AI022082 0.4172 -0.1295 -0.1492 0.0565 -0.1225 0.1089 -0.0497 0.1325 -0.0114 0.0533

240057_ KIAA0280 at protein AI653262 -0.2535 -0.0968 0.1244 0.4012 -0.0899 0.0799 -0.1341 0.3577 -0.0825 0.3851

240094 Hypothetical AL042660 -0.2989 -0.1012 0.0873 0.4959 -0.0912 0.0811 -0.1539 0.4104 -0.1011 0.4718

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at protein

-4 DJ971N18.2

Transcribed locus, weakly similar to

XP_209041.2

KIAAl 503

240165_ protein [Homo at sapiens] AI678013 -0.6068 0.1882 0.054 0.0754 0.1692 -0.1504 0.0293 -0.078 -0.0143 0.0667

CDNA

240246_ FLJ44826 fis, AW29472 at clone 2 0.342 -0.1408 0.067 0.0435 -0.1353 0.1202 -0.0246 0.0655 0.0089 -0.0416

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 1 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

BRACE30467

'Jy -4 62 'Jy

CDNA

FLJ12931 fis, clone

240263_ NT2RP200486 -5.00E- at 1 N74924 0.5676 -0.1718 -0.1383 0.0027 -0.1584 0.1408 -0.0456 0.1215 04 0.0025 pyrin and HIN 240413_ domain family, at member 1 AI827431 0.1612 0.1321 0.1079 0.6234 0.1196 -0.1063 0.194 -0.5173 0.1297 -0.6051

240593_ Calcium/calmo x at dulin- R98767 0.4595 -0.0827 -0.1694 -0.093 -0.077 0.0685 0.0026 -0.0069 0.0187 -0.0871

Table 6: Group of 1645 genes fhat are differentially expressed in healthy donors „ SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score dependent protein kinase

(CaM kinase)

II delta

240594_ Chromodomain at protein, Y-like W86659 0.2436 -0.1365 -0.064 0.173 -0.1307 0.1162 -0.0891 0.2377 -0.0355 0.1658

240652_ at T91029 0.3213 -0.1883 -0.0552 0.222 -0.1806 0.1606 -0.1091 0.2908 -0.0453 0.2113

Cancer

240718_ susceptibility AW30338 at candidate 1 4 -0.419 0.152 0.1065 0.0733 0.1431 -0.1272 0.0584 -0.1557 0.0147 -0.0686

240721 Bridging BE672858 -0.5215 0.1513 -0.0143 0.1512 0.1411 -0.1254 0 -1.00E- -0.0301 0.1406

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at integrator 3 04 RAS guanyl

-4

240862_ releasing at protein 4 AA923524 -0.4674 0.042 0.0929 0.2834 0.0374 -0.0332 -0.0618 0.1647 -0.0557 0.2601

240870_ Histone at deacetylase 4 AI056293 -0.4195 0.0118 -0.14 0.5386 0.0106 -0.0094 -0.1345 0.3587 -0.1101 0.514 Solute carrier family 8 (sodium/calciu

241041_ m exchanger), at member 1 BF223010 0.188 -0.2073 -0.1391 0.4918 -0.1961 0.1743 -0.1776 0.4735 -0.1015 0.4737

241133 Tcellreceptor AI016855 0.4977 -0.1291 -0.1387 -0.119 0.1058 -0.0234 0.0624 0.0075 -0.035

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at beta chain 0.0381 (TCRB)

OO mRNA, TCRB-BV27 J2-4 BC2 allele

241195_ 2.00E- at AI791152 0.454 -0.1954 04 0.0502 -0.1858 0.1651 -0.0654 0.1745 -0.01 0.0469

CDNA FLJ42259 fis, clone

241365_ TKIDN201128 at 9 AA002140 0.4408 -0.0315 0.052 -0.423 -0.0287 0.0255 0.0974 -0.2598 0.0858 -0.4006

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

V-ets erythroblastosi s virus E26 oncogene

241435_ homolog 1 at (avian) AA702930 0.4251 -0.0865 0.0485 0.2568 -0.0791 0.0703 0.0439 -0.1172 0.0512 -0.2391

Chromosome 5

241494_ open reading AW02734 at frame 12 2 0.3623 -0.1678 0.1611 0.0833 -0.1605 0.1427 -0.022 0.0586 0.0169 -0.0789

241652_ Lin-7 homolog x_at A (C. elegans) T82147 -0.3551 0.1272 0.0013 0.0278 0.1212 -0.1078 0.0243 -0.0647 -0.0057 0.0265

241734 serum response AI391443 0.1954 0.1196 -0.0183 0.1112 -0.0988 0.1612 -0.43 0.1049 -0.4893

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score)-, RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at factor binding 0.5041

OO protein 1 O solute carrier family 8 (sodium/calciu

241752_ m exchanger), at member 1 AA094434 -0.3002 0.0228 0.0038 0.2467 0.0212 -0.0189 -0.0556 0.1482 -0.0503 0.2347 calcium/calmo dulin- dependent

241871_ protein kinase at IV AL529104 0.3994 0.0451 -0.012 0.5229 0.0406 -0.0361 0.1418 -0.3782 0.1069 -0.4987

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

241916_ Phospholipid at scramblase l AI984040 -0.6718 0.4107 -0.1849 0.2205 0.3826 -0.3401 0.1591 -0.4244 0.0398 -0.1855

Z-DNA

242020_ binding protein s_at 1 AI925506 -0.6543 0.4931 -0.1708 -0.472 0.4664 -0.4146 0.2415 -0.6441 0.0855 -0.3989

242051_ Transcribed at locus AI695695 0.2677 0.039 0.0826 0.4612 0.0352 -0.0313 0.1299 -0.3465 0.0945 -0.4408

242059_ Ethanolamine AW97663 at kinase 1 1 0.2987 -0.0518 -0.1093 0.0666 -0.0494 0.0439 0.0041 -0.0108 0.0137 -0.064

Similar to 4OS 242099_ ribosomal at protein S3 T83938 0.4687 -0.0754 -0.0081 0.2771 -0.0689 0.0613 0.051 -0.136 0.0554 -0.2584

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score hypothetical protein

LOC200030 /// hypothetical

242191_ LOC400781 /// at AGl protein AI701905 0.4016 -0.0695 0.066 0.2947 -0.0637 0.0566 0.0569 -0.1516 0.0592 -0.2765

XIAP

242234_ associated at factor-1 AI859280 -0.4009 0.4282 -0.1911 0.5422 0.4046 -0.3597 0.2454 -0.6544 0.1015 -0.4736 242289_ AW96241 at — 3 0.2185 0.0368 0.1789 0.4968 0.0339 -0.0302 0.1353 -0.3609 0.1034 -0.4823 242335 FP15737 AA382004 -0.3543 0.0728 -0.0653 0.2363 0.067 -0.0595 -0.0408 0.1087 -0.0475 0.2217

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at

$ 242343_ Zinc ringer x_at protein 518 H57111 0.4839 -0.1896 -0.1134 0.1131 -0.1768 0.1572 -0.0785 0.2094 -0.0223 0.1039

Nipped-B

242352_ homolog AW27226 at (Drosophila) 2 0.3859 -0.1947 0.0663 0.0551 -0.1881 0.1672 -0.0637 0.1699 -0.0112 0.0524 serine/threonin e/tyrosine

242408_ interacting AW96893 at protein 5 0.2322 0.0877 -0.096 0.3822 0.0819 -0.0728 0.1228 -0.3274 0.0789 -0.3682

242429_ zinc finger at protein 567 BF435183 0.345 0.0263 -0.1434 0.2899 0.0245 -0.0218 0.0801 -0.2137 0.0593 -0.2766

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

242457_ Transcribed AW45110

O £C at locus 7 0.0885 -0.093 -0.1728 0.3228 -0.0882 0.0784 -0.1037 0.2766 -0.067 0.3126

242463_ zinc finger x_at protein 600 AI620827 0.427 -0.0919 0.1441 0.3364 -0.0838 0.0745 0.0626 -0.1669 0.0674 -0.3147

242509_ MGCl 7624 at protein R71072 0.4771 -0.171 -0.1295 0.086 -0.161 0.1431 -0.0675 0.1799 -0.0172 0.0801

Family with sequence 242594 similarity 44, at member A AI889584 -0.4715 0.0968 0.1661 0.0708 0.0906 -0.0806 0.0069 -0.0184 -0.0142 0.0665

242625 — radical s- AWl 8984 - at adenosyl 3 -1.0103 0.8426 -0.258 0.9509 0.7856 -0.6983 0.4721 -1.259 0.153 -0.7139

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score methionine

Ul

OO domain containing 2 242648_ kelch-like 8 at (Drosophila) BE858995 -0.4538 0.01 0.0549 0.3911 0.009 -0.008 -0.0986 0.263 -0.0786 0.3668

242761_ zinc finger s_at protein 420 AI061288 0.2695 0.0191 0.1225 0.4484 0.0177 -0.0157 0.1193 -0.3182 0.0929 -0.4336 zinc finger,

242776_ CCHC domain at containing 6 AA584428 -0.391 0.1629 -0.1477 0.1132 0.1522 -0.1353 0.0127 -0.0338 -0.0225 0.1049

242808_ at — AI733287 -0.4441 0.0365 -0.1579 0.5151 0.0331 -0.0294 -0.1222 0.3258 -0.1051 0.4903

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

242827_ Transcribed

& x_at locus AA806368 0.4457 -0.2822 -0.1214 0.4073 -0.2607 0.2317 -0.1791 0.4776 -0.0789 0.3684

242859_ Transcription at factor CP2 BE156563 0.3968 -0.1964 0.1045 0.0116 -0.1861 0.1654 -0.0525 0.1399 -0.0023 0.0108

Chromosome

19 open

242877_ reading frame at 13 AI821399 0.372 -0.2061 -0.0207 0.1839 -0.1942 0.1726 -0.1054 0.281 -0.0364 0.1701

242898_ - at — AI494047 -0.3639 0.3137 -0.1296 0.3343 0.2986 -0.2654 0.1642 -0.4379 0.065 -0.3033

242907_ guanylate - at binding protein BF509371 -0.5072 0.2687 -0.0886 0.1052 0.2486 -0.221 0.0974 -0.2598 0.0198 -0.0924

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

2, interferon- inducible

242916_ centrosomal at protein 1 AA642477 0.4233 -0.1013 -0.2058 0.0293 -0.0956 0.085 -0.0343 0.0916 -0.0059 0.0277

Phosphatidylin ositol-3- phosphate/phos phatidylinositol 242926_ 5-kinase, type at πi AI798124 0.3702 -0.1217 -0.1113 0.0477 -0.1161 0.1032 -0.0436 0.1164 -0.0097 0.0455

242943_ ST8 alpha-N¬ at acetyl- AA352113 -0.5973 0.2208 0.0716 0.0383 0.2 -0.1778 0.0654 -0.1744 0.0072 -0.0337

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score neuraminide alpha-2,8- 00 sialyltransferas e 4

DEAD (Asp-

Glu-Ala-Asp)

242961_ box x_at polypeptide 58 AI304317 -0.1365 0.2044 -0.0597 -0.346 0.1964 -0.1746 0.1368 -0.3648 0.0712 -0.3323

243178_ AW96970 at 3 -0.3269 -0.0078 -0.0312 0.3899 -0.0071 0.0063 -0.1007 0.2685 -0.0796 0.3716

243222_ Full-length AW29534 at cDNA clone 0 -0.674 0.1733 -0.0773 0.3112 0.1559 -0.1386 -0.0368 0.0981 -0.0603 0.2812

Table 6: Group of 1645 genes that are differentiaϊly expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

CS0DF024YN

14 of Fetal brain of Homo sapiens

(human)

PABPl- dependent poly

A-speciflc

243233_ ribonuclease at subunit PAN3 AI701943 0.3042 -0.1454 0.1019 0.0258 -0.1403 0.1247 -0.031 0.0828 0.0053 -0.0247

243256_ MAP kinase AW79636 at interacting 4 -0.321 0.0275 -0.1695 0.4228 0.0248 -0.0221 -0.0985 0.2626 -0.0859 0.4009

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score serine/threonin S O≤ e kinase 1

Chromosome 7 243271_ open reading at frame 6 AI064690 -0.5642 0.382 -0.2032 0.2377 0.3617 -0.3215 0.1617 -0.4311 0.0443 -0.2068

243332_ at — BE972639 0.5166 -0.1468 -0.1989 0.0474 -0.1368 0.1216 -0.0533 0.1422 -0.0094 0.0439

243489_ at — BF514098 0.5741 -0.1492 -0.0561 0.1435 -0.1367 0.1215 -0.0015 0.0039 0.0281 -0.1311

YYl

243561 associated at factor 2 AA651631 0.3564 -0.1787 -0.1212 0.2236 -0.1701 0.1512 -0.108 0.2879 -0.0454 0.2117

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Activating ζg 243581_ transcription AWl 1722 at factor 6 9 -0.3715 0.0773 -0.1145 0.2893 0.0726 -0.0645 -0.057 0.152 -0.0592 0.2764 hypothetical

243589_ protein at LOC284058 AI823453 0.5885 -0.247 -0.0543 0.1007 -0.2318 0.2061 -0.0914 0.2438 -0.0197 0.0918

Similar to

FRGl protein

243689_ (FSHD region s_at gene 1 protein) AI681945 0.364 -0.0197 -0.2021 0.1304 -0.0184 0.0164 0.0299 -0.0797 0.0265 -0.1237

243729_ CDNA at FLJ37931 fis, AI457984 0.4315 -0.0878 0.1052 0.3146 -0.0798 0.0709 0.0567 -0.1512 0.0628 -0.2931

Table 6: Group of 1645 genes that are differentially expressed in hsa, thy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score clone

'Jl CTONG20043 κ>

97

SUMOl/sentri

243768_ n specific at protease 6 AA026388 0.4656 -0.1645 -0.1408 0.0914 -0.1528 0.1358 -0.0676 0.1803 -0.018 0.0841

CDNA clone

243835_ IMAGE:48380 at 03, partial cds BE467787 0.3713 -0.0201 0.1295 0.4563 -0.0183 0.0162 0.1091 -0.2909 0.0933 -0.4355

243842_ Checkpoint at suppressor 1 BE463896 0.5676 -0.1212 -0.2965 0.0203 -0.1097 0.0975 -0.0378 0.1009 -0.0039 0.0183

243878 Forkhead box AI248610 0.4363 -0.0961 -0.2065 0.0027 -0.09 0.08 -0.026 0.0694 -5.00E- 0.0026

-

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at Pl 04 a 243908 Zinc finger at protein 638 AI308174 0.4392 -0.1573 -0.0761 0.0373 -0.149 0.1324 -0.0515 0.1373 -0.0075 0.035

243932_ Transcribed at locus AI286254 0.2915 0.0213 0.0283 0.3864 0.0199 -0.0177 0.1035 -0.276 0.08 -0.3733

Serologically defined colon

243963_ cancer antigen at 8 AI473707 0.5297 -0.2967 -0.0526 0.2925 -0.2831 0.2517 -0.1578 0.4207 -0.0579 0.27

SNF2 histone

243964_ linker PHD at RING helicase AI631201 0.5741 -0.2617 0.2733 0.1605 -0.2453 0.2181 -0.0248 0.066 0.0313 -0.146

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

Eukaryotic translation

244015_ initiation factor at 4 gamma, 3 AA704163 -0.1597 -0.0834 -0.0848 0.4696 -0.0771 0.0685 -0.1548 0.4127 -0.0976 0.4553

244042_ x_at — AA883831 0.4152 0.0042 -0.147 0.3001 0.0039 -0.0034 0.0812 -0.2165 0.0613 -0.2859

Protein kinase, interferon- inducible double

244047_ stranded RNA at dependent AA447714 0.358 -0.016 0.0484 -0.375 -0.0148 0.0132 0.0952 -0.2538 0.0769 -0.3589

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score activator similar to cell

Ul recognition

244065_ molecule AWOl 675 at CASPR3 1 - -00..331199 --00..00008899 --00..00447744 00..44000033 -0.0083 0.0074 -0.1071 0.2857 -0.0828 0.3866

Chromosome 9

244094_ open reading - at frame 93 AA406237 0.3357 -0.0027 -0.024 0.3178 -0.0025 0.0022 0.0835 -0.2226 0.0655 -0.3057

Methionyl

244185_ aminopeptidase - at 2 AA921841 0.4238 -0.0963 0.1118 0.2904 -0.0888 0.079 0.0485 -0.1292 0.0585 -0.2729

244218 Staphylococcal AI374686 -0.3001 -0.0401 -0.0514 0.4677 -0.0364 0.0324 -0.1368 0.3648 -0.096 0.4481

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at nuclease domain containing 1 Special AT- rich sequence binding protein 1 (binds to nuclear matrix/scaffold

244267_ -associating at DNA's) AA237039 0.7308 -0.215 -0.1086 -0.08 -0.1967 0.1748 -0.0352 0.0938 0.0154 -0.0718

244313 Transcribed AI052659 -0.5543 0.0366 0.1622 0.3211 0.0321 -0.0285 -0.0729 0.1945 -0.0623 0.2906

Tab! Ie 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at locus

V-raf-1 murine

-4 leukemia viral

244373_ oncogene at homolog l AI740571 -0.4627 0.0373 0.0188 0.3622 0.0335 -0.0298 -0.0863 0.2302 -0.0722 0.337

244375_ AW87360 at Enah/Vasp-like 6 0.5953 -0.1001 -0.0194 0.3316 -0.0864 0.0768 0.0589 -0.157 0.063 -0.2941

244383_ at AI283051 0.3551 -0.2001 -0.0234 0.188 -0.1919 0.1706 -0.1028 0.2741 -0.0381 0.1779

244398_ zinc finger x_at protein 684 BE328243 -0.4101 0.3575 -0.2845 -0.254 0.3433 -0.3052 0.1616 -0.4309 0.0487 -0.2271

244482 Eukaryotic AI753104 0.3526 -0.3455 0.101 0.4586 -0.3346 0.2974 -0.2356 0.6282 -0.0919 0.4289

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (hipus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score at translation initiation factor

OO

IA, Y-linked

Tumor protein

244536_ p53 binding at protein, 2 AA702963 -0.3508 0.0413 -0.0741 0.3249 0.0385 -0.0342 -0.0749 0.1998 -0.0666 0.3109

Rho GTPase

244548_ activating at protein 26 AI189587 -0.0859 -0.0644 -0.1871 0.441 -0.0598 0.0532 -0.1373 0.366 -0.0917 0.4277

Spectrin repeat

244568_ containing, at nuclear AL035992 0.3362 -0.1804 -0.0625 0.1925 -0.1736 0.1543 -0.0987 0.2633 -0.0394 0.1838

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score envelope 2 Friend

VO

244592_ leukemia virus at integration 1 BE675040 0.2405 -0.1672 -0.0594 0.2537 -0.1603 0.1424 -0.1091 0.2909 -0.0521 0.2431 Protein inhibitor of

244633_ activated at STAT, 2 AA404996 0.1107 -0.196 -0.0733 0.4783 -0.1817 0.1615 -0.1729 0.4611 -0.0976 0.4557 Transcribed locus,

244674_ moderately 5.00E- 1.00E- -5.00E- at similar to AA936428 0.4414 -0.1799 0.0234 04 -0.169 0.1502 -0.0462 0.1231 04 04

Table 6: Group of 1645 genes that are differentially expressed m healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

XP_496299.1 o hypothetical o protein

LOC148206

[Homo sapiens]

244753_ Actinin, alpha at 4 BF000430 0.2897 -0.1969 -0.0769 0.2987 -0.1854 0.1648 -0.132 0.3519 -0.06 0.2802

Phosphatidyl

244826_ ositol transfer at protein, beta R24061 0.3511 -0.1228 -0.0319 -0.006 -0.1157 0.1028 -0.0311 0.083 0.0012 -0.0056

244871 ubiquitin AW26835 -0.3327 -0.0063 -0.0719 0.431 -0.0056 0.005 -0.1135 0.3026 -0.0874 0.4079

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score)_* RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score s_at specific 7 o protease 32

244889_ AW59224 at — 2 -0.5726 0.1673 -0.2193 0.3588 0.1493 -0.1328 -0.0488 0.1302 -0.0695 0.3243

CD24 antigen

(small cell lung carcinoma cluster 4 266_s_at antigen) L33930 -0.239 -0.0299 -0.3311 0.6464 -0.0267 0.0238 -0.1656 0.4416 -0.1336 0.6236 cleavage and polyadenylatio 33132_at n specific U37012 0.3705 -0.0465 0.0909 0.3476 -0.0433 0.0385 0.075 -0.2 0.0712 -0.3324

Table 6: Group of 1645 genes that are differentially expressed in healthy donors , SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score factor 1, g 16OkDa

CD52 antigen (CAMPATH-I 34210_at antigen) N90866 0.2675 0.0227 0.1003 0.4346 0.0207 -0.0184 0.1125 -0.3001 0.0892 -0.4161

37145_at granulysin M85276 0.5411 -0.1212 0.2284 0.4579 -0.109 0.0969 0.0838 -0.2236 0.0911 -0.4249 butyrophilin, subfamily 3, -

38241 — at member A3 U90548 -0.077 0.2873 -0.0539 0.6345 0.2604 -0.2315 0.2321 -0.6189 0.1266 -0.5909

39248_at aquaporin 3 N74607 0.2191 0.0896 0.1342 0.5953 0.0804 -0.0715 0.1715 -0.4574 0.1233 -0.5752

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score peroxiredoxin

§ 39729_at 2 L19185 0.3681 -0.0315 0.183 0.4738 -0.0282 0.0251 0.1106 -0.2948 0.0959 -0.4473

SET translocation (myeloid leukemia- 40189_at associated) M93651 0.3047 0.007 0.126 0.4559 0.0062 -0.0055 0.1156 -0.3082 0.0926 -0.4319

44673 at sialoadhesin N53555 -0.4433 0.407 -0.2904 0.3458 0.3909 -0.3475 0.1852 -0.4939 0.0652 -0.3043

- sema domain, immunoglobuli -

46665_at n domain (Ig), AI949392 0.4107 -0.0779 0.134 0.3471 -0.0708 0.0629 0.0683 -0.182 0.0696 -0.3248

Table 6: Group of 1645 genes that are differentially expressed in healthy donors, SLB patients (lupus score), RA patients., and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score transmembrane o domain (TM) and short cytoplasmic domain,

(semaphorin)

4C hypothetical protein

53720_at FLJl 1286 AI862559 -0.2596 0.3737 -0.1439 0.5886 0.3438 -0.3056 0.2444 -0.6517 0.1109 -0.5174 KIAAl 196 55872_at protein AI493119 0.3463 -0.0024 0.0229 0.3748 -0.0021 0.0019 0.094 -0.2508 0.0762 -0.3554

Table 6: Group of 1645 genes that are dϊffereiitialiy expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score low density o lipoprotein

Ul receptor adaptor protein -3.00E- 2.00E-

57082_at 1 A AAA11669977880 0.39 04 0.0762 0.4772 04 0.1227 -0.3272 0.0961 -0.4485 hypothetical

58780_s protein

_at FLJ10357 R42449 -0.3387 0.0026 0.0231 0.3221 0.0024 -0.0021 -0.0804 0.2143 -0.0656 0.3061

AFFX- signal AFFX-

HUMIS transducer and HUMISG

GF3 A/M activator of F3A/M979

97935_3 transcription 1, 35_3 -0.4821 0.3611 -0.1119 0.3553 0.3378 -0.3003 0.1845 -0.492 0.0659 -0.3076

Table 6: Group of 1645 genes that are differentially expressed in healthy donors. SLE patients (lupus score), RA patients.. and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

_at 9IkDa

§ AFFX- signal HUMIS transducer and AFFX- GF3A/M activator of HUMISG 97935_5 transcription 1, F3A/M979 _at 9IkDa 35_5 -0.2983 0.3243 -0.21 0.3533 0.3131 -0.2783 0.1726 -0.4602 0.0699 -0.3264

AFFX- signal HUMIS transducer and AFFX- GF3A/M activator of HUMISG 97935_ transcription 1, F3A/M979 MA_at 9IkDa 35_MA -0.3585 0.3285 -0.1584 0.3519 0.3135 -0.2787 0.1721 -0.459 0.0683 -0.3188 AFFX- signal AFFX- -0.5104 0.4097 -0.1752 0.3876 -0.3446 0.2044 -0.5451 0.0731 -0.3411

Table 6: Group of 1645 genes that are differential] y expressed in healthy donors, SLE patients (lupus score), RA patients, and WG patients.

1 2 3 4 5 6 7 8 9 10 11 12 13

Representa Healthy

Probe tive Public Donor Lupus RA WG Lupus Other Lupus WG Other 3 WG Set ID Gene Title ID score score score score score 3 score score score score score

HUMIS transducer and HUMISG 0.3945

GF3A/M activator of F3A/M979

97935_ transcription 1, 35_MB

MB at 9IkDa

o

o

ON

4-

-4

κ>

Ul

K>

o

ON

KJ

Table 1OA: Positive Spearman Correlation of BVAS scores with gene fragments. The expression of these genes is increased when the disease activity in WG is increased.

Accession Correl. P-

# Number Gene Names Corr. Coeff value

1 NM_007219 Ring finger protein 24 0.733 2.69E-06

2 AL562528 Ubiquitin-conjugating enzyme E2, 0.729 3.23E-06 Table 1OA: Positive Spearman Correlation of BVAS scores with gene fragments. The expression of these genes is increased when the disease activity in WG is increased.

Accession Correl. P-

# Number Gene Names Corr. Coeff value

Jl (UBC6 homolog, yeast)

V-ets erythroblastosis virus E26

3 AL575509 oncogene homolog 2 (avian) 0.728 3.46E-06 4 AI760166 Lymphocyte alpha-kinase 0.728 3.47E-06 5 U41070 Leukotriene B4 receptor 0.724 4.18E-06

B-cell CLL/lymphoma 6 (zinc

6 NM_001706 finger protein 51) 0.719 5.23E-06

7 AI538394 Hypothetical protein FLJ14001 0.714 6.34E-06 8 AW592242 Similar to CGl 5828-PA 0.713 6.72E-06 9 NM_007246 Kelch-like 2, Mayven (Drosophila) 0 0..770088 8.25E-06 10 AW264036 Hypothetical LOC389185 0.706 8.96E-06

Acyl-CoA synthetase long-chain

11 NM_001995 family member 1 0.693 1.58E-05

Solute carrier family 22 (organic

12 NM_003059 cation transporter), member 4 0.691 1.70E-05

Transcribed locus, moderately

13 AK025534 similar to XP_375099.1 0.690 1.74E-05

14 AI768563 Rho GTPase activating protein 26 0.689 1.82E-05

15 AW295340 Lymphocyte alpha-kinase 0.688 1.86E-05

16 L32185 Solute carrier family 11 member 1 0.686 2.06E-05

Nuclear factor (erythroid-derived

17 L13974 2), 45kDa 0.684 2.19E-05

Solute carrier family 2 (facilitated

18 NM_006931 glucose transporter), member 3 0.679 2.72E-05 19 NM_000717 Carbonic anhydrase IV 0.677 2.91E-05

Nuclear factor, interleukin 3

20 NM_005384 regulated 0.676 2.95E-05 Table 1OA: Positive Spearman Correlation of BVAS scores with gene fragments. The expression of these genes is increased when the disease activity in WG is increased.

Accession Carrel. P-

# Number Gene Names Corr. Coeff value

21 W60806 0.676 2.96E-05

22 AI084056 Transcribed locus 0.673 3.30E-05

B-cell CLL/lymphoma 6 (zinc

23 S67779 finger protein 51) 0.673 3.33E-05 24 AI452715 Zinc finger protein 608 0.673 3.36E-05

25 NM_018324 Thioesterase domain containing 1 0.673 3.39E-05

Maltase-glucoamylase (alpha-

26 NM_004668 glucosidase) 0.668 4.09E-05

Staphylococcal nuclease domain

27 AI374686 containing 1 0.667 4.22E-05 28 ALl 36944 Solute carrier family 40, member 1 0 0..666677 4.24E-05 29 AF 177765 0.664 4.62E-05 30 AI767388 0.664 4.71E-05

V-ets erythroblastosis virus E26

31 NM_005239 oncogene homolog 2 (avian) 0.661 5.14E-05 32 BC004564 Docking protein 3 0.660 5.32E-05

CDNA FLJl 3601 fis, clone

33 AL049435 PLACE1010069 0.660 5.42E-05

Table 1OB: Negative Spearman Correlation of BVAS scores with gene fragments. The expression of these genes is decreased, when the activity of WG is increased.

Accession Correl. P-

Number Gene Names Corr. Coeff value

BE217880 Interleukin 7 receptor -0.755 2.12E-05

NM_006159 NEL-like 2 (chicken) -0.738 2.46E-04

Killer cell lectin-like receptor

U30610 subfamily D, member 1 -0.727 1.45E-04 Table 1OB: Negative Spearman Correlation of BVAS scores with gene fragments. The expression of these genes is decreased, when the activity of WG is increased.

Accession Correl. P-

# Number Gene Names Corr. Coeff value

Chromosome 16 open reading

4 NM_024600 frame 30 -0.725 4.75E-05 5 NM_000436 3-oxoacid CoA transferase 1 -0.720 2.60E-04 6 BE042354 Lactate dehydrogenase B -0.720 9.41E-05 7 L34703 T cell receptor alpha chain -0.719 1.20E-04 8 AA976536 Brix domain containing 1 -0.717 2.17E-05 9 AI761658 Hypothetical protein FLJ20315 -0.714 1.26E-05

V-ets erythroblastosis virus E26

10 BE218980 oncogene homolog 1 (avian) -0.713 2.79E-05

Mannosidase, alpha, class 1C,

11 NM_020379 member 1 -0.712 5.01E-05 12 NM_006720 Actin binding LIM protein 1 -0.711 3.28E-04 13 NM_021129 Pyrophosphatase (inorganic) -0.710 5.15E-05 14 AF043899 Bridging integrator 1 -0.707 8.08E-05

Serine hydroxymethyltransferase 2

15 AWl 90316 (mitochondrial) -0.704 8.33E-05 16 D13720 IL2-inducible T-cell kinase -0.698 1.28E-04

Nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent

17 AI770171 2 -0.697 1.44E-05

18 AK025298 Autism susceptibility candidate 2 -0.695 1.10E-04

19 AA169780 LDL receptor adaptor protein -0.694 9.23E-07

20 AW450363 ADP-ribosylation factor-like 7 -0.692 2.78E-04

Cirrhosis, autosomal recessive 6

21 AL578336 (cirhin) -0.692 7.47E-06

22 NM_02102 Ribosomal protein L36a -0.691 2.79E-04

23 N NMM_00115544114 Ribosomal protein L36 -0.691 4.41E-05 Table 1OB: Negative Spearman Correlation of BVAS scores with gene fragments. The expression of these genes is decreased, when the activity of WG is increased. Accession Carrel. P-

# Number Gene Names Corr. Coeff value

24 BE465433 Hypothetical protein BC008322 -0.691 1.66E-05

Ankylosis, progressive homolog

25 AA854943 (mouse) -0.688 3.13E-05

26 AB051458 KIAA 1671 protein -0.687 2.57E-05

27 BC001051 ADP-ribosylation factor-like 7 -0.686 2.74E-04

CD2 antigen (p50), sheep red

28 NM_0017έ blood cell receptor -0.685 2.03E-04

29 AA541630 Runt-related transcription factor 3 -0.684 2.37E-04

30 N NMM__00221166443 Tribbles homolog 2 (Drosophila) -0.684 2.74E-04

31 AI745230 Transcribed locus -0.681 9.77E-06

32 T65020 Transcribed locus -0.680 1.91E-05

Developmentally regulated GTP

33 BF223206 binding protein 2 -0.679 2.55E-04

34 AF204231 Golgin-67 -0.678 1.88E-04

Protein kinase, cAMP-dependent,

35 AAl 30247 catalytic, beta -0.678 2.65E-04

36 U87558 Bridging integrator 1 -0.677 1.51E-04

CD3Z antigen, zeta polypeptide

37 J04132 (TiT3 complex) -0.676 1.58E-04

Ras protein-specific guanine

38 AI912976 nucleotide-releasing factor 2 -0.676 1.59E-05

39 AF036906 Linker for activation of T cells -0.676 1.29E-04

Lymphoid enhancer-binding factor

40 AF288571 1 -0.675 3.58E-05

41 AL021786 Integral membrane protein 2A -0.674 2.61E-04

B-cell CLL/lymphoma HB (zinc

42 NM_022898 finger protein) -0.674 4.48E-05 Table 1OB: Negative Spearman Correlation of BVAS scores with gene fragments. The expression of these genes is decreased, when the activity of WG is increased. Accession Correl. P-

# Number Gene Names Corr. Coeff value 43 NM_016337 Enah/Vasp-like -0.673 5.26E-05

Serologically defined colon cancer

44 W60810 antigen 33 -0.671 3.05E-05

T cell receptor beta chain BV20S1 45 AL559122 BJ1-5 BCl -0.671 1.01E-04

Killer cell lectin-like receptor

46 AB009597 subfamily D, member 1 -0.669 1.95E-04 47 NM_000986 Ribosomal protein L24 -0.668 3.55E-04 48 NM_001009 Ribosomal protein S5 -0.666 3.54E-04 49 N25986 -0.666 2.00E-05 50 AL121934 -0.665 5.28E-05 51 BE314601 Hypothetical protein HSPCl 11 -0.665 8.80E-05 Butyrophilin, subfamily 3, member

52 U90548 A3 -0.664 3.63E-06

Lymphocyte-specific protein

53 NM_005356 tyrosine kinase -0.663 2.32E-04

Killer cell lectin-like receptor

54 NM_002258 subfamily B, member 1 -0.663 7.86E-05

Tumor necrosis factor receptor

55 U94506 superfamily, member 25 -0.662 1.29E-04 (Major histocompatibility complex, class II, DR beta 3, Major histocompatibility complex, class

56 AJ297586 II, DR beta 4) -0.662 7.36E-05

57 BF217539 Lectin, mannose-binding, 1 -0.661 2.92E-05 FUS interacting protein (serine-

58 AF047448 arginine rich) 1 -0.661 1.51E-04 Table 1OB: Negative Spearman Correlation of BVAS scores with gene fragments. The expression of these genes is decreased, when the activity of WG is increased.

Accession Carrel. P-

# Number Gene Names Corr. Coeff value

59 M12423 T cell receptor alpha locus -0.660 1.70E-04

(Heterogeneous nuclear ribonucleoprotein Al, Similar to Heterogeneous nuclear ribonucleoprotein Al (Helix- destabilizing protein) (Single- strand binding protein) (hnRNP core protein Al) (HDP-I) (Topoisomerase-inhibitor

60 X79536 suppressed)) -0.660 8.19E-05 61 AF 164622 Golgin-67 -0.660 1.47E-04

Table 12: Comparison of clinical and demographic parameters between patients belonging the low and high IFN-regulated gene groups. ^aAll values are provided as the number of positive patients per group, with the exception of Age, SLEDAI score and SLEDAI score (truncated) in which the mean and (SD) are indicated; ¹³NS indicates not significant; ^CC - Caucasian, B — Black, O — Other; number of patients positive for either arthritis or myositis; ^enumber of patients positive for either urinary casts, hematuria, proteinuria or pyuria; Wmber of patients positive for either rash, alopecia or mucosal ulcers; ^gSLEDAI score (truncated) is defined as the SLEDAI score less the contributions by low complement and increased DNA binding

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lo% ' IFN group vs. the high-

IFN group The 659 probes correspond to 297 genes.

> low IFN MgIi IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

Fc fragment of IgG, high affinity Ia,

21451 l_x_at FCGRlA L03419 -1.1317 0.6552 -0.2105 0.1339 receptor(CD64)

Fc fragment of IgG, high affinity Ia,

216950_s_at FCGRlA X14355 -1.0677 0.6181 -0.1225 0.0779 receptor(CD64)

213294_at Hypothetical protein FLJ38348 FLJ38348 AV755522 -0.9996 0.5787 0.0473 -0.0301

Chromosome 7 open

243271_at C7orf6 AI064690 -0.9341 0.5408 -0.6366 0.4051 reading frame 6 peroxisomal proliferator-

228230_at PRIC285 ALl 21829 -0.9173 0.5311 0.0623 -0.0397 activated receptor A interacting complex 285

DKFZP564F05

212333_at DKFZP564F0522 protein AL049943 -0.8993 0.5207 -0.022 0.014

22

218085_at chromatin modifying protein 5 CHMP5 NMJH5961 -0.8775 0.508 -0.4444 0.2828

Table 13: List of the 659 Gene Probes with Corresponding CentroM Scores for Classifying SLE - Healthy and the kro ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

218304_s_at oxysterol binding protein-like 11 OSBPLI l NM_022776 -0.8705 0.504 0.1602 -0.1019 interferon, alpha-inducible protein (clone IFI-

205483_s_at G1P2 NMjxmoi -0.8584 0.497 -0.9014 0.5736 15K)

ON

212185_x_at metallothionein 2A MT2A NM_005953 -0.8549 0.4949 -0.3994 0.2542

225415_at deltex 3 -like (Drosophila) DTX3L AA577672 -0.8402 0.4864 -0.459 0.2921 interferon-induced protein with tetratricopeptide repeats 1 /// interferon-

203153_at IFITl NMJ)01548 -0.8098 0.4689 -0.8238 0.5242 induced protein with tetratricopeptide repeats

1 1

20241 l_at interferon, alpha-inducible protein 27 IFI27 NM_005532 -0.8035 0.4652 -0.9187 0.5846

201470_at glutathione S-transferase omega 1 GSTOl NM_004832 -0.8007 0.4636 -0.1832 0.1166

206026_s_at tumor necrosis factor, alpha-induced protein 6 TNFAIP6 NM_007115 -0.7918 0.4584 -0.255 0.1623

214453_s_at interferon-induced protein 44 IFI44 NM_006417 -0.784 0.4539 -0.9491 0.604

218085_at chromatin modifying protein 5 CHMP5 NM_015961 -0.7822 0.4529 -0.3927 0.2499

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ϊD Gene Name Symbol Ace, No. SLE score group group score score score interferon-induced protein with

229450_at IFIT3 AI075407 -0.7815 0.4525 -0.7178 0.4568 tetratricopeptide repeats 3

78383_at Topoisomerase I binding, arginine/serine-rich TOPORS AI150117 -0.78 0.4516 0.0836 -0.0532

4-

226603_at chromosome 7 open reading frame 6 C7orf6 BE966604 -0.7795 0.4513 -0.6931 0.4411

226702_at hypothetical protein LOC 129607 LOC129607 AI742057 -0.7776 0.4502 -0.9359 0.5956

206025_s_at tumor necrosis factor, alpha-induced protein 6 TNFAIP6 AWl 88198 -0.7748 0.4486 -0.262 0.1667 tumor necrosis factor (ligand) superfamily,

202687_s_at member 10 /// tumor necrosis factor (ligand) TNFSFlO U57059 -0.7662 0.4436 -0.3212 0.2044 superfamily, member 10

Tumor necrosis factor (ligand) superfamily,

214329_x_at member 10 /// Tumor necrosis factor (ligand) TNFSFlO AW474434 -0.7604 0.4402 -0.38 0.2418 superfamily, member 10

222986_s_at scotin SCOTIN BC001463 -0.7595 0.4397 0.0283 -0.018

204415_at interferon, alpha-inducible protein (clone IFI- G1P3 NM_022873 -0.7584 0.4391 -0.0599 0.0381

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ^r IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN jtieaitiiy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

6-16) tumor necrosis factor (ligand) superfamily,

223502_s_at TNFSF 13B AF134715 -0.7563 0.4378 -0.323 0.2055 member 13b interferon-induced protein with

204747_at IFIT3 NMJ)Ol 549 -0.751 0.4348 -0.7699 0.4899 tetratricopeptide repeats 3

20858 l_x_at metallothionein IX MTlX NM_005952 -0.7505 0.4345 -0.3343 0.2127

228152_s_at hypothetical protein FLJ31033 FLJ31033 AK023743 -0.747 0.4325 -0.3443 0.2191

208966_x_at interferon, gamma-inducible protein 16 IFIl 6 AF208043 -0.7468 0.4323 -0.3534 0.2249

202837_at FLN29 gene product FLN29 NM_006700 -0.7461 0.4319 -0.2178 0.1386

235276_at Epithelial stromal interaction 1 (breast) EPSTIl AA781795 -0.7456 0.4317 -0.7704 0.4903

214453_s_at interferon-induced protein 44 IFI44 NM_006417 -0.7406 0.4288 -1.0111 0.6434 solute carrier family 23 (nucleobase

209236_at SLC23A2 AL389886 -0.7386 0.4276 0.0167 -0.0106 transporters), member 2

Table 13; List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the k«v IFN group vs. the high

IFN group >. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. IMo. SLE score group group score score score serine (or cysteine) proteinase inhibitor, clade

200986_at G (Cl inhibitor), member 1, (angioedema, SERPINGl NM_000062 -0.7381 0.4273 -0.6162 0.3921 hereditary)

4_

204439_at interferon-induced protein 44-like IFI44L NM_006820 -0.7348 0.4254 -1.4373 0.9147

235276_at Epithelial stromal interaction 1 (breast) EPSTIl AA781795 -0.7342 0.4251 -0.8115 0.5164 tumor necrosis factor (ligand) superfamily,

223502_s_at TNFSF13B AF134715 -0.7309 0.4231 -0.3263 0.2076 member 13b

204439_at interferon-induced protein 44-like IFI44L NM_006820 -0.7297 0.4224 -0.9813 0.6245

N-ethylmaleimide-sensitive factor attachment

20875 l_at NAPA BCOOl 165 -0.729 0.4221 0.0624 -0.0397 protein, alpha

213294_at Hypothetical protein FLJ38348 FLJ38348 AV755522 -0.7286 0.4218 -0.5528 0.3518 peroxisomal proliferator-activated receptor A

228230_at PRIC285 AL121829 -0.7255 0.42 -0.4661 0.2966 interacting complex 285

224957_at cDNA sequence BC022357 BC022357 AL572206 -0.7251 0.4198 -0.0395 0.0251

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lovs ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score „ similar to Interferon-induced transmembrane

216565_x_at LOC391020 ALl 21994 -0.7153 0.4141 -0.2301 0.1464 protein 3 (Interferon-inducible protein 1-8U) eukaryotic translation initiation factor 2-alpha

20421 l_x_at EIF2AK2 NM_002759 -0.7039 0.4075 -0.5452 0.347 kinase 2

239979_at Epithelial stromal interaction 1 (breast) EPSTIl BE645480 -0.7015 0.4061 -0.7884 0.5017

223577_x_at PRO 1073 protein PRO1073 AA827878 -0.7 0.4053 -0.181 0.1152 interferon-induced protein with

229450_at IFIT3 AI075407 -0.6984 0.4043 -0.7166 0.456 tetratricopeptide repeats 3

202343_x_at cytochrome c oxidase subunit Vb COX5B NMJ)01862 -0.6968 0.4034 -0.1134 0.0722 radical S-adenosyl methionine domain

213797_at RSAD2 AI337069 -0.6945 0.4021 -1.1284 0.7181 containing 2

235276_at Epithelial stromal interaction 1 (breast) EPSTIl AA781795 -0.6919 0.4006 -0.7842 0.499

202430_s_at phospholipid scramblase 1 PLSCRl NM_021105 -0.692 0.4006 -0.503 0.3201

208855_s_at serine/threonine kinase 24 (STE20 homolog, STK24 AF083420 -0.6882 0.3985 -0.0585 0.0372

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ' IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

AffylD Gene Name Symbol Ace. No. SLE score group group score score score yeast)

225919_s_at chromosome 9 open reading frame 72 C9orf72 AI832598 -0.6863 0.3973 -0.0935 0.0595 radical S-adenosyl methionine domain

242625_at RSAD2 AWl 89843 -0.6852 0.3967 -1.1837 0.7533 containing 2 dehydrogenase/reductase (SDR family)

219799_s_at DHRS9 NM_005771 -0.6815 0.3945 -0.2696 0.1715 member 9 radical S-adenosyl methionine domain

213797_at RSAD2 AI337069 -0.6808 0.3942 -1.0289 0.6548 containing 2

233425_at zinc finger, CCHC domain containing 2 ZCCHC2 AU147903 -0.6791 0.3932 -0.8697 0.5534

20241 l_at interferon, alpha-inducible protein 27 IFI27 NM_005532 -0.678 0.3925 -0.8661 0.5511

211012_s_at promyelocytic leukemia PML BC000080 -0.6774 0.3922 -0.356 0.2265

Poly (ADP-ribose) polymerase family,

227807_at PARP9 AI738416 -0.6684 0.3869 -0.2206 0.1404 member 9

239979_at Epithelial stromal interaction 1 (breast) EPSTIl BE645480 -0.6681 0.3868 -1.0319 0.6567

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ? IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol _ Ace, No. SLE score group group score score score

221827_at chromosome 20 open reading frame 18 C20orfl8 BE788439 -0.6673 0.3864 -0.3455 0.2198

219356_s_at chromatin modifying protein 5 CHMP5 NM_016410 -0.6654 0.3852 -0.3687 0.2346

DEAD (Asp-Glu-Ala-Asp) box polypeptide

242961_x_at DDX58 AI304317 -0.6603 0.3823 -0.0821 0.0522 58 eukaryotic translation initiation factor 2-alpha

20421 l_x_at EIF2AK2 NM_002759 -0.6604 0.3823 -0.4852 0.3088 kinase 2 tumor necrosis factor (ligand) superfamily,

223501_at TNFSF 13B AWl 51360 -0.6573 0.3806 -0.4563 0.2904 member 13b myxovirus (influenza virus) resistance 2

204994_at MX2 NM_002463 -0.6569 0.3803 -0.3939 0.2507 (mouse) guanine nucleotide binding protein (G

207157_s_at GNG5 NM_005274 -0.6426 0.372 -0.1859 0.1183 protein), gamma 5 interferon-induced protein with

226757_at IFIT2 AA131041 -0.6418 0.3716 -0.6274 0.3993 tetratricopeptide repeats 2

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ¹1FN group vs. the high

IFN grout. >. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

205098_at chemokine (C-C motif) receptor 1 CCRl AI421071 -0.6407 0.3709 -0.5611 0.3571

SCO cytochrome oxidase deficient homolog 2

205241_at SCO2 NM_005138 -0.6367 0.3686 -0.3668 0.2334 (yeast)

226941_at Activating transcription factor 6 ATF6 BF439325 -0.6346 0.3674 -0.2223 0.1415

232645_at hypothetical protein LOC153684 LOC153684 AW665885 -0.6297 0.3646 -0.0224 0.0143

Signal transducer and activator of

232375_at STATl AI539443 -0.6282 0.3637 -0.2377 0.1513 transcription 1, 9IkDa

225415_at deltex 3 -like (Drosophila) DTX3L AA577672 -0.6258 0.3623 -0.3625 0.2307 interferon-induced protein with tetratricopeptide repeats 1 /// interferon-

203153_at IFITl NM_pO1548 -0.6243 0.3614 -0.8062 0.513 induced protein with tetratricopeptide repeats

1 1

221345_at G protein-coupled receptor 43 GPR43 NM_005306 -0.6232 0.3608 -0.2163 0.1376

212185_x_at metallothionein 2 A MT2A NM_005953 -0.6198 0.3588 0.0888 -0.0565

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the km IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ϊD Gene Name Symbol Ace. No. SLE score group group score score score

218400_at 2 -5 -oligoadenylate synthetase 3, 10OkDa OAS3 NM_006187 -0.6171 0.3573 -0.8285 0.5273 interferon, alpha-inducible protein (clone IFI-

205483_j5_at G1P2 NM_005101 -0.6161 0.3567 -0.9313 0.5927 15K)

4- caspase 1, apoptosis-related cysteine protease

211367_s_at CASPl U13699 -0.6135 0.3552 -0.4356 0.2772 (interleukin 1, beta, convertase)

Transcribed locus, moderately similar to

235220_at XP_517655.1 similar to KIAA0825 protein — BG168199 -0.6124 0.3546 -0.3387 0.2155

[Pan troglodytes]

218618_s_at fibronectin type III domain containing 3 B FNDC3B NM_022763 -0.6114 0.354 -0.1889 0.1202

Likely ortholog of mouse acyl-Coenzyme A

239277_at ACATE2 AI559696 -0.6068 0.3513 -0.4803 0.3056 thioesterase 2, mitochondrial

224957_at cDNA sequence BC022357 BC022357 AL572206 -0.606 0.3509 -0.1159 0.0738

202145_at lymphocyte antigen 6 complex, locus E LY6E NM_002346 -0.6047 0.3501 -1.009 0.6421

22470 l_at poly (ADP-ribose) polymerase family, PARP14 AA056548 -0.596 0.3451 -0.5456 0.3472

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy arid the kro ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes. <•

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score member 14

222986_s_at scotin SCOTIN BC001463 -0.5955 0.3448 -0.3965 0.2523

219209_at interferon induced with helicase C domain 1 IFIHl NM_022168 -0.5952 0.3446 -0.7018 0.4466

Ul 227458_at CD274 antigen PDCDlLGl AI608902 -0.5951 0.3445 -0.5119 0.3258

228050_at Src-associated protein SAW FLJl 2787 AA046406 -0.5941 0.344 -0.2897 0.1844

219352_at hect domain and RLD 6 HERC6 NMJU7912 -0.593 0.3433 -0.6414 0.4082

202863__at nuclear antigen SpIOO SPlOO NMJ)03113 -0.5927 0.3431 -0.3765 0.2396

214059_at Interferon-induced protein 44 IFI44 BE049439 -0.5918 0.3426 -0.0172 0.011 interferon-induced protein with

203595_s_at IFIT5 N47725 -0.5873 0.34 -0.7444 0.4737 tetratricopeptide repeats 5

210797_s_at 2 -5 '-oligoadenylate synthetase-like OASL AF063612 -0.5868 0.3397 -0.6916 0.4401

213350_at Ribosomal protein SI l RPSIl BF680255 -0.5864 0.3395 -0.3412 0.2171

204225_at histone deacetylase 4 HDAC4 NM_006037 -0.5851 0.3387 -0.2898 0.1844

221943_x_at Ribosomal protein L38 RPL38 AW303136 -0.5851 0.3387 -0.4185 0.2663

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

202008_s_at nidogen (enactin) NID NM_002S08 -0.5847 0.3385 -0.1285 0.0817

220492_s_at otoferlin OTOF NM_004802 -0.5843 0.3383 -0.0177 0.0112

218773_s_at methionine sulfoxide reductase B2 MSRB2 NM_012228 -0.5825 0.3372 -0.1194 0.076

Os 217933_s_at leucine aminopeptidase 3 LAP3 NM_015907 -0.5811 0.3364 -0.6709 0.4269

219863_at hect domain and RLD 5 HERC5 NM_016323 -0.5784 0.3349 -0.9824 0.6252

205552_s_at 2',5 -oligoadenylate synthetase 1, 40/46kDa OASl NM_002534 -0.5779 0.3346 -0.8845 0.5628

223062_s_at phosphoserine aminotransferase 1 PSATl BC004863 -0.577 0.3341 -0.5011 0.3189

230179_at hypothetical protein LOC285812 LOC285812 N52572 -0.5756 0.3332 -0.4227 0.269

225076_s_at KIAAl 404 protein KIAA1404 AAl 50460 -0.5746 0.3327 -0.2216 0.141

Transcribed locus, weakly similar to

240165_at XP_209041.2 KIAAl 503 protein [Homo — AI678013 -0.5743 0.3325 -0.4119 0.2621 sapiens]

21921 l_at ubiquitin specific protease 18 USP 18 NM_017414 -0.5744 0.3325 -1.0738 0.6833

213199_at DKFZP586P0123 protein DKFZP586P01 AL080220 -0.5728 0.3316 -0.4504 0.2866

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low IFN group vs. the high

BFN group. The 659 probes correspond to 297 genes.

low IFN high IFN jcieaitiiy

Affy BD Gene Name Symbol Ace. Ko. SLE score group score score score

23

218400_at 2 -5 -oligoadenylate synthetase 3, 10OkDa OAS3 NM_006187 -0.5724 0.3314 -0.9572 0.6091

223298_s_at 5 -nucleotidase, cytosolic III NT5C3 AF312735 -0.5717 0.331 -0.2299 0.1463

Ul -4 228570_at BTB (POZ) domain containing 11 BTBDIl BF510581 -0.5718 0.331 0.1547 -0.0984

223062_s_at phosphoserine aminotransferase 1 PSATl BC004863 -0.5718 0.331 -0.3949 0.2513

232563_at zinc finger protein 684 ZNF684 AW275016 -0.5718 0.331 -0.5135 0.3268

227354_at FLJ37858 protein FLJ37858 BF589359 -0.5706 0.3303 -0.1473 0.0937

Nance-Horan syndrome (congenital cataracts

228933_at NHS BF111819 -0.5697 0.3298 -0.4038 0.257 and dental anomalies)

219559_at chromosome 20 open reading frame 59 C20orf59 NM_022082 -0.5694 0.3296 -0.2289 0.1456

212285_s_at agrin AGRN AW008051 -0.568 0.3289 -0.6139 0.3907

231956_at KIAA1618 KIAA1618 AA976354 -0.5681 0.3289 -0.6082 0.387

Fc fragment of IgG, high affinity Ia, receptor

214511_x_at FCGRlA L03419 -0.5669 0.3282 -0.1567 0.0997 (CD64)

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low IFN group vs. the high IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

AffyID Gene Name Symbol Ace. No. SLE score group group score score score

223577_x_at PRO 1073 protein PRO 1073 AA827878 -0.5662 0.3278 -0.2247 0.143

233425_at zinc finger, CCHC domain containing 2 ZCCHC2 AU147903 -0.5661 0.3277 -0.663 0.4219

212531_at lipocalin 2 (oncogene 24p3) LCN2 NM_005564 -0.5647 0.3269 -0.4259 0.271 poly (ADP-ribose) polymerase family,

223220_s_at PARP9 AF307338 -0.5642 0.3266 -0.4421 0.2814 member 9

204170_s_at CDC28 protein kinase regulatory subunit 2 CKS2 NMJ)01827 -0.564 0.3265 -0.4924 0.3134

44673_at sialoadhesin SN N53555 -0.5633 0.3261 -1.0109 0.6433

78383_at Topoisomerase I binding, arginine/serine-rich TOPORS AI150117 -0.5626 0.3257 -0.355 0.2259

Metastasis associated lung adenocarcinoma

228582_x_at MALATl AI475544 -0.5615 0.3251 -0.28 0.1782 transcript 1 (non-coding RNA) 209546_s_at apolipoprotein L, 1 APOLl AF323540 -0.5598 0.3241 -0.4161 0.2648

MCM4 minichromosome maintenance 222036_s_at MCM4 AI859865 -0.5596 0.324 -0.4585 0.2918 deficient 4 (S. cerevisiae) 222532 at signal recognition particle receptor, B subunit SRPRB BF983948 -0.5595 0.3239 -0.1972 0.1255

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

201649_at ubiquitin-conjugating enzyme E2L 6 UBE2L6 NM_004223 -0.5593 0.3238 -0.3627 0.2308

22529 l_at polyribonucleotide nucleotidyltransferase 1 PNPTl AI967971 -0.5574 0.3227 -0.57 0.3627

213524_s_at putative lymphocyte G0/G1 switch gene G0S2 NM_015714 -0.5568 0.3223 -0.4215 0.2683

Ul

<o 230354_at Transcribed locus — BG236273 -0.5561 0.3219 -0.3847 0.2448

Transcribed locus, weakly similar to

241368_at NP_003148.1 NIMA (never in mitosis gene — All 90693 -0.556 0.3219 0.0465 -0.0296 a)-related kinase 4 [Homo sapiens]

Poly (ADP-ribose) polymerase family,

235157_at PARP 14 AW297731 -0.5547 0.3212 -0.8667 0.5515 member 14

224589_at — — BF223193 -0.5531 0.3202 -0.4285 0.2727

226702_at hypothetical protein LOC 129607 LOC 129607 AI742057 -0.5532 0.3202 -0.9896 0.6297

208966_x_at interferon, gamma-inducible protein 16 IFI16 AF208043 -0.5521 0.3196 -0.3623 0.2306

202595_s_at leptin receptor overlapping transcript-like 1 LEPROTLl AF161461 -0.5496 0.3182 -0.472 0.3003

223952_x_at dehydrogenase/reductase (SDR family) DHRS9 AF240698 -0.5494 0.3181 -0.3798 0.2417

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ϊD Gene Name Symbol Ace. Ko. SLE score group group score score score member 9 -

MCM4 minichromosome maintenance

222036_s_at MCM4 AI859865 -0.5495 0.3181 -0.0903 0.0575

Os deficient 4 (S. cerevisiae) O\

O serine/threonine kinase 24 (STE20 homolog,

208855_s_at STK24 AF083420 -0.5495 0.3181 0.0169 -0.0107 yeast)

MCM6 minichromosome maintenance

201930_at deficient 6 (MIS5 homolog, S. pombe) (S. MCM6 NM_005915 -0.5492 0.318 -0.4464 0.2841 cerevisiae)

218618_s_at fibronectin type III domain containing 3B FNDC3B NM_022763 -0.549 0.3178 -0.3711 0.2362

219356_s_at chromatin modifying protein 5 CHMP5 NM_016410 -0.5476 0.317 -0.5562 0.354

237544_at Transcribed locus — BF508786 -0.547 0.3167 -0.4772 0.3037

212356_at KIAA0323 KIAA0323 AB002321 -0.5465 0.3164 -0.0164 0.0104

MCM6 minichromosome maintenance

201930_at MCM6 NM_005915 -0.5447 0.3154 -0.4378 0.2786 deficient 6 (MIS5 homolog, S. pombe) (S.

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ^r IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN Mgh IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score cerevisiae)

240718_at Cancer susceptibility candidate 1 CASCl AW303384 -0.5441 0.315 -0.4522 0.2878

235175_at guanylate binding protein 4 GBP4 BG260886 -0.5437 0.3148 -0.1063 0.0676

YDD 19 protein /// chromosome 6 open YDD 19 ///

215207_x_at reading frame 68 /// similar to hypothetical C6orf68 /// BF695847 -0.543 0.3144 -0.4448 0.2831 protein, MGC:7199 LOC440128

210797_s_at 2 -5 -oligoadenylate synthetase-like OASL AF063612 -0.5414 0.3135 -0.9108 0.5796

219684_at 28kD interferon responsive protein IFRG28 NM_022147 -0.5403 0.3128 -0.8232 0.5238

218915_at neurofibromin 2 (bilateral acoustic neuroma) NF2 NM_016418 -0.5399 0.3126 -0.4305 0.274

244398_x_at zinc finger protein 684 ZNF684 BE328243 -0.5372 0.311 -0.5321 0.3386

SCO cytochrome oxidase deficient homolog 2

205241_at SC02 NM_005138 -0.5369 0.3109 -0.3725 0.237 (yeast)

235276_at Epithelial stromal interaction 1 (breast) EPSTIl AA781795 -0.5365 0.3106 -0.6529 0.4155

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low < IFN group vs. the high

IFN gi'ouf ). The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

230314_at Similar to hypothetical protein 628 — AW014557 -0.5365 0.3106 -0.5232 0.333

201649_at ubiquitin-conjugating enzyme E2L 6 UBE2L6 NM_004223 -0.5359 0.3103 -0.4191 0.2667

48117_at hypothetical protein BCOl 1981 LOCI 12869 AAl 60496 -0.5357 0.3101 -0.4525 0.2879

230314_at Similar to hypothetical protein 628 — AW014557 -0.5357 0.3101 -1.0033 0.6385

218400_at 2 -5'-oligoadenylate synthetase 3, 10OkDa OAS3 NM_006187 -0.5353 0.3099 -1.1506 0.7322

225076_s_at KIAAl 404 protein KIAA1404 AAl 50460 -0.5351 0.3098 -0.1802 0.1147

241916_at Phospholipid scramblase 1 PLSCRl AI984040 -0.5347 0.3096 -0.7703 0.4902

241016_at Cullin 3 CUL3 AI017888 -0.5328 0.3085 -0.4724 0.3006

Solute carrier family 4 (anion exchanger),

242030_at SLC4A1AP AI934909 -0.5319 0.308 -0.1395 0.0888 member 1, adaptor protein

228151_at Transcribed locus — BF970431 -0.5319 0.3079 -0.4747 0.3021

201641_at bone marrow stromal cell antigen 2 BST2 NM_004335 -0.5314 0.3076 -0.5593 0.3559

219209_at interferon induced with helicase C domain 1 IFIHl NM_022168 -0.5305 0.3071 -0.6925 0.4407

230354_at Transcribed locus — BG236273 -0.5302 0.3069 -0.3427 0.2181

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lo% ¹ IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group ~ score score score

218872_at hypothetical protein FLJ20607 TSC NMJ) 17899 -0.5299 0.3068 0.1437 -0.0915

203243_s_at PDZ and LIM domain 5 PDLIM5 NM__006457 -0.53 0.3068 -0.1515 0.0964

ON myxovirus (influenza virus) resistance 2

204994_at MX2 NMJ⁾02463 -0.5297 0.3067 0.0073 -0.0047 (mouse)

234986_at Glutamate-cysteine ligase, modifier subunit GCLM AA630626 -0.5296 0.3066 -0.3822 0.2432 membrane-spanning 4-domains, subfamily A,

224358_s_at member 7 /// membrane-spanning 4-domains, MS4A7 AF237916 -0.5278 0.3055 -0.4836 0.3077 subfamily A, member 7 interferon, alpha-inducible protein (clone IFI-

204415_at G1P3 NM_022873 -0.5273 0.3053 -1.0987 0.6992 6-16)

23533 l_x_at polycomb group ring finger 5 PCGF5 AI341142 -0.5272 0.3052 -0.4676 0.2976 -

230645_at FERM domain containing 3 FRMD3 BFl 10588 -0.5267 0.3049 -0.14 0.0891

DEAD (Asp-Glu-Ala-Asp) box polypeptide

218943_s_at DDX58 NM_014314 -0.5264 0.3048 -0.582 0.3704 58

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ^r IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

242446_at chromosome 6 open reading frame 163 C6orfl63 AI033106 -0.5256 0.3043 -0.4608 0.2932 peroxisomal proliferator-activated receptor A

228230_at PRIC285 AL121829 -0.5249 0.3039 -0.5806 0.3695 interacting complex 285

33850_at microtubule-associated protein 4 MAP4 W28892 -0.5248 0.3038 -0.4072 0.2592

216246_at Ribosomal protein S20 RPS20 AFl 13008 -0.5248 0.3038 0.0307 -0.0195

235106_at mastermind-like 2 (Drosophila) MAML2 AW847318 -0.5235 0.3031 -0.4755 0.3026

209684_at Ras and Rab interactor 2 RIN2 ALl 36924 -0.5233 0.303 -0.5062 0.3221

222154_s_at DNA polymerase-transactivated protein 6 DNAPTP6 AK002064 -0.5232 0.3029 -0.5788 0.3683

238739_at Transcribed locus — AW902062 -0.5229 0.3027 -0.3886 0.2473

222816_s_at zinc finger, CCHC domain containing 2 ZCCHC2 BE676543 -0.5223 0.3024 -0.5538 0.3524

202028_s_at ribosomal protein L38 RPL38 BC000603 -0.5217 0.3021 -0.4832 0.3075

219426_at eukaryotic translation initiation factor 2C, 3 EIF2C3 NM_024852 -0.5217 0.3021 -0.4482 0.2852 membrane-spanning 4-domains, subfamily A,

224358_s_at MS4A7 AF237916 -0.5215 0.3019 -0.4998 0.3181 member 7 /// membrane-spanning 4-domains,

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the km ^r IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score subfamily A, member 7

243271_at Chromosome 7 open reading frame 6 C7orf6 AI064690 -0.5208 0.3015 -0.5667 0.3606

ON 238743_at Hypothetical protein FLJ38348 FLJ38348 BG251692 -0.5207 0.3015 -0.4359 0.2774

Ui

DEAD (Asp-Glu-Ala-Asp) box polypeptide

218943_s_at DDX58 NM_014314 -0.5206 0.3014 -0.4341 0.2762 58 solute carrier family 23 (nucleobase

209236_at SLC23A2 AL389886 -0.5206 0.3014 -0.4802 0.3056 transporters), member 2

232666_at 2-5 -oligoadenylate synthetase 3, 10OkDa OAS3 R13458 -0.52 0.301 -0.061 0.0388

213293_s_at tripartite motif-containing 22 TRIM22 AA083478 -0.5185 0.3002 -0.5672 0.3609

222154_s_at DNA polymerase-transactivated protein 6 DNAPTP6 AK002064 -0.5177 0.2997 -1.0887 0.6928

201545_s_at poly(A) binding protein, nuclear 1 PABPNl NM_004643 -0.517 0.2993 -0.1674 0.1065 guanylate binding protein 2, interferon-

242907_at GBP2 BF509371 -0.5166 0.2991 -0.4255 0.2708 inducible

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the krø ^r IEN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

228151_at Transcribed locus — BF970431 -0.5166 0.2991 -0.4011 0.2552

222986_s_at scotin SCOTIN BC001463 -0.5164 0.2989 -0.3278 0.2086 caspase 1, apoptosis-related cysteine protease

211367_s_at CASPl U13699 -0.5161 0.2988 -0.4477 0.2849 (interleukin 1, beta, convertase)

202595_s_at leptin receptor overlapping transcript-like 1 LEPROTLl AF161461 -0.5156 0.2985 -0.2161 0.1375

DEAD (Asp-Glu-Ala-Asp) box polypeptide

218943_s_at DDX58 NMJU4314 -0.5153 0.2983 -0.4631 0.2947 58

233591_at CDNA: FLJ23098 fis, clone LNG07440 — AK026751 -0.515 0.2982 -0.4556 0.2899

204225_at histone deacetylase 4 HDAC4 NM_006037 -0.5144 0.2978 -0.2752 0.1751

215221_at Forkheadbox Pl FOXPl AK025064 -0.5142 0.2977 -0.3321 0.2113

202010_s_at zinc finger protein 410 ZNF410 NM_021188 -0.5141 0.2976 -0.4983 0.3171

219559_at chromosome 20 open reading frame 59 C20orf59 NM_022082 -0.5139 0.2975 -0.4112 0.2616

Transcribed locus, moderately similar to

235220_at — BG168199 -0.5125 0.2967 -0.4542 0.289 XP_517655.1 similar to KIAA0825 protein

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lo% ^r IFN group vs. the high

EFN grout. ). The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Afly ED Gene Name Symbol Ace, No. SLE score group group score score score

[Pan troglodytes]

209684_at Ras and Rab interactor 2 RIN2 AL136924 -0.5108 0.2957 -0.5028 0.3199

202869_at 2',5'-oligoadenylate synthetase 1, 40/46kDa OASl NM_016816 -0.5107 0.2956 -0.9604 0.6112

-4 peroxisomal proliferator-activated receptor A

228230_at PRIC285 AL121829 -0.5089 0.2946 -0.4983 0.3171 interacting complex 285 guanylate binding protein 1, interferon-

202270_at inducible, 67kDa /// guanylate binding protein GBPl NM_002053 -0.5083 0.2943 -0.542 0.3449

1, interferon-inducible, 67kDa

212356_at KIAA0323 KIAA0323 AB002321 -0.5082 0.2942 -0.4297 0.2734

215221_at Forkheadbox Pl FOXPl AK025064 -0.5078 0.294 -0.4586 0.2919

202636_at ring finger protein 103 RNF103 NM_005667 -0.5077 0.2939 -0.4071 0.259

212657_s_at interleukin 1 receptor antagonist ILlRN U65590 -0.5074 0.2938 -0.3295 0.2097

203091_at far upstream element (FUSE) binding protein FUBPl NM_003902 -0.5074 0.2937 -0.2572 0.1637

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the krø ^r IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes. -

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

1

226941_at Activating transcription factor 6 ATF6 BF439325 -0.5064 0.2932 -0.4555 0.2899

33850_at microtubule-associated protein 4 MAP4 W28892 -0.5065 0.2932 -0.392 0.2494 oe 202863_at nuclear antigen SpIOO SPlOO NM_003113 -0.5063 0.2931 -0.4572 0.291 nm_014143 PDCDlLGl PDCDlLGl nm_014143 -0.5063 0.2931 -0.039 0.0248

227347_x_at hairy and enhancer of split 4 (Drosophila) HES4 NM_021170 -0.5053 0.2926 -0.5448 0.3467

232222_at chromosome 18 open reading frame 49 C18orf49 AK000229 -0.5045 0.2921 -0.4824 0.307

235643_at chromosome 7 open reading frame 6 C7orf6 BE886225 -0.5043 0.292 -0.7368 0.4689

Homo sapiens, clone IMAGE:5261213,

228315_at — AI632728 -0.5042 0.2919 -0.4722 0.3005 mRNA

218986_s_at hypothetical protein FLJ20035 FLJ20035 NM_017631 -0.5043 0.2919 -1.0228 0.6509

220019_s_at zinc finger protein 224 ZNF224 NM_005774 -0.5031 0.2912 -0.4884 0.3108

226603_at chromosome 7 open reading frame 6 C7orf6 BE966604 -0.5007 0.2899 -0.6608 0.4205

201202_at proliferating cell nuclear antigen PCNA NM_002592 -0.5002 0.2896 -0.4078 0.2595

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low IFN group vs. the high BFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

205569_at lysosomal-associated membrane protein 3 LAMP3 NM_014398 -0.4999 0.2894 -0.5254 0.3344

232563_at zinc finger protein 684 ZNF684 AW275016 -0.4998 0.2894 -0.4666 0.2969

205099_s_at chemokine (C-C motif) receptor 1 CCRl NMJ)01295 -0.4974 0.288 -0.5734 0.3649

ON

223298_s_at 5 -nucleotidase, cytosolic III NT5C3 AF312735 -0.497 0.2878 -0.3114 0.1981

210312_s_at intraflagellar transport protein IFT20 IFT20 BC002640 -0.4971 0.2878 -0.4439 0.2825

225919_s_at chromosome 9 open reading frame 72 C9orf72 AI832598 -0.496 0.2872 -0.0697 0.0443

203713_s_at lethal giant larvae homolog 2 (Drosophila) LLGL2 NM__004524 -0.4954 0.2868 -0.1498 0.0953

219352_at hect domain and RLD 6 HERC6 NM_017912 -0.4947 0.2864 -0.7943 0.5054

206075_s_at casein kinase 2, alpha 1 polypeptide CSNK2A1 NM__001895 -0.4943 0.2862 -0.0804 0.0512

202446_s_at phospholipid scramblase 1 PLSCRl AI825926 -0.4944 0.2862 -0.5523 0.3514

223414_s_at hypothetical protein FLJ20425 LYAR ALl 36750 -0.4939 0.286 -0.5189 0.3302 transporter 1 , ATP-binding cassette, sub- 202307 s at TAPl NM_000593 -0.4929 0.2854 -0.3272 0.2082

^{~ ~} family B (MDR/TAP)

204615_x_at isopentenyl-diphosphate delta isomerase IDIl NM 004508 -0.4929 0.2853 -0.3952 0.2515

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lo% r IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

202446_s_at phospholipid scramblase 1 PLSCRl AI825926 -0.4926 0.2852 -0.5449 0.3468

ATPase, H+ transporting, lysosomal 42kDa,

202872_at ATP6V1C1 AW024925 -0.4907 0.2841 -0.0117 0.0074 Vl subunit C, isoform 1

-4

O guanylate binding protein 2, interferon-

242907_at GBP2 BF509371 -0.4902 0.2838 -0.3055 0.1944 inducible

220492_s_at otoferlin OTOF NM_004802 -0.4892 0.2832 -0.5692 0.3622

22529 l_at polyribonucleotide nucleotidyltransferase 1 PNPTl AI967971 -0.4891 0.2832 -0.5774 0.3674 guanylate binding protein 1, interferon-

202270_at inducible, 67kDa /// guanylate binding protein GBPl NM_002053 -0.4885 0.2828 -0.5127 0.3263

1, interferon-inducible, 67kDa

CDNA FLJ12226 fis, clone

215995_x_at — AUl 47598 -0.4878 0.2824 -0.0319 0.0203 MAMMAlOOl 143

CD44 antigen (homing function and Indian

204489_s_at CD44 NM_000610 -0.4871 0.282 -0.1748 0.1112 blood group system)

Table 13: List of the 659 Gene Probes with Corresponding Ceiitroid Scores for Classifying SLE - Healthy and the low IFN group vs. the high IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

202010_s_at zinc finger protein 410 ZNF410 NM_021188 -0.4864 0.2816 -0.1666 0.106

206133_at XIAP associated factor-1 HSXIAPAFl NM_017523 -0.486 0.2814 -1.0225 0.6507

ON 219863_at hect domain and RLD 5 HERC5 NM_016323 -0.4858 0.2813 -0.9398 0.5981 -4

219684_at 28kD interferon responsive protein IFRG28 NM_022147 -0.4853 0.281 -0.6293 0.4005

DKFZP564F05

212333_at DKFZP564F0522 protein AL049943 -0.4851 0.2808 -0.4155 0.2644

22

230036_at chromosome 7 open reading frame 6 C7orf6 BE669858 -0.4848 0.2806 -0.6662 0.4239 201641_at bone marrow stromal cell antigen 2 BST2 NM_004335 -0.4841 0.2803 -0.5741 0.3654

Poly (ADP-ribose) polymerase family,

235157_at PARP14 AW297731 -0.484 0.2802 -0.6805 0.433 member 14 225416_at Ring finger protein 12 RNF12 N58188 -0.4822 0.2792 -0.4884 0.3108

Chromosome 9 open reading frame 10 239391_at C9orflOOS AA195528 -0.4818 0.2789 -0.4318 0.2748 opposite strand 201233 at proteasome (prosome, macropain) 26 S PSMD 13 NM 002817 -0.4806 0.2783 -0.4661 0.2966

Table 13: List of the 659 Gene Probes wifb. Corresponding CentroM Scores for Classifying SLE - Healthy and the kro ^r IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No, „ SLE score group group

^* score score score subunit, non-ATPase, 13

219519_s_at sialoadhesin /// sialoadhesin SN NM_023068 -0.48 0.2779 -0.2982 0.1898

230866_at cysteinyl leukotriene receptor 1 CYSLTRl BE549540 -0.4789 0.2773 -0.4419 0.2812 βs -J κ> 202430_s_at phospholipid scramblase 1 PLSCRl NM_021105 -0.4787 0.2771 -0.5775 0.3675

235574_at guanylate binding protein 4 GBP4 AW392952 -0.4782 0.2768 -0.5294 0.3369

209593_s_at torsin family 1, member B (torsin B) TORlB AF317129 -0.4772 0.2763 -0.3978 0.2531

229625_at Guanylate binding protein 5 GBP5 BG545653 -0.4765 0.2759 -0.3255 0.2072

204860_s_at baculoviral IAP repeat-containing 1 BIRCl AI817801 -0.4762 0.2757 -0.0731 0.0465

242898_at — — AI494047 -0.4754 0.2752 -0.5215 0.3319

205875_s_at three prime repair exonuclease 1 TREXl NM_016381 -0.4745 0.2747 -0.3673 0.2337 programmed cell death 4 (neoplastic

202730_s_at PDCD4 NM_014456 -0.474 0.2744 -0.5141 0.3271 transformation inhibitor)

230179_at hypothetical protein LOC285812 LOC285812 N52572 -0.4731 0.2739 -0.3495 0.2224

20875 l_at N-ethylmaleimide-sensitive factor attachment NAPA BCOOl 165 -0.4719 0.2732 -0.0139 0.0088

Table 13: List of the 659 Gene Probes with Corresponding Centroid Seores for Classifying SLE - Healthy and the lo% ^r IFN group vs. the high

BFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

AffyID Gene Name Symbol Ace, No. SLE score group group score score score protein, alpha proteasome (prosome, macropain) subunit,

202243_s_at PSMB4 NM_002796 -0.472 0.2732 -0.0524 0.0334 beta type, 4

Acyl-CoA synthetase long-chain family

201660_at ACSL3 AL525798 -0.4717 0.2731 -0.4581 0.2915 member 3

225076_s_at KIAA1404 protein KIAA1404 AAl 50460 -0.4711 0.2728 -0.1942 0.1236

235573_at Heat shock 105kDa/l 1OkDa protein 1 HSPHl AL536101 -0.4706 0.2725 -0.4773 0.3037

221827_at chromosome 20 open reading frame 18 C20orfl8 BE788439 -0.4702 0.2722 -0.3412 0.2171

225065_x_at hypothetical protein MGC40157 MGC40157 AI826279 -0.469 0.2715 -0.0123 0.0078

206115_at early growth response 3 EGR3 NM_004430 -0.4683 0.2711 -0.2114 0.1345

228607_at 2 -5 -oligoadenylate synthetase 2, 69/7IkDa OAS2 AI651594 -0.4671 0.2704 -0.2311 0.147

227347_x_at hairy and enhancer of split 4 (Drosophila) HES4 NM_021170 -0.4665 0.2701 -0.4279 0.2723 radical S-adenosyl methionine domain

242625_at RSAD2 AWl 89843 -0.4655 0.2695 -0.5963 0.3795 containing 2

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lo% ' IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

206332_s_at interferon, gamma-inducible protein 16 IFIl 6 NM_005531 -0.4649 0.2692 -0.3371 0.2145

218915_ at neurofibromin 2 (bilateral acoustic neuroma) NF2 NM_016418 -0.4646 0.269 -0.4903 0.312

20482 ljat butyrophilin, subfamily 3, member A3 BTN3A3 NM_006994 -0.4632 0.2682 -0.3222 0.2051

-4

4- 235386_at Hypothetical protein LOC285535 LOC285535 AWl 62768 -0.4628 0.2679 -0.5241 0.3335

DEAD (Asp-Glu-Ala-Asp) box polypeptide

222793_at DDX58 AK023661 -0.4618 0.2674 -0.6291 0.4003 58

219684_at 28kD interferon responsive protein IFRG28 NM_022147 -0.4618 0.2673 -0.7793 0.4959

205003_at dedicator of cytokinesis 4 DOCK4 NMJH4705 -0.4617 0.2673 -0.2767 0.1761

204326_x_at metallothionein IX MTlX NM_002450 -0.4611 0.2669 -0.3016 0.1919

205552_s_at 2',5 -oligoadenylate synthetase 1, 40/46kDa OASl NM_002534 -0.4604 0.2665 -0.6074 0.3865

232222_at chromosome 18 open reading frame 49 C18orf49 AK000229 -0.4603 0.2665 -0.371 0.2361

241916_at Phospholipid scramblase 1 PLSCRl AI984040 -0.4602 0.2664 -0.442 0.2812

232563_at zinc finger protein 684 ZNF684 AW275016 -0.4596 0.2661 -0.3976 0.253

218429_s_at hypothetical protein FLJl 1286 FLJl 1286 NM_018381 -0.4584 0.2654 -0.349 0.2221

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group - score score score

214059_at Interferon-induced protein 44 IFI44 BE049439 -0.4583 0.2653 -0.2716 0.1728 early growth response 2 (Krox-20 homolog,

205249_at EGR2 NM_000399 -0.4568 0.2645 -0.5052 0.3215 Drosophila)

Ul programmed cell death 4 (neoplastic

202730_s_at PDCD4 NM_014456 -0.4567 0.2644 -0.4788 0.3047 transformation inhibitor)

N-acetylneuraminic acid synthase (sialic acid

218189_s_at NANS NM_018946 -0.4562 0.2641 -0.5146 0.3275 synthase)

204698_at interferon stimulated gene 2OkDa ISG20 NM_002201 -0.4559 0.2639 -0.2701 0.1719

242020_s_at Z-DNA binding protein 1 ZBPl AI925506 -0.4549 0.2633 -0.2891 0.184

DEAD (Asp-Glu-Ala-Asp) box polypeptide

218943_s_at DDX58 NM_014314 -0.4545 0.2631 -0.6489 0.4129 58

228617_at XIAP associated factor- 1 HSXIAPAFl AA142842 -0.454 0.2628 -0.8417 0.5356 phorbol- 12-myristate- 13 -acetate-induced

204286_s_at PMAIPl NM_021127 -0.4524 0.2619 -0.4558 0.2901 protein 1

Table 13: List of the 659 Gene Probes with Corresponding Centrøid Scores for Classifying SLE - Healthy and the low IFN group vs. the high IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Afiy ID Gene Name Symbol Ace, ^"No. SLE score group group score score score

204972_at 2 -5 -oligoadenylate synthetase 2, 69/7IkDa OAS2 NM_016817 -0.451 0.2611 -0.9839 0.6261 235106_at mastermind-like 2 (Drosophila) MAML2 AW847318 -0.4506 0.2608 -0.4507 0.2868 dehydrogenase/reductase (SDR family)

219799_s_at DHRS9 NM_005771 -0.4488 0.2598 -0.5079 0.3232 member 9 212657_s_at interleukin 1 receptor antagonist ILlRN U65590 -0.4486 0.2597 -0.3135 0.1995 mitochondrial ribosomal protein SIl /// 211595_s_at MRPSIl AB049944 -0.4485 0.2597 -0.4736 0.3014 mitochondrial ribosomal protein SI l pro-oncosis receptor inducing membrane

211967_at PORIMIN BG538627 -0.4484 0.2596 -0.3479 0.2214 injury gene

NM_014143 PDCDlLGl PDCDlLGl NM_014143 -0.4473 0.2589 -0.3963 0.2522 222816_s_at zinc finger, CCHC domain containing 2 ZCCHC2 BE676543 -0.447 0.2588 -0.5859 0.3728 224835_at hypothetical protein KIAA1434 KIAA1434 ALl 09935 -0.4455 0.2579 0.0352 -0.0224

ATPase, H+ transporting, lysosomal 42kDa,

202874 s at ATP6V1C1 NM 001695 -0.4452 0.2577 -0.3962 0.2521

Vl subunit C, isoform 1

Table 13: List of the 659 Gene Probes with Corresponding Centrøid Scores for Classifying SLE - Healthy and the km ^r IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

- low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

226326_at polycomb group ring ringer 5 PCGF5 AI798098 -0.445 0.2576 -0.5073 0.3228

235256_s_at galactose mutarotase (aldose 1-epimerase) GALM BE788984 -0.4442 0.2572 -0.4146 0.2638

-4 218543_s_at zinc finger CCCH type domain containing 1 ZC3HDC1 NM_022750 -0.4437 0.2569 -0.5997 0.3816

-4

231747_at cysteinyl leukotriene receptor 1 CYSLTRl NM_006639 -0.4436 0.2568 -0.5314 0.3382

202863_at nuclear antigen SpIOO SPlOO NM_003113 -0.4426 0.2562 -0.2786 0.1773

225710_at CDNA FLJ34013 fis, clone FCBBF2002111 — H99792 -0.4424 0.2561 -0.2677 0.1703

242020_s_at Z-DNA binding protein 1 ZBPl AI925506 -0.4424 0.2561 -0.4899 0.3118

210797_s_at 2 -5 '-oligoadenylate synthetase-like OASL AF063612 -0.4409 0.2552 -0.8782 0.5589

202869_at 2 ',5 '-oligoadenylate synthetase 1, 40/46kDa OASl NMJ)16816 -0.4405 0.255 -0.8316 0.5292 interferon-induced protein with

203596_s_at IFIT5 NM_012420 -0.4404 0.2549 -0.5348 0.3403 tetratricopeptide repeats 5 phorbol- 12-myristate- 13-acetate-induced

204285_s_at PMAIPl AI857639 -0.4402 0.2549 -0.4883 0.3107 protein 1

20687 l_at elastase 2, neutrophil ELA2 NMJ)01972 -0.4401 0.2548 -0.3927 0.2499

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low IFN group vs. the high IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

239988_at Hect domain and RLD 6 HERC6 AA708470 -0.4399 0.2547 -0.3896 0.2479 interferon-induced protein with 203596_s_at IFIT5 NM_012420 -0.4394 0.2544 -0.6745 0.4292

ON tetratricopeptide repeats 5 OO 224225_s_at ets variant gene 7 (TEL2 oncogene) ETV7 AF218365 -0.4386 0.2539 -0.5499 0.3499

Nance-Horan syndrome (congenital cataracts 228933_at NHS BF111819 -0.4383 0.2538 -0.493 0.3137 and dental anomalies) succinate dehydrogenase complex, subunit B,

202675_at SDHB NM_003000 -0.4382 0.2537 -0.387 0.2463 iron sulfur (Ip)

232645_at hypothetical protein LOCI 53684 LOCI 53684 AW665885 -0.4381 0.2536 0.0307 -0.0195

232666_at 2 -5 -oligoadenylate synthetase 3, 10OkDa OAS3 R13458 -0.4376 0.2533 -0.2767 0.1761

230036_at chromosome 7 open reading frame 6 C7orf6 BE669858 -0.4374 0.2532 -0.5206 0.3313

202438_x_at iduronate 2-sulfatase (Hunter syndrome) IDS BF346014 -0.4372 0.2531 -0.4341 0.2763

243122_at PARK2 co-regulated PACRG Hl 8468 -0.4371 0.2531 -0.1811 0.1152

209593 s at torsin family 1, member B (torsin B) TORlB AF317129 -0.4372 0.2531 -0.4146 0.2638

Table 13: List of the 659 Gene Probes with Corresponding Ceritroid Scores for Classifying SLE - Healthy and the kro ' IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

» low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. IMo. SLE score group group score score score

241916_at Phospholipid scramblase 1 PLSCRl AI984040 -0.4371 0.253 -0.739 0.4703 succinate dehydrogenase complex, subunit B,

202675_at SDHB NM_003000 -0.4367 0.2528 -0.1027 0.0653

ON iron sulfur (Ip)

218872_at hypothetical protein FLJ20607 TSC NM_017899 -0.4354 0.2521 -0.4883 0.3107

231769_at F-box protein 6 FBX06 AF129536 -0.4353 0.252 -0.6288 0.4002

21921 l_at ubiquitin specific protease 18 USPl 8 NM_017414 -0.4353 0.252 -0.8174 0.5201 dehydrogenase/reductase (SDR family)

223952_x_at DHRS9 AF240698 -0.4351 0.2519 -0.3268 0.2079 member 9 signal transducer and activator of

225636_at STAT2 H98105 -0.4351 0.2519 -0.5636 0.3587 transcription 2, 113kDa peroxisomal proliferator-activated receptor A

232787_at PRIC285 AK023724 -0.4346 0.2516 -0.3397 0.2162 interacting complex 285

204615_x_at isopentenyl-diphosphate delta isomerase IDIl NM_004508 -0.4341 0.2513 -0.4493 0.2859

Table 13: List of the 659 Gene Probes with Corresponding CentroM Scores for Classifying SLE - Healthy and the low IFN group ¥s. the high

EFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score family with sequence similarity 21, member

211068_x_at C /// family with sequence similarity 21, FAM21C BC006456 -0.434 0.2512 -0.0538 0.0342 member C

O

48117_at hypothetical protein BCOl 1981 LOCI 12869 AAl 60496 -0.4309 0.2495 -0.3508 0.2232

TRAF-interacting protein with a forkhead-

226117_at TIFA AA195074 -0.4303 0.2491 -0.364 0.2316 associated domain interferon-induced protein with

203596_s_at IFIT5 NM_012420 -0.4301 0.249 -0.4927 0.3136 tetratricopeptide repeats 5

236285_at Hypothetical protein BC009980 MGC16635 AI631846 -0.4294 0.2486 -0.4342 0.2763 proteasome (prosome, macropain) subunit,

202243_s_at PSMB4 NM_002796 -0.428 0.2478 -0.1383 0.088 beta type, 4

TRAF-interacting protein with a forkhead-

226117_at TIFA AA195074 -0.4278 0.2476 -0.4651 0.296 associated domain

212531_at lipocalin 2 (oncogene 24p3) LCN2 NM_005564 -0.4275 0.2475 -0.2304 0.1466

Table 13: List of the 659 Gene Probes with. Corresponding Centroid Scores for Classifying SLE - Healthy and the km ' IFN group vs. the high

IFN grouj: >. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

Likely ortholog of mouse acyl-Coenzyme A

239277_at ACATE2 AI559696 -0.4272 0.2473 -0.3233 0.2057 tbioesterase 2, mitochondrial

Myristoylated alanine-rich protein kinase C

ON 00 225897_at MARCKS AI709406 -0.4263 0.2468 -0.3241 0.2062 substrate tumor necrosis factor (ligand) superfamily,

223501_at TNFSF 13B AW151360 -0.4263 0.2468 -0.4651 0.296 member 13b

MovlO, Moloney leukemia virus 10, homolog

223849_s_at MOVlO BC002548 -0.4258 0.2465 -0.3791 0.2412 (mouse) myxo virus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) ///

202086_at MXl NMJ302462 -0.425 0.2461 -0.7102 0.452 myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)

223599_at tripartite motif-containing 6 TRIM6 AF220030 -0.424 0.2455 -0.3535 0.2249

202837_at FLN29 gene product FLN29 NM_006700 -0.4238 0.2454 -0.3898 0.248

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ^r IFN group vs. the high

EFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy lD Gene Name Symbol Ace. No. SLE score group group score score score

201202_at proliferating cell nuclear antigen PCNA NM_002592 -0.4225 0.2446 -0.3532 0.2248

215338_s_at natural killer-tumor recognition sequence NKTR AI688640 -0.4212 0.2439 -0.4657 0.2964 translocated promoter region (to activated

20173 l_s_at TPR NM_003292 -0.4212 0.2438 -0.4785 0.3045 κ» MET oncogene) chemokine (C-X-C motif) ligand 1

204470_at (melanoma growth stimulating activity, CXCLl NM_001511 -0.4202 0.2433 -0.0397 0.0252 alpha)

242234_at XIAP associated factor- 1 HSXIAPAFl AI859280 -0.4197 0.243 -0.4483 0.2853 far upstream element (FUSE) binding protein

203091_at FUBPl NM_003902 -0.4193 0.2428 -0.5597 0.3562 1 nm_002046 GAPDH GAPDH nm_002046 -0.4193 0.2428 0.0673 -0.0428 carcinoembryonic antigen-related cell

209498_at CEACAMl X16354 -0.4191 0.2426 -0.5186 0.33 adhesion molecule 1 (biliary glycoprotein)

235256_s_at galactose mutarotase (aldose 1-epimerase) GALM BE788984 -0.4188 0.2424 -0.4477 0.2849

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low r IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

Wiskott-Aldrich syndrome protein interacting

231182_at WASPIP BF446719 -0.4187 0.2424 -0.2794 0.1778 protein

206026_s_at tumor necrosis factor, alpha-induced protein 6 TNFAIP6 NM_007115 -0.4183 0.2422 -0.2915 0.1855

206026_s_at tumor necrosis factor, alpha-induced protein 6 TNFAIP6 NM_007115 -0.4178 0.2419 -0.2665 0.1696

202996_at polymerase (DNA-directed), delta 4 POLD4 NM_021173 -0.4177 0.2418 0.1547 -0.0984

227755_at CDNA clone IMAGE:4077090, partial cds — AA042983 -0.4169 0.2413 -0.1824 0.1161

212916_at PHD finger protein 8 PHF8 AW249934 -0.4167 0.2413 -0.0924 0.0588 poly (ADP-ribose) polymerase family,

223220_s_at PARP9 AF307338 -0.4168 0.2413 -0.568 0.3614 member 9 peptidylglycine alpha-amidating

214620_x_at PAM BF038548 -0.4148 0.2402 -0.0529 0.0337 monooxygenase

223298_s_at 5 -nucleotidase, cytosolic III NT5C3 AF312735 -0.4145 0.24 -0.3215 0.2046

Protein tyrosine phosphatase, non-receptor

241930_x_at PTPNIl AA223204 -0.412 0.2385 -0.3441 0.219 type 11 (Noonan syndrome 1)

Table 13: List of the 659 Gene Probes with Corresponding CentroM Scores for Classifying SLE - Healthy and the lo% ^r IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ED Gene Name Symbol Ace, No. SLE score group group score score score

211965_at zinc finger protein 36, C3H type-like 1 ZFP36L1 BE620915 -0.4106 0.2377 -0.363 0.231

241910_x_at Hypothetical LOC400590 LOC400590 AI610396 -0.4104 0.2376 -0.4741 0.3017 transporter 1, ATP-binding cassette, sub¬

202307_s_at TAPl NM_000593 -0.4103 0.2375 -0.2447 0.1557 family B (MDR/TAP)

Wiskott-Aldrich syndrome protein interacting

231182_at WASPIP BF446719 -0.4095 0.2371 -0.3497 0.2225 protein

202018_s_at lactotransferrin LTF NM_002343 -0.4085 0.2365 -0.2496 0.1588

226702_at hypothetical protein LOCI 29607 LOC129607 AI742057 -0.408 0.2362 -0.3854 0.2453

206553_at 2 -5 -oligoadenylate synthetase 2, 69/7IkDa OAS2 NM_002535 -0.4077 0.236 -0.4816 0.3065 chemokine (C-X-C motif) ligand 1

204470_at (melanoma growth stimulating activity, CXCLl NM_001511 -0.4067 0.2355 -0.2494 0.1587 alpha)

211506_s_at interleukin 8 IL8 AF043337 -0.4067 0.2354 -0.1176 0.0748

211012_s_at promyelocyte leukemia PML BC000080 -0.4059 0.235 -0.572 0.364

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No, SLE score group group score score score

215338_s_at natural killer-tumor recognition sequence NKTR AI688640 -0.4052 0.2346 -0.5168 0.3289

242020_s_at Z-DNA binding protein 1 ZBPl AI925506 -0.4045 0.2342 -0.5481 0.3488

225291_at polyribonucleotide nucleotidyltransferase 1 PNPTl AI967971 -0.4036 0.2337 -0.3701 0.2355

90 Ui DEAD (Asp-Glu-Ala-Asp) box polypeptide

242961_x_at DDX58 AI304317 -0.4027 0.2331 -0.362 0.2303 58

206461_x_at metallothionein IH MTlH NM_005951 -0.4026 0.2331 -0.3327 0.2117

224835_at hypothetical protein KIAAl 434 KIAAl 434 ALl 09935 -0.4024 0.233 -0.0237 0.0151

205569_at lysosomal-associated membrane protein 3 LAMP3 NM_014398 -0.4012 0.2323 -0.2814 0.1791

226702_at hypothetical protein LOC129607 LOC129607 AI742057 -0.4008 0.2321 -0.4217 0.2684

228617_at XIAP associated factor- 1 HSXIAPAFl AA142842 -0.3999 0.2315 -0.9428 0.6 family with sequence similarity 21, member

211068_x_at C /// family with sequence similarity 21, FAM21C BC006456 -0.3995 0.2313 -0.1436 0.0914 member C

235643_at chromosome 7 open reading frame 6 C7orf6 BE886225 -0.3993 0.2312 -0.6216 0.3956

Table 13: List of the 659 Gene Probes with Corresponding Cetrtrøid Scores for Classifying SLE - Healthy and the lov* IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

228152_s_at hypothetical protein FLJ31033 FLJ31033 AK023743 -0.3992 0.2311 -0.4422 0.2814

212380_at KIAA0082 KIAA0082 D43949 -0.3991 0.2311 -0.4902 0.312 upstream binding transcription factor, KNA

ON 00 225982_at UBTF BG341575 -0.399 0.231 -0.4599 0.2926 polymerase I

35156_at hypothetical protein LOC203069 LOC203069 AL050297 -0.3968 0.2297 -0.3422 0.2178

226106_at ring finger protein 141 RNF141 AI307808 -0.3963 0.2294 0.0466 -0.0296

240718_at Cancer susceptibility candidate 1 CASCl AW303384 -0.3955 0.229 -0.474 0.3016

211582_x_at leukocyte specific transcript 1 LSTl AF000424 -0.3955 0.229 0.0954 -0.0607

241916_at Phospholipid scramblase 1 PLSCRl AI984040 -0.3954 0.2289 -0.3711 0.2361 proteasome (prosome, macropain) subunit,

202659_at PSMBlO NM_002801 -0.3954 0.2289 -0.1831 0.1165 beta type, 10

219364_at likely ortholog of mouse Dlllgp2 LGP2 NM_024119 -0.395 0.2287 -0.3415 0.2173 nm_001101 actin, beta ACTB nm_001101 -0.3947 0.2285 0.0625 -0.0398

231182_at Wiskott-Aldrich syndrome protein interacting WASPIP BF446719 -0.3945 0.2284 -0.378 0.2406

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lav, ^r IFN group Λ?S. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ϊD Gene Name Symbol Acc» No, SLE score group group score score score protein

TRAF-interacting protein with a forkhead-

226117_at TIFA AA195074 -0.3943 0.2283 -0.392 0.2495 associated domain

-4 218821_at aminopeptidase-like 1 NPEPLl AL139349 -0.3942 0.2282 -0.1542 0.0981

218986_s_at hypothetical protein FLJ20035 FLJ20035 NM_017631 -0.3937 0.228 -0.7727 0.4917 guanylate binding protein 1, interferon-

231577_s_at GBPl AW014593 -0.3937 0.2279 -0.2978 0.1895 inducible, 67kDa makorin, ring finger protein, 1 /// makorin,

201285_at MKRNl NM_013446 -0.3937 0.2279 0.2148 -0.1367 ring finger protein, 1

240718_at Cancer susceptibility candidate 1 CASCl AW303384 -0.3934 0.2278 -0.1202 0.0765

219691_at sterile alpha motif domain containing 9 SAMD9 NMJ) 17654 -0.3926 0.2273 -0.5612 0.3571

Myristoylated alanine-rich protein kinase C

225897_at MARCKS AI709406 -0.3921 0.227 -0.3269 0.208 substrate

Table 13: List of the 659 Gene Probes with Corresponding Centrøid Scores for Classifying SLE - Healthy and the km ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ϊD Gene Name Symbol Ace. No. SLE score group group score score score myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) ///

202086_at MXl NM_002462 -0.3919 0.2269 -0.4502 0.2865 myxovirus (influenza virus) resistance 1,

ON OC 00 interferon-inducible protein p78 (mouse) peroxisomal proliferator-activated receptor A

232787_at PRIC285 AK023724 -0.3914 0.2266 -0.1064 0.0677 interacting complex 285

213293_s_at tripartite motif-containing 22 TRIM22 AA083478 -0.3912 0.2265 -0.4792 0.3049

235574_at guanylate binding protein 4 GBP4 AW392952 -0.3909 0.2263 -0.2966 0.1887

218304_s_at oxysterol binding protein-like 11 OSBPLI l NM_022776 -0.3906 0.2262 -0.0523 0.0333

202996_at polymerase (DNA-directed), delta 4 POLD4 NM_021173 -0.3904 0.226 -0.0491 0.0312

242234_at XIAP associated factor- 1 HSXIAPAFl AI859280 -0.39 0.2258 -0.818 0.5206

236285_at Hypothetical protein BC009980 MGC16635 AI631846 -0.3899 0.2257 -0.3783 0.2407 translocated promoter region (to activated

201731_s_at TPR NM_003292 -0.3895 0.2255 -0.4513 0.2872 MET oncogene)

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the krø > IFN group vs. the high

EFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

204821_at butyrophilin, subfamily 3, member A3 BTN3A3 NM_006994 -0.3888 0.2251 -0.3683 0.2344 interferon-induced protein with

217502_at IFIT2 BE888744 -0.3852 0.223 -0.4314 0.2745 tetratricopeptide repeats 2

<o 229625_at Guanylate binding protein 5 GBP5 BG545653 -0.3849 0.2228 -0.3883 0.2471

202438_x_at iduronate 2-sulfatase (Hunter syndrome) IDS BF346014 -0.3848 0.2228 -0.4041 0.2572

204326_x_at metallothionein IX MTlX NM_002450 -0.3849 0.2228 0.1542 -0.0981 lectin, galactoside-binding, soluble, 3 binding

200923_at LGALS3BP NM_005567 -0.3839 0.2222 -0.3592 0.2286 protein

211012_s_at promyelocyte leukemia PML BC000080 -0.3829 0.2217 -0.4167 0.2652

209417_s_at interferon-induced protein 35 IFI35 BC001356 -0.3826 0.2215 -0.6746 0.4293

236285_at Hypothetical protein BC009980 MGC16635 AI631846 -0.3814 0.2208 -0.2971 0.1891

213524_s_at putative lymphocyte G0/G1 switch gene G0S2 NMJ)15714 -0.3811 0.2206 -0.3125 0.1989

202018_s_at lactotransferrin LTF NM_002343 -0.3808 0.2204 -0.1595 0.1015

Table 13: List of the 659 Gene Probes with Corresponding Certtroid Scores for Classifying SLE - Healthy and the kro ¹ IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

AffyID Gene Name Symbol Ace. No, SLE score group group score score score

YDD 19 protein /// chromosome 6 open YDD19 ///

215207_x_at reading frame 68 /// similar to hypothetical C6orf68 /// BF695847 -0.3807 0.2204 -0.1763 0.1122 protein, MGC:7199 LOC440128

211506_s_at interleukin 8 IL8 AF043337 -0.3795 0.2197 -0.4244 0.2701

223599_at tripartite motif-containing 6 TRIM6 AF220030 -0.3783 0.219 -0.4328 0.2754 poly (ADP-ribose) polymerase family,

22470 l_at PARP14 AA056548 -0.3775 0.2185 -0.5831 0.3711 member 14 phorbol- 12-myristate- 13 -acetate-induced

204285_s_at PMAIPl AI857639 -0.3769 0.2182 -0.4717 0.3001 protein 1

228439_at hypothetical protein BC012330 MGC20410 AW083820 -0.376 0.2177 -0.4718 0.3002

204972_at 2 -5 -oligoadenylate synthetase 2, 69/7IkDa OAS2 NMJ)16817 -0.3751 0.2172 -0.8922 0.5678

232034_at hypothetical protein LOC203274 LOC203274 ALl 17607 -0.3741 0.2166 -0.1186 0.0755

202636_at ring finger protein 103 RNF 103 NM_005667 -0.3728 0.2158 -0.0513 0.0327

205099_s_at chemokine (C-C motif) receptor 1 CCRl NMJ)01295 -0.3724 0.2156 -0.6835 0.435

Table 13: List of the 659 Gene Probes with. Corresponding CentroM Scores for Classifying SLE - Healthy and the low ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group , score score score *

235106_at mastermind-like 2 (Drosophila) MAML2 AW847318 -0.3716 0.2151 -0.365 0.2323

223298_s_at 5 -nucleotidase, cytosolic III NT5C3 AF312735 -0.3707 0.2146 -0.306 0.1947

227458_at CD274 antigen PDCDlLGl AI608902 -0.3688 0.2135 -0.2397 0.1525

Os

^O

202864_s_at nuclear antigen SpIOO SPlOO NM_003113 -0.3686 0.2134 -0.5133 0.3266

225919_s_at chromosome 9 open reading frame 72 C9orf72 AI832598 -0.3661 0.2119 -0.0821 0.0522

232034_at hypothetical protein LOC203274 LOC203274 ALl 17607 -0.3653 0.2115 -0.4401 0.2801

238423_at synaptotagmin-like 3 SYTL3 AI674404 -0.3643 0.2109 -0.0652 0.0415

Metastasis associated lung adenocarcinoma

228582_x_at MALATl AI475544 -0.3622 0.2097 -0.4641 0.2954 transcript 1 (non-coding RNA)

235106_at mastermind-like 2 (Drosophila) MAML2 AW847318 -0.3614 0.2093 -0.3485 0.2218

206332_s_at interferon, gamma-inducible protein 16 IFI16 NM_005531 -0.3612 0.2091 -0.3909 0.2488

207777_s_at SP 140 nuclear body protein SP140 NM_007237 -0.3599 0.2084 -0.3072 0.1955

230405_at hypothetical gene supported by AL713721 LOC441109 AI143416 -0.3592 0.2079 -0.4388 0.2793

211506_s_at interleukin 8 IL8 AF043337 -0.3587 0.2077 -0.3752 0.2388

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lø\* ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group ^* score score score interferon-induced protein with

203595_s_at IFIT5 N47725 -0.3581 0.2073 -0.3981 0.2533 tetratricopeptide repeats 5

N-acyl-phosphatidylethanolamine-

ON 238722_x_at NAPE-PLD AI460037 -0.358 0.2073 -0.5065 0.3223

VO hydrolyzing phospholipase D

206553_at 2 -5 -oligoadenylate synthetase 2, 69/7IkDa OAS2 NM_002535 -0.358 0.2072 -0.5231 0.3329

206461_x_at metallothionein IH MTlH NM_005951 -0.3574 0.2069 -0.3245 0.2065

44673_at sialoadhesin SN N53555 -0.3568 0.2065 0.0051 -0.0033

211012_s_at promyelocytic leukemia PML BC000080 -0.3566 0.2064 -0.4942 0.3145

230405_at hypothetical gene supported by AL713721 LOC441109 AI143416 -0.3564 0.2063 -0.4254 0.2707

202343_x_at cytochrome c oxidase subunit Vb COX5B NMJ)01862 -0.3552 0.2057 -0.1056 0.0672

206133_at XIAP associated factor-1 HSXIAPAFl NM_017523 -0.3548 0.2054 -0.7706 0.4904

202863_at nuclear antigen SpIOO SPlOO NM_003113 -0.3527 0.2042 -0.5733 0.3648

222816_s_at zinc finger, CCHC domain containing 2 ZCCHC2 BE676543 -0.3516 0.2035 -0.7492 0.4768

223758_s_at general transcription factor HH, polypeptide GTF2H2 BC005345 -0.3508 0.2031 -0.3739 0.2379

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lo% ^r IFN group vs. the high

IFN group t. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

2, 44kDa

209546_j3_at apolipoprotein L, 1 APOLl AF323540 -0.348 0.2015 -0.0314 0.02

Signal transducer and activator of

232375_at STATl AI539443 -0.348 0.2015 -0.4078 0.2595 transcription 1, 9IkDa

217933_s_at leucine aminopeptidase 3 LAP3 NMJ) 15907 -0.3478 0.2014 -0.6815 0.4337

238423_at synaptotagmin-like 3 SYTL3 AI674404 -0.3474 0.2012 -0.2923 0.186

22853 l_at sterile alpha motif domain containing 9 SAMD9 AA741307 -0.3471 0.2009 -0.6863 0.4367

227458_at CD274 antigen PDCDlLGl AI608902 -0.3459 0.2003 -0.3989 0.2538

243768_at SUMOl/sentrin specific protease 6 SENP6 AA026388 -0.3447 0.1996 -0.391 0.2488

230405_at hypothetical gene supported by AL713721 LOC441109 AI143416 -0.3426 0.1984 -0.3384 0.2153 tumor necrosis factor (ligand) superfamily,

202687_s_at member 10 /// tumor necrosis factor (ligand) TNFSFlO U57059 -0.3416 0.1978 -0.4054 0.258 superfamily, member 10

218543_s_at zinc finger CCCH type domain containing 1 ZC3HDC1 NM_022750 -0.3412 0.1976 -0.3219 0.2049

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ^r IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

226326_at polycomb group ring finger 5 PCGF5 AI798098 -0.3392 0.1964 -0.35 0.2227

209417_s_at interferon-induced protein 35 IFI35 BC001356 -0.3378 0.1956 -0.9221 0.5868 inhibitor of DNA binding 2, dominant negative helix-loop-helix protein /// inhibitor

201566_x_at ID2 /// ID2B D13891 -0.331 0.1917 -0.1373 0.0874 of DNA binding 2B, dominant negative helix- loop-helix protein general transcription factor IIH, polypeptide

223758_s_at GTF2H2 BC005345 -0.3298 0.1909 -0.3885 0.2472 2, 44kDa

205230_at rabphilin 3 A homolog (mouse) RPH3A NM_014954 -0.3292 0.1906 0.1572 -0.1

231956_at KIAA1618 KIAA1618 AA976354 -0.3274 0.1895 -0.5951 0.3787

20858 l_x_at metallothionein IX MTlX NM_005952 -0.3268 0.1892 -0.1222 0.0778 transporter 2, ATP-binding cassette, sub¬

225973_at TAP2 AA573502 -0.3268 0.1892 -0.3314 0.2109 family B (MDR/TAP)

227458_at CD274 antigen PDCDlLGl AI608902 -0.3247 0.188 -0.3075 0.1957

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lo% 11FN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ϊD Gene Name Symbol Ace. No. SLE score group group ^•score score score unc-93 homolog Bl (C. elegans) /// unc-93

220998_s_at UNC93B1 NM_030930 -0.3227 0.1868 -0.2518 0.1603 homolog Bl (C. elegans) protein phosphatase IK (PP2C domain

Os 235061_at PPMlK AV706522 -0.322 0.1864 -0.5004 0.3184 containing)

205875_s_at three prime repair exonuclease 1 TREXl NMJ)16381 -0.3193 0.1849 -0.3648 0.2321

225506_at KIAA1468 KIAA1468 AA523958 -0.3171 0.1836 -0.1065 0.0678 makorin, ring finger protein, 1 /// makorin,

201285_at MKRNl NM_013446 -0.3144 0.182 0.2148 -0.1367 ring finger protein, 1

233880_at chromosome 17 open reading frame 27 C17orf27 AL161961 -0.3127 0.181 0.163 -0.1037

219364_at likely ortholog of mouse Dl Ilgp2 LGP2 NM_024119 -0.3103 0.1796 -0.6334 0.4031

233880_at chromosome 17 open reading frame 27 C17orf27 AL161961 -0.3093 0.1791 -0.5651 0.3596

Protein tyrosine phosphatase, non-receptor

241930_x_at PTPNIl AA223204 -0.3075 0.178 0.1847 -0.1175 type 11 (Noonan syndrome 1) nrn_002046 GAPDH GAPDH nm_002046 -0.3061 0.1772 0.0451 -0.0287

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ' IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

HeaMry

Affy ϊD Gene Name Symbol Ace. No. SLE score group group score score score

229194_at polycomb group ring finger 5 PCGF5 AL045882 -0.3055 0.1769 -0.2737 0.1742

22853 l_at sterile alpha motif domain containing 9 SAMD9 AA741307 -0.303 0.1754 -0.5053 0.3216

Poly (ADP-ribose) polymerase family,

ON 227807_at PARP9 AI738416 -0.3026 0.1752 -0.4629 0.2946 member 9 unc-93 homolog Bl (C. elegans) /// unc-93

220998_s_at UNC93B1 NM_O3O93O -0.302 0.1749 -0.358 0.2278 homolog B 1 (C. elegans)

238581_at Guanylate binding protein 5 GBP5 BG271923 -0.3016 0.1746 -0.3405 0.2167

210797_s_at 2 -5 -oligoadenylate synthetase-like OASL AF063612 -0.301 0.1743 -0.5705 0.3631

233880_at chromosome 17 open reading frame 27 C17orf27 AL161961 -0.2997 0.1735 -0.4461 0.2839

53720_at hypothetical protein FLJl 1286 FLJl 1286 AI862559 -0.2995 0.1734 -0.4728 0.3008 transporter 2, ATP-binding cassette, sub¬

225973_at TAP2 AA573502 -0.2982 0.1726 -0.2936 0.1868 family B (MDR/TAP)

202145_at lymphocyte antigen 6 complex, locus E LY6E NMJ302346 -0.2976 0.1723 -0.7986 0.5082

209762_x_at SPIlO nuclear body protein SPI lO AF280094 -0.2936 0.17 -0.307 0.1954

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the kro ' IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affytt) Gene Name Symbol Aøc, No. SLE score group group score score score

208965_s_at interferon, gamma-inducible protein 16 IFI16 BG256677 -0.2926 0.1694 -0.3069 0.1953

211582_x_at leukocyte specific transcript 1 LSTl AF000424 -0.2904 0.1681 0.1598 -0.1017

Metastasis associated lung adenocarcinoma

ON 228582_x_at MALATl AI475544 -0.2881 0.1668 -0.2362 0.1503 -4 transcript 1 (non-coding RNA)

206075_s_at casein kinase 2, alpha 1 polypeptide CSNK2A1 NMJ)G 1895 -0.287 0.1662 0.1335 -0.085

TRAF-interacting protein with a forkhead-

226117_at TIFA AAl 95074 -0.2861 0.1656 -0.4011 0.2552 associated domain

208436_s_at interferon regulatory factor 7 IRF7 NM_004030 -0.2811 0.1627 -0.5262 0.3348

221345_at G protein-coupled receptor 43 GPR43 NM_005306 -0.2792 0.1617 -0.3941 0.2508

228439_at hypothetical protein BC012330 MGC20410 AW083820 -0.2788 0.1614 -0.1168 0.0743

238739_at Transcribed locus — AW902062 -0.2735 0.1584 -0.0973 0.0619

211456_x_at Similar to 60S ribosomal protein L35 — AF333388 -0.2699 0.1562 -0.3174 0.202

230866_at cysteinyl leukotriene receptor 1 CYSLTRl BE549540 -0.2672 0.1547 -0.4348 0.2767

219862_s_at nuclear prelamin A recognition factor NARF NM_012336 -0.2658 0.1539 -0.0486 0.0309

Table 13: . List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE -Healthy and the krø ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score leucine-rich repeats and calponin homology

90610_at LRCH4 AI654857 -0.2626 0.152 -0.1083 0.0689 (CH) domain containing 4

205098_at chemokine (C-C motif) receptor 1 CCRl AI421071 -0.2619 0.1516 -0.5891 0.3749

OO

222986_s_at scotin SCOTIN BC001463 -0.2612 0.1512 -0.3355 0.2135

228607_at 2 -5 -oligoadenylate synthetase 2, 69/7IkDa OAS2 AI651594 -0.2604 0.1507 -0.4565 0.2905

224148_at FYN binding protein (FYB-120/130) FYB AFl 16653 -0.2596 0.1503 -0.4377 0.2786 guanylate binding protein 1, interferon-

202269_x_at inducible, 67kDa /// guanylate binding protein GBPl BC002666 -0.2581 0.1494 -0.605 0.385

1, interferon-inducible, 67kDa

204698_at interferon stimulated gene 2OkDa ISG20 NM_002201 -0.2555 0.1479 -0.277 0.1762

230405_at hypothetical gene supported by AL713721 LOC441109 AI143416 -0.2524 0.1461 -0.4762 0.303

209762_x_at SPl 10 nuclear body protein SPIlO AF280094 -0.252 0.1459 -0.3651 0.2323

201752_s_at adducin 3 (gamma) ADD3 AI763123 -0.2491 0.1442 -0.1284 0.0817

208965_s_at interferon, gamma-inducible protein 16 IFI16 BG256677 -0.248 0.1436 -0.2367 0.1506

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the km ^r IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score groitp group score score score

Homo sapiens, clone IMAGE:5261213,

228315_at — AI632728 -0.2451 0.1419 -0.3623 0.2305 mRNA

225929_s_at chromosome 17 open reading frame 27 C17orf27 AA233374 -0.2439 0.1412 -0.4656 0.2963

ON

VO vo 222816_s_at zinc finger, CCHC domain containing 2 ZCCHC2 BE676543 -0.2404 0.1392 -0.3639 0.2316

-1.00E-

243904_at CDNA clone IMAGE:5287121, partial cds — AA204752 -0.2335 0.1352 1.00E-04 04

225466_at hypothetical protein FLJ36874 FLJ36874 BG291961 -0.2308 0.1336 -0.1896 0.1206 interferon-induced protein with

226757_at IFIT2 AA131041 -0.2308 0.1336 -0.5333 0.3394 tetratricopeptide repeats 2

201470_at glutathione S-transferase omega 1 GSTOl NM_004832 -0.2294 0.1328 -0.1674 0.1065 proteasome (prosome, macropain) subunit,

202659_at PSMBlO NM_002801 -0.2257 0.1306 -0.4003 0.2547 beta type, 10 splicing factor proline/glutamine rich

201585_s_at SFPQ BG035151 -0.2255 0.1305 -0.1367 0.087 (polypyrimidine tract binding protein

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the lo% ' IFN group vs. the high

EFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score associated)

231363_at hypothetical LOC149018 LOC149018 AA776758 -0.2223 0.1287 0.0539 -0.0343

208436_s_at interferon regulatory factor 7 IRF7 NM_004030 -0.2213 0.1281 -0.3231 0.2056

-4

O O 207777_s_at SP 140 nuclear body protein SP140 NM_007237 -0.2206 0.1277 -0.1978 0.1258 pro-oncosis receptor inducing membrane

211967_at POMMIN BG538627 -0.2127 0.1231 -0.4602 0.2929 injury gene nm_001l01 actin, beta ACTB nm_001101 -0.2103 0.1217 0.0619 -0.0394 leucine-rich repeats and calponrn homology

90610_at LRCH4 AI654857 -0.2097 0.1214 -0.0589 0.0375 (CH) domain containing 4

219691_at sterile alpha motif domain containing 9 SAMD9 NM_017654 -0.2095 0.1213 -0.5476 0.3485

222745_s_at chromosome 15 open reading frame 29 C15orf29 AI924685 -0.2093 0.1212 0.0633 -0.0403

226106_at ring finger protein 141 RNF141 AI307808 -0.2085 0.1207 0.0084 -0.0053

210889_s_at Fc fragment of IgG, low affinity lib, receptor FCGR2B M31933 -0.2083 0.1206 -0.1844 0.1173

Table 13: List of the 659 Gene Probes wifh Corresponding Centroid Scores for Classifying SLE - Healthy and the low ^r IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Acc, No. SLE score group group score score score

(CD32)

226163_at zinc ringer and BTB domain containing 9 ZBTB9 AW291499 -0.2073 0.12 -0.2775 0.1766

225929_s_at chromosome 17 open reading frame 27 C17orf27 AA233374 -0.2068 0.1197 -0.5626 0.358

² 211965_at zinc finger protein 36, C3H type-like 1 ZFP36L1 BE620915 -0.2036 0.1178 0.1379 -0.0877 phorbol- 12-myristate- 13 -acetate-induced

204286_s_at PMAIPl NM_021127 -0.1995 0.1155 -0.3285 0.209 protein 1 transporter 2, ATP-binding cassette, sub¬

225973_at TAP2 AA573502 -0.1988 0.1151 -0.3556 0.2263 family B (MDR/TAP)

203148_s_at tripartite motif-containing 14 TRIM14 NM_014788 -0.1984 0.1148 -0.3729 0.2373 lectin, galactoside-binding, soluble, 3 binding

200923_at LGALS3BP NM_005567 -0.1968 0.1139 -0.6008 0.3823 protein transporter 2, ATP-binding cassette, sub¬

225973_at TAP2 AA573502 -0.1955 0.1132 -0.3261 0.2075 family B (MDR/TAP)

225897_at Myristoylated alanine-rich protein kinase C MARCKS AI709406 -0.1913 0.1107 -0.3005 0.1912

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the kra ^r IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score substrate

225076_s_at KIAA1404 protein KIAA1404 AAl 50460 -0.1885 0.1091 -0.1652 0.1051

O 202864_s_at nuclear antigen SpIOO SPlOO NM_003113 -0.1841 0.1066 -0.4121 0.2622 interferon-induced protein with

204747_at IFIT3 NMJ)Ol 549 -0.183 0.1059 -0.2825 0.1798 tetratricopeptide repeats 3 guanylate binding protein 1, interferon-

231577_s_at GBPl AW014593 -0.179 0.1036 -0.3982 0.2534 inducible, 67kDa

220924_s_at solute carrier family 38, member 2 SLC38A2 NMJ 18976 -0.1783 0.1032 -0.1148 0.073

222982_x_at solute carrier family 38, member 2 SLC38A2 AF298897 -0.1749 0.1013 -0.0747 0.0476 splicing factor proline/glutamine rich

201585_s_at (polypyrimidine tract binding protein SFPQ BG035151 -0.1738 0.1006 -0.1752 0.1115 associated)

227354_at FLJ37858 protein FLJ37858 BF589359 -0.1715 0.0993 -0.1046 0.0665

234344_at RAP2C, member of RAS oncogene family RAP2C AF093744 -0.1716 0.0993 -0.2356 0.1499

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the krø ' IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

Metastasis associated lung adenocarcinoma

228582_x_at MALATl AI475544 -0.168 0.0973 -0.322 0.2049 transcript 1 (non-coding RNA)

210705_s_at tripartite motif-containing 5 TRIM5 AF220028 -0.1676 0.097 -0.2947 0.1875

-4

O

225466_at hypothetical protein FLJ36874 FLJ36874 BG291961 -0.1673 0.0969 -0.1047 0.0666 phorbol- 12-myristate- 13 -acetate-induced

204286_s_at PMAIPl NM_021127 -0.1659 0.096 -0.4403 0.2802 protein 1

Transcribed locus, weakly similar to

240165_at XP_209041.2 KIAAl 503 protein [Homo — AI678013 -0.1656 0.0959 -0.1141 0.0726 sapiens]

229194_at polycomb group ring finger 5 PCGF5 AL045882 -0.1653 0.0957 -0.2243 0.1427

222745_s_at chromosome 15 open reading frame 29 C15orf29 AI924685 -0.1633 0.0945 -0.235 0.1496

232034_at hypothetical protein LOC203274 LOC203274 ALl 17607 -0.1586 0.0918 -0.099 0.063

213735_s_at cytochrome c oxidase subunit Vb COX5B AI557312 -0.1563 0.0905 -0.0728 0.0463

222498_at 5-azacytidine induced 2 AZI2 AI809206 -0.1553 0.0899 -0.1374 0.0874

Table 13: List of the 659 Gene Probes with Corresponding Ceiitrøid Scores for Classifying SLE - Healthy and the krø ' IFN group vs. the high

IFN grou] 3. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

219519_s_at sialoadhesin /// sialoadhesin SN NM_023068 -0.1552 0.0898 -0.1044 0.0664

218429_s_at hypothetical protein FLJl 1286 FLJl 1286 NM_018381 -0.1514 0.0876 -0.5309 0.3378 interferon-induced protein with

217502_at IFIT2 BE888744 -0.1504 0.0871 -0.4882 0.3107 tetratricopeptide repeats 2

223434_at guanylate binding protein 3 GBP3 ALl 36680 -0.1504 0.087 -0.2569 0.1635

243768_at SUMOl/sentrin specific protease 6 SENP6 AA026388 -0.148 0.0857 -0.1068 0.068 tumor necrosis factor (ligand) superfamily,

202688_at member 10 /// tumor necrosis factor (ligand) TNFSFlO NM_003810 -0.1463 0.0847 -0.2718 0.1729 superfamily, member 10

211965_at zinc finger protein 36, C3H type-like 1 ZFP36L1 BE620915 -0.1436 0.0831 -0.0166 0.0106

225710_at CDNA FLJ34013 fis, clone FCBBf 2002111 — H99792 -0.1434 0.083 -0.291 0.1852 tumor necrosis factor (ligand) superfamily,

202688_at member 10 /// tumor necrosis factor (ligand) TNFSFlO NM_003810 -0.1412 0.0817 -0.2527 0.1608 superfamily, member 10

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name SymboJ Ace. No. SLE score group group score score score

226459_at phosphoinositide-3 -kinase adaptor protein 1 PIK3AP1 AW575754 -0.1357 0.0785 -0.1768 0.1125

223434_at guanylate binding protein 3 GBP3 ALl 36680 -0.1343 0.0778 -0.4497 0.2861

210705_s_at tripartite motif-containing 5 TRIM5 AF220028 -0.1277 0.0739 -0.2328 0.1481

O Ul guanylate binding protein 1 , interferon-

202269_x_at inducible, 67kDa /// guanylate binding protein GBPl BC002666 -0.115 0.0666 -0.3264 0.2077

1, interferon-inducible, 67kDa

235276_at Epithelial stromal interaction 1 (breast) EPSTIl AA781795 -0.1145 0.0663 -0.5644 0.3592

219862_s_at nuclear prelamin A recognition factor NARF NM_012336 -0.1098 0.0636 0.0877 -0.0558

211965_at zinc finger protein 36, C3H type-like 1 ZFP36L1 BE620915 -0.1036 0.06 -0.033 0.021

204326_x_at metallothionein IX MTlX NM_002450 -0.1025 0.0594 -0.2759 0.1756

224225_s_at ets variant gene 7 (TEL2 oncogene) ETV7 AF218365 -0.0981 0.0568 -0.3087 0.1964

207500_at caspase 5, apoptosis-related cysteine protease CASP5 NM_004347 -0.0968 0.056 -0.1082 0.0689

201901_s_at YYl transcription factor YYl Z14077 -0.0956 0.0553 -0.0237 0.0151

204155_s_at KIAA0999 protein KIAA0999 AA044154 -0.0915 0.053 0.1763 -0.1122

Table 13: List of the 659 Gene Probes with Corresponding Cenrrøid Scores for Classifying SLE - Healthy and the lo% ' IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score søore score

234344_at RAP2C, member of RAS oncogene family RAP2C AF093744 -0.0899 0.052 -0.2131 0.1356

227755_at CDNA clone IMAGE:4077090, partial cds — AA042983 -0.0887 0.0513 0.1572 -0.1

Myristoylated alanine-rich protein kinase C

O 225897_at MARCKS AI709406 -0.0645 0.0373 -0.3644 0.2319 substrate nm_002046 GAPDH GAPDH nm_002046 -0.0641 0.0371 0.0572 -0.0364

22593 l_s_at chromosome 17 open reading frame 27 C17orf27 AI954660 -0.0636 0.0368 -0.4988 0.3174

233880_at chromosome 17 open reading frame 27 C17orf27 AL161961 -0.0628 0.0364 -0.0993 0.0632 similar to Interferon-induced transmembrane

216565_x_at LOC391020 AL121994 -0.0515 0.0298 -0.2263 0.144 protein 3 (Interferon-inducible protein 1-8U)

220924_s_at solute carrier family 38, member 2 SLC38A2 NMJ)18976 -0.0492 0.0285 -0.3439 0.2188 prostaglandin-endoperoxide synthase 2

204748_at (prostaglandin G/H synthase and PTGS2 NM_000963 -0.0432 0.025 -0.1112 0.0708 cyclooxygenase) nm J⁾Ol 101 actin, beta ACTB nm_001101 -0.0405 0.0235 -0.0374 0.0238

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ' IFN group vs. the high

IFN group. The 659 probes correspond to 29? genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score dehydrogenase/reductase (SDR family)

224009__x_at DHRS9 AF240697 -0.032 0.0185 -0.4023 0.256 member 9

203148_s_at tripartite motif-containing 14 TRIM14 NMJ014788 -0.0209 0.0121 -0.3437 0.2187

-4

O -4 prostaglandin-endoperoxide synthase 2

204748_at (prostaglandin G/H synthase and PTGS2 NM_000963 -0.0107 0.0062 -0.0653 0.0416 cyclooxygenase)

228304_at Transcribed locus — BE674118 -0.0094 0.0055 -0.494 0.3143

Fc fragment of IgG, low affinity lib, receptor

210889_s_at FCGR2B M31933 -0.0074 0.0043 -0.0562 0.0358 (CD32)

-4.00E-

22529 l_at polyribonucleotide nucleotidyltransferase 1 PNPTl AI967971 2.00E-04 -0.2462 0.1567 04

238581_at Guanylate binding protein 5 GBP5 BG271923 0.0036 -0.0021 -0.3892 0.2477

MovlO, Moloney leukemia virus 10, homolog

223849_s_at MOVlO BC002548 0.0065 -0.0038 0.1396 -0.0888 (mouse)

Table 13: List of the 659 Gene Probes with Corresponding Cβntroid Scores for Classifying SLE - Healthy and the lovi r IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes. -

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace, No. SLE score group group score score score

226459_at phosphoinositide-3 -kinase adaptor protein 1 PIK3AP1 AW575754 0.007 -0.004 -0.2444 0.1555

203243_s_at PDZ and LIM domain 5 PDLIM5 NM_006457 0.0181 -0.0105 -0.0349 0.0222

223414_s_at hypothetical protein FLJ20425 LYAR ALl 36750 0.02 -0.0116 -0.0805 0.0512

209762_x_at SP 110 nuclear body protein SPI lO AF280094 0.0218 -0.0126 -0.3762 0.2394

38241_at butyrophilin, subfamily 3, member A3 BTN3A3 U90548 0.0286 -0.0166 -0.2835 0.1804

22593 l_s_at chromosome 17 open reading frame 27 C17orf27 AI954660 0.032 -0.0185 -0.5955 0.379

N-ethylmaleimide-sensitive factor attachment

20875 l_at NAPA BCOOl 165 0.0354 -0.0205 -0.2196 0.1398 protein, alpha inhibitor of DNA binding 2, dominant negative helix-loop-helix protein /// inhibitor

201566_x_at ID2 /// ID2B D13891 0.04 -0.0231 -0.1337 0.0851 of DNA binding 2B, dominant negative helix- loop-helix protein

212380_at KIAA0082 KIAA0082 D43949 0.0537 -0.0311 -0.415 0.2641

232034_at hypothetical protein LOC203274 LOC203274 ALl 17607 0.0698 -0.0404 -0.1727 0.1099

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the low ^r IFN group vs. the high

IFN group . The 659 probes correspond to 297 genes.

low BFN high IFN

Healthy

Afify ID Gene Name Symbol Ace. No. SLE score group group score score score

226459_at phosphoinositide-3-kinase adaptor protein 1 PIK3AP1 AW575754 0.0936 -0.0542 -0.2059 0.131 signal transducer and activator of

225636_at STAT2 H98105 0.105 -0.0608 -0.4244 0.2701 transcription 2, 113fcDa

-4 carcinoembryonic antigen-related cell

209498_at CEACAMl X16354 0.1453 -0.0841 -0.1825 0.1162 adhesion molecule 1 (biliary glycoprotein)

222982_x_at solute carrier family 38, member 2 SLC38A2 AF298897 0.1535 -0.0889 -0.2609 0.166 serine (or cysteine) proteinase inhibitor, clade

200986_at G (Cl inhibitor), member 1, (angioedema, SERPINGl NM_000062 0.169 -0.0979 -0.3548 0.2258 hereditary)

200775_s_at heterogeneous nuclear ribonucleoprotein K HNRPK BC000355 0.1711 -0.099 -0.0165 0.0105

242020_s_at Z-DNA binding protein 1 ZBPl AI925506 0.2008 -0.1162 -0.1633 0.1039

Transcribed locus, weakly similar to

241368_at NP_003148.1 NIMA (never in mitosis gene — All 90693 0.2086 -0.1208 0.0487 -0.031 a)-related kinase 4 [Homo sapiens]

Table 13: List of the 659 Gene Probes with Corresponding Centroid Scores for Classifying SLE - Healthy and the krø IFN group vs. the high

IFN group. The 659 probes correspond to 297 genes.

low IFN high IFN

Healthy

Affy ID Gene Name Symbol Ace. No. SLE score group group score score score

Wiskott-Aldrich syndrome protein interacting

231182_at WASPIP BF446719 0.2171 -0.1257 0.1822 -0.1159 protein nm_001101 actin, beta ACTB nm_001101 0.2393 -0.1386 0.0685 -0.0436

-4

O 205230_at rabphilin 3A homolog (mouse) RPH3A NM_014954 0.24 -0.139 0.1039 -0.0661

38241_at butyrophilin, subfamily 3, member A3 BTN3A3 U90548 0.4705 -0.2724 -0.3407 0.2168

225065_x_at hypothetical protein MGC40157 MGC40157 AI826279 0.4868 -0.2819 -0.0358 0.0228

200775_s_at heterogeneous nuclear ribonucleoprotein K HNRPK BC000355 0.5889 -0.3409 -0.2715 0.1728

-4

-4

4-

-4 'Jl

-4 -4

VO

Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease. Affy ID Symbol Ace. No.

200923_at LGALS3BP NM_005567 200923_at LGALS3BP NM_005567 200986_at SERPINGl NM_000062 201202_at PCNA NM_002592 201202_at PCNA NM_002592 201285_at MKRNl NM_013446 201285 at MKRNl NM 013446 ID2 ///

201566 x at D13891 ID2B 201585_s_at SFPQ BG035151

201930_at MCM6 NM_005915

202008_s_at NID NM_002508

202010_s_at ZNF410 NM_021188

202018_s_at LTF NM_002343

202018_s_at LTF NM_002343

202086_at MXl NM_002462

202086_at MXl NM_002462

202145_at LY6E NM_002346 202145_at LY6E NM_002346

202269_x_at GBPl BC002666 202269_x_at GBPl BC002666 202270 at GBPl NM 002053 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease. AfEy ID Symbol Ace. No.

202270_at GBPl NM_ _.002053

202411_at IFI27 NM_ .005532

202411_at IFI27 NM_ _,005532

202430_ _s_at PLSCRl NM_ 021105

202438_ _x_at IDS BF346014

202446_ _s_at PLSCRl AI825926

202446_ _s_at PLSCRl AI825926

202595_.s_at LEPROTLl AF161461

202659_.at PSMBlO NM_. 002801

202688_at TNFSFlO NM_ 003810

202863_,at SPlOO NM_ 003113

202863_at SPlOO NM_ _003113

202863_.at SPlOO NM_ 003113

202869_.at OASl NM_ 016816

202869_.at OASl NM_ 016816

202872_.at ATP6V1C1 AW024925

202996_.at POLD4 NM_. _021173

203091_.at FUBPl NM_. 003902

203148_. _s_at TRIM14 NM_. _014788

203153_.at IFITl NM_. 001548

203153_.at IFITl NM_. _001548

203595_. _s_at IFIT5 N47725

203595_. _s_at IFIT5 N47725

203596_. _s_at IFIT5 NM_. _012420

203596 s at IFIT5 NM 012420 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease.

Affy ID Symbol Ace. No.

203596_ s_at IFIT5 NM_ 012420

203713_ s_at LLGL2 NM_ _.004524

204155_ s_at KIAA0999 AA044154

204225_ at HDAC4 NM_ 006037

204285_ s_at PMAIPl AI857639

204286_ _s_at PMAIPl NM_ 021127

204286_ s_at PMAIPl NM_ 021127

204286_ s_at PMAIPl NM_ _.021127

204326_ x_at MTlX NM_ 002450

204326_ x_at MTlX NM_ 002450

204326_ x_at MTlX NM. 002450

204415_ at G1P3 NM_ 022873

204415_ at G1P3 NM. _022873

204439_ at IFI44L NM_ 006820

204439_ at IFI44L NM. 006820

204470_ at CXCLl NM_. _001511

204615_ x_at IDIl NM_. _004508

204747_ at IFIT3 NM. 001549

204748_ at PTGS2 NM_ 000963

204748_ at PTGS2 NM_ _000963

204972_ at OAS2 NM_ 016817

204972_ _.at OAS2 NM_ _016817

205003_ at DOCK4 NM_ 014705

205099_ _s_at CCRl NM_ _001295

205230_ .at RPH3A NM_ 014954

205230 at RPH3A NM 014954 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease.

Affy ID Symbol Ace. No.

205483_s_at G1P2 NM_005101

205483_s_at G1P2 NM_005101

205552_s_at OASl NM_002534

205552_s_at OASl NM_002534

205569_at LAMP3 NM_014398

205569_at LAMP3 NM_014398

205875_s_at TREXl NM_016381

205875_s_at TREXl NM_016381

206025_s_at TNFAIP6 AWl 88198

206026_s_at TNFAIP6 NM_007115

206026_s_at TNFAIP6 NM_007115

206026_s_at TNFAIP6 NM_007115

206075_s_at CSNK2A1 NMJ)Ol 895

206115_at EGR3 NM_004430

HSXIAPAF

206133 at NM_017523 1

HSXIAPAF

206133 at NM_017523 1

206461_x_at MTlH NM_005951

206461_x_at MTlH NM_005951

206553_at OAS2 NM_002535

206553_at OAS2 NM_002535

207500_at CASP5 NM_004347

207777_s_at SP140 NM_007237

20858 l_x_at MTlX NM_005952

208751 at NAPA BCOOl 165 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease. Affy ID Symbol Ace. No.

20875 l_at NAPA BCOOl 165 20875 l_at NAPA BCOOl 165 208965 js_at IFI16 BG256677 209236_at SLC23A2 AL389886 209417_s_at IFI35 BC001356 209417_s_at IFI35 BC001356

209498_at CEACAMl X16354

210705_s_at TRIM5 AF220028 210797_s_at OASL AF063612 210797_s_at OASL AF063612 210797_s_at OASL AF063612 210797_s_at OASL AF063612 211012_s_at PML BC000080

211367_s_at CASPl Ul 3699

211456_x_at AF333388

211506_s_at IL8 AF043337

211506_s_at IL8 AF043337

211506_s_at IL8 AF043337

211582_x_at LSTl AF000424

211965_at ZFP36L1 BE620915

211967_at PORIMIN BG538627

212185_x_at MT2A NM_005953

212285_s_at AGRN AW008051

DKFZP564

212333_at AL049943

F0522 212380 at KIAA0082 D43949 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease. Affy ID Symbol Ace. No.

212531_at LCN2 NM_005564

212916_at PHF8 AW249934

213293_s_at TRIM22 AA083478

213294_at FLJ38348 AV755522

213524_s_at G0S2 NMJ)15714

213524_s_at G0S2 NM_015714

213797_at RSAD2 AI337069

213797_at RSAD2 AI337069

214059_at IFI44 BE049439

214453_s_at IFI44 NM_006417

214453_s_at IFI44 NM_006417

21451 l_x_at FCGRlA L03419

21451 l_x_at FCGRlA L03419

214620_x_at PAM BF038548

215221_at FOXPl AK025064

216950_s_at FCGRlA X14355

217502_at IFIT2 BE888744

217502_at IFIT2 BE888744

217933_s_at LAP3 NM_015907

217933_s_at LAP3 NM_015907

218085_at CHMP5 NM_015961

218304_s_at OSBPLIl NM_022776

218400_at OAS3 NM_006187

218400_at OAS3 NM_006187

218400_at OAS3 NM_006187

218618 s at FNDC3B NM 022763 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease.

Affy ID Symbol Ace. No.

218943_s_at DDX58 NM_014314

218943_s_at DDX58 NM_014314

218986_s_at FLJ20035 NM_017631

218986_s_at FLJ20035 NM_017631

219209_at IFIHl NM_022168

21921 l_at USP18 NM_017414

21921 l_at USP18 NM_017414

219352_at HERC6 NM_017912

219352_at HERC6 NM_017912

219356_s_at CHMP5 NM_016410

219356_s_at CHMP5 NM_016410

219364_at LGP2 NM_024119

219426_at EIF2C3 NM_024852

219519_s_at SN NM_023068

219559_at C20orf59 NM_022082

219684__at IFRG28 NM_022147

219684__at IFRG28 NM_022147

219684_at IFRG28 NM_022147

219691_at SAMD9 NM_017654

219799_s_at DHRS9 NM_005771

219799_s_at DHRS9 NM_005771

219863_at HERC5 NM_016323

219863_at HERC5 NMJ)16323

220492_s_at OTOF NM_004802

220924 _s_at SLC38A2 NM_018976

220924 s at SLC38A2 NM 018976 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease.

Affy ID Symbol Ace. No.

221827_at C20orfl8 BE788439

222154_s_at DNAPTP6 AK002064

222154_s_at DNAPTP6 AK002064

222498_at AZI2 AI809206

222532_at SPvPRB BF983948

222745_s_at C15orf29 AI924685

222745_s_at C15orf29 AI924685

222793_at DDX58 AK023661

222816_s_at ZCCHC2 BE676543

222816_s_at ZCCHC2 BE676543

222816_s_at ZCCHC2 BE676543

222982_x_at SLC38A2 AF298897

222982_x_at SLC38A2 AF298897

222986_s_at SCOTIN BC001463

223062_s_at PSATl BC004863

223220_s_at PARP9 AF307338

223298_s_at NT5C3 AF312735

223298_s_at NT5C3 AF312735

223414_s_at LYAR AL136750

223434 jit GBP3 _. ALl 36680

223501_at TNFSF13B AW151360

223501__at TNFSF13B AW151360

223577_x_at PRO1073 AA827878

223577_x_at PRO1073 AA827878

223599_at TRIM6 AF220030 .

223599 at TRIM6 AF220030 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease.

Affy ID Symbol Ace. No.

223758_ s_at GTF2H2 BC005345

223849_ _s_at MOVlO BC002548

223849_ s_at MOVlO BC002548

223952_ x_at DHRS9 AF240698

223952_ x_at DHRS9 AF240698

224009_ _x_at DHRS9 AF240697

224225_ _s_at ETV7 AF218365

224225_ s_at ETV7 AF218365

224589_ at NR1I3 BF223193

225065_ x_at MGC40157 AI826279

225076_ s_at KIAA1404 AAl 50460

225291_ at PNPTl AI967971

225291_ at PNPTl AI967971

225291_ at PNPTl AI967971

225291_ at PNPTl AI967971

225466_ at FLJ36874 BG291961

225636_ at STAT2 H98105

225710_ at — H99792

225710_ at — H99792

225897_ at MARCKS AI709406

225897_ at MARCKS AI709406

225897_ at MARCKS AI709406

225897_ at MARCKS AI709406

225919_ s_at C9orf72 AI832598

225919_ _s_at C9orf72 AI832598

225931 s at C17orf27 AI954660 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease.

Affy ID Symbol Ace. No.

225973_ _.at TAP2 AA573502

225973_ _.at TAP2 AA573502

225973_ at TAP2 AA573502

226106_ at RNF141 AI307808

226117_ at TIFA AA195074

226117_ at TIFA AA195074

226117_ _at TIFA AAl 95074

226117_ at TIFA AAl 95074

226459_ at PIK3AP1 AW575754

226603_ at C7orf6 BE966604

226702_ at LOC 129607 AI742057

226702_ at LOC 129607 AI742057

226702_ at LOC129607 AI742057

226702_ at LOC129607 AI742057

226757_ at IFIT2 AA131041

226757_ at IFIT2 AA131041

226941_ at ATF6 BF439325

227354_ at FLJ37858 BF589359

227458_ _at PDCDlLGl AI608902

227458_ at PDCDlLGl AI608902

227458_ at PDCDlLGl AI608902

227458_ at PDCDlLGl AI608902

227755_ at — AA042983

227807_^ _at PARP9 AI738416

227807_ at PARP9 AI738416

228050 at FLJ12787 AA046406 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease. Affy ID Symbol Ace. No.

228230_at PRIC285 ALl 21829 228230_at PRIC285 ALl 21829 228304_at BE674118 228439_at MGC20410 AW083820 22853 l_at SAMD9 AA741307 22853 l_at SAMD9 AA741307 228570 at BTBDI l BF510581

228582_x_at MALATl AI475544 228582 x at MALATl AI475544

228582_ _x_at MALATl AI475544

228582_ x_at MALATl AI475544

228607_ at OAS2 AI651594

228607_ at OAS2 AI651594

HSXIAPAF

228617_. at AA142842 1

HSXIAPAF

228617_, at AA142842 1

229194_ at PCGF5 AL045882

229194_ at PCGF5 AL045882

229450_ at IFIT3 AI075407

229450_ _at IFIT3 AI075407

229625_. at GBP5 BG545653

229625_. at GBP5 BG545653

230036_. _at C7orf6 BE669858

230036 at C7orf6 BE669858 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease. Affy ID Symbol Ace. No.

230179_at LOC285812 N52572

230314_at AW014557

230405_at LOC441109 AI143416

230405_at LOC441109 AI143416

230405_at LOC441109 AI143416

230405_at LOC441109 AI143416

230645_at FRMD3 BFl 10588

230866_at BE549540

231182_at WASPIP BF446719

231182_at WASPIP BF446719

231182_at WASPIP BF446719

231182_at WASPIP BF446719

231363_at LOC149018 AA776758

231577_s_at GBPl AWO 14593

231577_s_at GBPl AW014593

231747_at CYSLTRl NM_006639

231769_at FBXO6 AF129536

231956_at KIAA1618 AA976354

231956_at KIAA1618 AA976354

232034_at LOC203274 ALl 17607

232222_at C18orf49 AK000229

232375_at STATl AI539443

232563_at ZNF684 AW275016

232563_at ZNF684 AW275016

232563 at ZNF684 AW275016

232645 at LOC153684 AW665885 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease.

Affy ID Symbol Ace. No.

232645_at LOC153684 AW665885

232666_at OAS3 Rl 3458

232666_at OAS3 R13458

232787_at PRIC285 AK023724

232787_at PRIC285 AK023724

233425_at ZCCHC2 AU147903

233591_at — AK026751

233880_at C17orf27 AL161961

233880_at C17orf27 AL161961

233880_at C17orf27 AL161961

234344_at RAP2C AF093744

234986_at GCLM AA630626

23506 l_at PPMlK AV706522

235106_at MAML2 AW847318

235106_at MAML2 AW847318

235106_at MAML2 AW847318

235106_at MAML2 AW847318

235157_at PARP14 AW297731

235157_at PARP 14 AW297731

235256_s_at GALM BE788984

235256_s_at GALM BE788984

235276_at — AA781795

235276_at — AA781795

235276_at — AA781795

235276_at — AA781795

235276 at — AA781795 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease. Affy ID Symbol Ace. No.

235574_at GBP4 AW392952

235574_at GBP4 AW392952

235643_at C7orf6 BE886225

236285_at MGC16635 AI631846

236285_at MGC16635 AI631846

238423_at SYTL3 AI674404

238581_at GBP5 BG271923

238581_at GBP5 BG271923

238722_x_at NAPE-PLD AI460037

238739_at — AW902062

239277_at ACATE2 AI559696

239277_at ACATE2 AI559696

239979_at EPSTIl BE645480

239979_at EPSTIl BE645480

239988_at HERC6 AA708470

240718_at CASCl AW303384

240718_at CASCl AW303384

241368_at — All 90693

241368_at — All 90693

241916_at PLSCRl AI984040

241916_at PLSCRl AI984040

241916_at PLSCRl AI984040

241916_at PLSCRl AI984040

241930_x_at — AA223204

241930 x at AA223204 Table 15: 368 most variable gene probes and the associated probes in the SLE patient classification analysis in the descending order. The expression of genes provide the most variable genes that are useful in differentiating two SLE activity groups into high and low active SLE disease. Affy ID Symbol Ace. No.

242020_s_at ZBPl AI925506

242020_s_at ZBPl AI925506

242030_at SLC4A1AP AI934909 HSXIAPAF

242234 _at AI859280

1

HSXIAPAF

242234 _at AI859280 1

242625 _at RSAD2 AWl 89843

242907 at GBP2 BF509371

242961 x_at DDX58 AI304317

242961 _x_at DDX58 AI304317

243122 _at PACRG Hl 8468

243768 _at SENP6 AA026388

243768 _at SENP6 AA026388

243904 _at — AA204752

44673_ at SN N53555

44673_ at SN N53555

90610 at LRCH4 AI654857

PDCDlLGl PDCDlLGl NM 014143

Table 16: 53 genes that provide the most differentiation between healthy donor individuals,

SLE patients, WG patients and RA patients.

Affy ID Description Symbol Ace. No. serine (or cysteine) proteinase inhibitor,

200986 at SERPINGl NM 000062 clade G (Cl inhibitor), member 1, Table 16: 53 genes that provide the most differentiation between healthy donor individuals, SLE patients, WG patients and RA patients.

Affy ID Description Symbol Ace. No.

(angioedema, hereditary)

20241 l_at interferon, alpha-inducible protein 27 IFI27 NM_005532 202430_s_at phospholipid scramblase 1 PLSCRl NM_021105 tumor necrosis factor (ligand)

202687 s at TNFSFlO U57059 superfamily, member 10 202837_at FLN29 gene product FLN29 NM_006700 202863_at nuclear antigen Sp 100 SPlOO NM_003113 interferon-induced protein with

203153 at IFITl NM 001548 tetratricopeptide repeats 1 interferon-induced protein with

203595 s at IFIT5 N47725 tetratricopeptide repeats 5 eukaryotic translation initiation factor 2-

204211 x at EIF2AK2 NM_002759 alpha kinase 2 interferon, alpha-inducible protein (clone

204415 at G1P3 NM_022873

IFI-6-16) 204439_at interferon-induced protein 44-like IFI44L NM_006820 interferon-induced protein with

204747 at IFIT3 NM_001549 tetratricopeptide repeats 3 myxovirus (influenza virus) resistance 2

204994 at MX2 NM_002463

(mouse) 205098_at chemokine (C-C motif) receptor 1 CCRl AI421071

SCO cytochrome oxidase deficient

205241 at SCO2 NM_005138 liomolog 2 (yeast) interferon, alpha-inducible protein (clone

205483 s at G1P2 NMjxmoi

IFI-15K) tumor necrosis factor, alpha-induced

206025 s at TNFAIP6 AWl 88198 protein 6 206026_s_at tumor necrosis factor, alpha-induced TNFAIP6 NM 007115 Table 16: 53 genes that provide the most differentiation between healthy donor individuals,

SLE patients, WG patients and RA patients. Affy ID Description Symbol Ace. No. protein 6

208581_x_at metallothionein IX MTlX NM_005952 N-ethylmaleimide-sensitive factor 20875 l_at NAPA BCOOl 165 attachment protein, alpha 208966_x_at interferon, gamma-inducible protein 16 IFI16 AF208043 caspase 1, apoptosis-related cysteine 211367_s_at CASPl U13699 protease (interleukin 1, beta, convertase)

212185_x_at metallothionein 2A MT2A NM_005953 213294_at Hypothetical protein FLJ38348 FLJ38348 AV755522 radical S-adenosyl methionine domain

213797_at RSAD2 AI337069 containing 2

Tumor necrosis factor (ligand)

214329_x_at TNFSFlO AW474434 superfamily, member 10

214453_s_at interferon-induced protein 44 IFI44 NM_006417 21451 l_x_at Fc gamma receptor I FCGRlA L03419 similar to Interferon-induced

216565_x_at transmembrane protein 3 (Interferon- LOC391020 AL121994 inducible protein 1-8U) Fc fragment of IgG, high affinity Ia₅

216950_s_at FCGRlA X14355 receptor (CD64)

218085_at chromatin modifying protein 5 CHMP5 NMJ) 15961 219356_s_at chromatin modifying protein 5 CHMP5 NM_016410 dehydrogenase/reductase (SDR family)

219799_s_at DHRS9 NM_005771 member 9

222816_s_at zinc finger, CCHC domain containing 2 ZCCHC2 BE676543 222986_s_at scotin SCOTIN BC001463 223298_s_at 5 -nucleotidase, cytosolic III NT5C3 AF312735 223501 at tumor necrosis factor (ligand) TNFSF 13B AWl 51360 Table 16: 53 genes that provide the most differentiation between healthy donor individuals,

SLE patients, WG patients and RA patients. Affy ID Description Symbol Ace. No. superfamily, member 13b tumor necrosis factor (ligand)

223502_s_at TNFSF 13B AFl 34715 superfamily, member 13b nuclear receptor subfamily 1 , group I, 224589_at NR1I3 BF223193 member 3 poly (ADP-ribose) polymerase family,

224701_at PARP 14 AA056548 member 14

225415_at deltex 3 -like (Drosophila) DTX3L AA577672 226603_at chromosome 7 open reading frame 6 C7orf6 BE966604 226702_at hypothetical protein LOC 129607 LOC 129607 AI742057 Poly (ADP-ribose) polymerase family,

227807_at PARP9 AI738416 member 9

228152_s_at hypothetical protein FLJ31033 FLJ31033 AK023743 peroxisomal proliferator-activated

228230_at PRIC285 AL121829 receptor A interacting complex 285 interferon-induced protein with

229450_at IFIT3 AI075407 tetratricopeptide repeats 3

233425_at zinc finger, CCHC domain containing 2 ZCCHC2 AUl 47903 235276_at EST — AA781795

Likely ortholog of mouse acyl-

239277_at Coenzyme A thioesterase 2, ACATE2 AI559696 mitochondrial

239979_at Epithelial stromal interaction 1 (breast) EPSTIl BE645480 radical S-adenosyl methionine domain 242625_at RSAD2 AWl 89843 containing 2 243271 at Chromosome 7 open reading frame 6 C7orf6 AI064690 Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from aE disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

1 206553_at 2'-5'-oligoadenylate synthetase 2, 69/7IkDa NM_002535 0 0.2039 0 -0.6437

OO 219975 x a thioesterase domain containing 1 NM_018324 0 0 0

3 204439_.at interferon-induced protein 44-like NM_006820 -0.2864 0.3647 -0.0887 interferon-induced protein with tetratricopeptide

4 203153_. _at repeats 1 /// interferon-induced protein with NMJ)01548 -0.2158 0.3087 tetratricopeptide repeats 1

5 235276_.at AA781795 -0.5166 0.3153 0

6 213797_.at radical S-adenosyl methionine domain containing 2 AI337069 -0.4706 0.3731 -0.0877

203828 s a interleukin 32 /// interleukin 32 NM 004221 0 0

Table 17: List of 277 genes of Example 7, which is a gene list corrected for gender Mas by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

8 242625_at radical S-adenosyl methionine domain containing 2 AWl 89843 -0.4581 0.3478 -0.0024 -0.4609

205483_s_a

-4 9 interferon, alpha-inducible protein (clone IFI-15K) NM_005101 -0.1927 0.3004 0 -0.4382

233126_s_a

10 thioesterase domain containing 1 AKOOl 844 0 0 0 0 t

11 209409_at growth factor receptor-bound protein 10 D86962 0 0 0 0 231597 x a

12 AI371550 0.3791 0 0

13 226702_at hypothetical protein LOC 129607 AI742057 -0.3768 0.2905 0 209051 s a

14 ral guanine nucleotide dissociation stimulator AF295773 0 0 0

212768_s_a

15 olfactomedin 4 AL390736 0 0 t

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

16 21921 l_at ubiquitin specific protease 18 NM_017414 0 0.2502 -0.0281 -0.3643

17 202869_at 2 ',5 -oligoadenylate synthetase 1 , 40/46kDa NM_016816 0 0.2312 0 -0.3563

-4

O 18 202145_at lymphocyte antigen 6 complex, locus E NM_002346 -0.1159 0.2916 -0.0712 -( interferon-induced protein with tetratricopeptide

19 229450 at AI075407 -0.3219 0.2202 0 -( repeats 3

217775_s_a

20 retinol dehydrogenase 11 (all-trans and 9-cis) NM_016026 0 -( t

204388_s_a

21 monoamine oxidase A NM_000240 0 t

205552_s_a

22 2 ',5 -oligoadenylate synthetase 1 , 40/46kDa NM_002534 0.1319 0.2625 0 -I t

23 215248_at growth factor receptor-bound protein 10 AU145003 0 0 0 (

24 210999_s_a growth factor receptor-bound protein 10 U66065 0 0 0 (

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender Has by removing male control samples from all disease and healthy groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

25 218400_at 2 -5 -oligoadenylate synthetase 3, 10OkDa NM_006187 -0.1118 0.2588 -0.3029

Fc fragment of IgE, high affinity I, receptor for; alpha 211734_s_a

26 polypeptide /// Fc fragment of IgE, high affinity I, BC005912 receptor for; alpha polypeptide

202900_s_a

27 nucleoporin 88kDa NM_002532 0 -(

28 204972_at 2 '-5 -oligoadenylate synthetase 2, 69/7IkDa NM_016817 0 0.2204 -( interferon-induced protein with tetratricopeptide

29 204747 at NMJ)Ol 549 -0.2794 0.2608 -( repeats 3

214453_s_a

30 interferon-induced protein 44 NM_006417 -0.1619 0.2778 -0.0543 -< t

31 202859 x a interleukin δ NM 000584 0

Table 17: List of 211 genes of Example 7, which is a gene list corrected, for gender bias by removing male control samples from all disease and healthy control groups_*

R '

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k

32 219863_at hect domain and RLD 5 NM_016323 -0.2334 0.2748 0 -0.2701

-4

4- myxovirus (influenza virus) resistance 1, interferon- inducible protein p78 (mouse) /// myxovirus (influenza

33 202086 at NM_002462 -0 .1609 0.2559 0 virus) resistance 1, interferon-inducible protein p78 (mouse)

34 212793_ at dishevelled associated activator of morphogenesis 2 BF513244 0 0 0 A disintegrin-like and metalloprotease (reprolysin

35 236901_ at AA035730 0 0 0 type) with thrombospondin type 1 motif, 2

36 220418_ at ubiquitin associated and SH3 domain containing, A NM_018961 0 0 0

206177_ _s_a

37 arginase, liver NM_000045 0 0 0 t

38 227609 at epithelial stromal interaction 1 (breast) AA633203 -0 .2399 0.2476 0

Table 17: List of ^'277 genes of Example 1, which is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k

39 -0.2446

-4 major histocompatibility complex, class II, DQ beta 1 212998_x_a

40 /// major histocompatibility complex, class II, DQ beta AI583173 0 -C t

1

41 228617_at XIAP associated factor- 1 AA142842 -0.1706 0.2391 0 -( 222154 s a

42 DNA polymerase-transactivated protein 6 AK002064 0.2344 -0.0689 -( t

21184 l_s_a tumor necrosis factor receptor superfamily, member

43 U94510 0 0 -( t 25

209602 s a

44 GATA binding protein 3 AI796169 0 0

45 214059_at Interferon-induced protein 44 BE049439 -0.1582 0.2303 -0.0618

Table 17: List of ^'277 genes of Example 7, which is a gene list corrected for gender Mas by removing male control samples from all disease arid healthy control groups. R

Healthy SLE WG

A RA

ASy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

211506 s a

46 interleukin 8 AF043337 -0.2289 t

208858 s a likely ortholog of mouse membrane bound C2 domain

47 ^{~ ~} BC004998 0 0 t containing protein

223849_s_a

48 MovlO, Moloney leukemia virus 10, homolog (mouse) BC002548 -0.097 0.1931 t

219519_s_a

49 sialoadhesin /// sialoadhesin NM_023068 -0.0078 0.2103 -0.0702 t

202747_s_a

50 integral membrane protein 2 A NM_004867 0 0 0

210202_s_a

51 bridging integrator 1 U87558 0 0 0

52 208168_s_a chitinase 1 (chitotriosidase) NM_003465 0 0 0 i

snder bias by removing male control samples from all disease and

•healthy control gro ouuppss..

R ι ^"

Healthy SLE WG A RA

¹ Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k t

53 219684_at 28kD interferon responsive pro NM_022147 0 0.1371 0 -0.2011

« 54 227952_at Hypothetical protein FLJ90036 AI580142 0.2 0 0

55 219352 at hect domain and RLD 6 NM_017912 0 0.192 0 -(

56 203725_at growth arrest and DNA-damage-inducible, alpha NMJ)01924 0 0 0 0 219062 s a

57 zinc finger, CCHC domain containing 2 NMJ) 17742 0 0.1951 0 -( t

58 206133_at XIAP associated factor- 1 NMJ) 17523 0 0.187 0 -( hypothetical protein FLJ20701 /// hypothetical protein

59 219093 at NM_017933 0 0 0 -( FLJ20701

205875_s_a

60 three prime repair exonuclease 1 NM_016381 0 0.1406 0 -I

61 20241 l_at interferon, alpha-inducible protein 27 NM 005532 0 0.1891 -0.1462

aider bias by rem oving-male control samples from all disease and j healthy control gro ouuppss.. •

R ^{" "}

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

62 205660_at 2 -5 -oligoadenylate synthetase-like NM_003733 0 0.1887 0 -0.0339 interferon-induced protein with tetratricopeptide

63 226757 at AA131041 -0.1198 0.1874 0 0

ON repeats 2

203596_s_a interferon-induced protein with tetratricopeptide 64 NM 012420 0 0.1861 0 t repeats 5 early growth response 2 (Krox-20 homolog,

65 205249 at NM 000399 -0.1829 0.0143 0

Drosophila)

202446_s_a

66 phospholipid scramblase 1 AI825926 -0.1803 0.121 0

227347_x_a

67 hairy and enhancer of split 4 (Drosophila) NM 021170 0.1778

218943_s_a

68 DEAD (Asp-Glu- Ala-Asp) box polypeptide 58 NM 014314 -0.0459 0.1766 0

Table 17: List of 277 genes of Example 7, which is a gene list collected for gender bias by removing male control samples from all disease and healthy control groups,

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

69 233425_at zinc finger, CCHC domain containing 2 AUl 47903 -0.0483 0.175 0 0

70 219209_at interferon induced with helicase C domain 1 NM_022168 0 0.1473 0 -0.175

-4

4- -4 71 219298_at enoyl Coenzyme A hydratase domain containing 3 NM_024693 0 0 0 0

6-phosphofructo-2-kinase/fructose-2,6-biphosphatase

72 209992 at AB044805 0 0 0

219423_x_a tumor necrosis factor receptor superfamily, member

Full-length cDNA clone CS0DI014YH21 of Placenta

74 226311 at BF058422

Cot 25 -normalized of Homo sapiens (human)

6-phosphofructo-2-kinase/fructose-2,6-biphosphatase

75 226733 at AA587884 0 0 0

2

76 207802_at cysteine-rich secretory protein 3 NM__006061 -0.1604 0 0

77 203595_s_a interferon-induced protein with tetratricopeptide N47725 0 0.1595 0

Table 17: List of 211 genes of Example 7, which is a- gene list corrected for gender bias by removing male control samples torn all disease and healthy control groups.

R ^:

Healthy SLE WG

A RA

AfEy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k repeats 5

217147_ _s_a

7 7 /9Qy T cell receptor interacting molecule AJ240085 0 0 0 -( t

80 232222_at chromosome 18 open reading frame 49 AK000229 -0.059 0.1508 0

208436_. _s_a

81 interferon regulatory factor 7 NM_004030 0 0.1506 0 t

82 204857_at MADl mitotic arrest deficient-like 1 (yeast) NM_003550 0 0 0

224490_ _s_a hypothetical protein LOC284058 /// hypothetical

83 BC006271 0.1492 -0.0127 0 t protein LOC284058

84 239979_at Epithelial stromal interaction 1 (breast) BE645480 0 0.1486 0

85 219364 at likely ortholog of mouse Dl Ilgp2 NM 024119 0 0.1454 0

Table 17: List of ^'277 genes of Example 7, which is a gene list corrected for gender Mas by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k interferon-induced protein with tetratricopeptide

86 217502 at BE888744 0 0.1451 -0.0921 repeats 2

-4

219819_s_a

87 mitochondrial ribosomal protein S28 NM_014018 0 0 0 -(

88 21969 l_at sterile alpha motif domain containing 9 NMJ) 17654 0 0.1429 0 -( 205353 s a

89 prostatic binding protein NM 002567 0 0 0 -( t

234883 x a T-cell antigen receptor beta chain /// T cell receptor V

90 ^{~ ~} M97943 -< t beta6-D-J /// T cell receptor V-beta 6

203683_s_a

91 vascular endothelial growth factor B NM_003377 0 0 0 t

92 230036_at chromosome 7 open reading frame 6 BE669858 -0.0371 0.1343 0

93 228152_s_a hypothetical protein FLJ31033 AK023743 -0.1329 0.0852 0

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k

hypothetical protein LOC284058 /// hypothetical

-4 BC006271 Ul 94 224489 at 0.1319 0 0

O protein LOC284058

242020_s_a

95 Z-DNA binding protein 1 AI925506 -0.0979 0.1319 0 t

96 207269_at defensin, alpha 4, corticostatin NM_001925 0 0 0 210797 s a

97 2 -5 -oligoadenylate synthetase-like AF063612 0 0.131 0 t

217933_s_a

98 leucine aminopeptidase 3 NM_015907 0 0.118 0

99 221823_at hypothetical gene supported by AF038182; BC009203 A ALL556655774411 0 0 0

100 226603_at chromosome 7 open reading frame 6 BE966604 -0.0572 0.1177 0

101 200986_at serine (or cysteine) proteinase inhibitor, clade G (Cl N NMM_000000006622 0 0.117 0

t !

\ R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k inhibitor), member 1, (angioedema, hereditary)

-4 102 230354_at Transcribed locus BG236273 0 0 0 0.1169 Ul 218543 s a

103 zinc finger CCCH type domain containing 1 NM__022750 0 0.1166 0

104 219279_at dedicator of cytokinesis 10 NMJU7718 0 0 0

105 205569 at lysosomal-associated membrane protein 3 NMJH4398 0 0.1152 0

T cell receptor delta locus /// T-cell receptor-delta

106 213830 at AW007751 0 0 0 mRNA, 3'end.

107 213294_at Hypothetical protein FLJ38348 AV755522 -0.0567 0.1143 0

108 22853 l_at sterile alpha motif domain containing 9 AA741307 0 0.1117 0

109 231688_at Transcribed locus AW337833 0 0 0

110 243589_at hypothetical protein LOC284058 AI823453 0.1102 -0.0059 0

111 211012 s a promyelocytic leukemia BC000080 0 0.1088 0

Table 17: List of 277 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k t

211456_x_a

-4 AF333388 0 0.0608 0 - -(0.1087

Ul 112 i. Similar to 60S ribosomal protein L35

K> t

113 210607_at fins-related tyrosine kinase 3 ligand U03858 0 0 0 -(

114 228607_at 2 -5 -oligoadenylate synthetase 2, 69/7IkDa AI651594 0 0.1064 0 -(

115 239988_at Hect domain and RLD 6 AA708470 0 0.1059 0 214575 s a

116 azurocidin 1 (cationic antimicrobial protein 37) NM__001700 0 0 0 C t

117 223599_at tripartite motif-containing 6 AF220030 0 0.1053 0 202430 s a

118 phospholipid scramblase 1 NM_021105 -0.0668 0.1052 0

119 206871_at elastase 2, neutrophil NMJ)01972 0 0 0 (

120 213817_at CDNA FLJ13601 fis, clone PLACE1010069 AL049435 0 0 0 (

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender Mas by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k

S Sttaauuffeenn,, R RNA binding protein, homolog 2

121 229417 at W46994 -0.1038 0 0 0 (Drosophila) w 122 22470 l_at poly (ADP-ribose) polymerase family, member 14 AA056548 0 0.0997 0 223220 s a

123 poly (ADP-ribose) polymerase family, member 9 AF307338 -0.0991 0.0819 0 t

124 228439_at hypothetical protein BC012330 AW083820 -0.0968 0.0274 0

125 22529 l_at polyribonucleotide nucleotidyltransferase 1 AI967971 0 0.0944 0 proteinase 3 (serine proteinase, neutrophil, Wegener

126 207341 at NM_002777 0 0 0 granulomatosis autoantigen) 127 242234_at XIAP associated factor-1 AI859280 0 0.0923 0 220492 s a

128 otoferlin NM 004802 0 0.0909 0 t

129 221973_at CDNA clone IMAGE:5217021, with apparent retained AI983904 0 0 0

Table 17: List of ^'277 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups,

R

Healthy SLE WG

RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k intron

208087 s a

^ 130 ^{~ ~} Z-DNA binding protein 1 /// Z-DNA binding protein 1 NM_030776 0.0901

*! t

205099_s_a

131 chemokine (C-C motif) receptor 1 NM_001295 0 0.0527 0 -( t

231577_s_a guanylate binding protein 1 , interferon-inducible,

132 AW014593 0 0.0873 0 t 67kDa

208581_x_a

133 metallothionein IX NM_005952 0 0.0871 0

134 210262_at cysteine-rich secretory protein 2 M25532 0 0 0

135 204415_at interferon, alpha-inducible protein (clone IFI-6- 16) NM_022873 0 0.0852 0 209417 s a

136 interferon-induced protein 35 BC001356 0 0.085 0

g male control samples from all disease and healthy control groups. i

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

20977 l_x_a CD24 antigen (small cell lung carcinoma cluster 4

137 AA761181 0 0 0 0.0837 t antigen)

-4

$ 138 203547_at CD4 antigen (p55) /// CD4 antigen (p55) U47924 0 0 0 -I

216379_x_a CD24 antigen (small cell lung carcinoma cluster 4

139 AKOOO 168 0 0 0 ( antigen)

140 44673 at sialoadhesin N53555 0 0.0813 0 carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) ///

141 211657 at Ml 8728 0 carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)

219356_s_a

142 chromatin modifying protein 5 NM_016410 0 0.0797 0 t

143 206710_s_a erythrocyte membrane protein band 4.1 -like 3 NM 012307 0 0 0

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender Mas by removing male control samples from all disease and healthy control groups. R

Healthy SLE WG

RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k

peroxisomal proliferator-activated receptor A

-4 144 228 AL121829 -0.0273 0.0779 0 0 Ul 230 at interacting complex 285 growth factor independent IB (potential regulator of

145 208501 at NM_004188 0 0 0 -(

CDKNlA, translocated in CML)

146 230314_at Similar to hypothetical protein 628 AW014557 0 0.0778 0

214173_x_a

147 chromosome 19 open reading frame 2 AW514900 0 0 0

212657_s_a

148 interleukin 1 receptor antagonist U65590 0.0743 0

231530_s_a

149 chromosome 11 open reading frame 1 BG150085 0 0 0

150 AFFX- signal transducer and activator of transcription 1, AFFX- 0 0.0707 0

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender bias by removing fnale control samples from all disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k

HUMISGF3 9IkDa HUMISGF3A/M

A/M97935_ 97935 MB

-4 'M -4 MB_at guanylate binding protein 1, interferon-inducible, 151 202270_at 67kDa /// guanylate binding protein 1 , interferon- NM 002053 0 0.0696 0 inducible, 67kDa tumor necrosis factor (ligand) superfamily, member

152 223501 at AWl 51360 0.069

13b

207000 s a protein phosphatase 3 (formerly 2B), catalytic subunit,

153 - - NM_005605 0 -( t gamma isoform (calcineurin A gamma)

154 238581_at Guanylate binding protein 5 BG271923 0 0.0676 0

155 227210_at Scm-like with four mbt domains 2 T65020 0 0 0 -<

156 232666_at 2 -5 -oligoadenylate synthetase 3, 10OkDa R13458 0 0.0671 0

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender Mas by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

204891_s_a

157 lymphocyte-specific protein tyrosine kinase NM 005356 0 0 -0.0652

5 -nucleotidase, cytosolic III AF312735 0 0.0646 0 t

210915_x_a

159 T cell receptor beta constant 1 Ml 5564 -( t

160 211967_at pro-oncosis receptor inducing membrane injury gene B BGG553388662277 0 0.0579 0

161 212380_at KIAA0082 D43949 0 0.0331 0

162 238970_at Zinc finger RNA binding protein BF509781 0.0639 -0.0086 0

223502_s_a tumor necrosis factor (ligand) superfamily, member

163 AF134715 0 0.0628 0 t 13b 214551 s a

164 CD7 antigen (p41) NM 006137 0 0 0

g male control samples from all disease and healthy control groups.

1 R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

165 53720_at hypothetical protein FLJl 1286 AI862559 0 0.0622 0 0 signal transducer and activator of transcription 2,

-4 Ul 166 225636 at H98105 0 0.0616 0 0

113kDa

167 218919_at zinc finger, ANl -type domain 1 NM_024699 0 0 0 -(

168 231455_at FLJ42418 protein AA768888 0 0.0595 0

204286_s_a

169 phorbol- 12-myristate- 13 -acetate-induced protein 1 NM_021127 0.0465 t

212285_s_a

170 agrin AW008051 0.0586 0 t

20699 l_s_a

171 chemokine (C-C motif) receptor 5 NM_000579 t

172 236280_at Transcribed locus AI225238 0 0 0

173 203757_s_a carcinoembryonic antigen-related cell adhesion BC005008 0 0 0

Table 17: List of 277 genes of Example 7, which, is a gene list corrected for gender bias by removing male control samples from aU disease and healthy control groups.

R

Healthy SLE WG A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k t molecule 6 (non-specific cross reacting antigen)

-4 244398 x a

BE328243 0.0565

O 174 zinc finger protein 684

M-phase phosphoprotein 10 (U3 small nucleolar

175 212885 at AL545921 0 -( ribonucleoprotein)

22593 l_s_a

176 chromosome 17 open reading frame 27 AI954660 0 0.0561 0 t

177 20164 l_at bone marrow stromal cell antigen 2 NM_004335 0 0.0549 0

202968_s_a dual-specificity tyrosine-(Y)-phosphorylation

178 Y09216 0 0 0 t regulated kinase 2 217165 x a

179 metallothionein IF (functional) M10943 0 0.0536 0

180 217143_s_a T cell receptor alpha locus /// T cell receptor delta X06557 0 0 0

Table 17: List of ^'277 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from aE disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k t locus

210847_x_a tumor necrosis factor receptor superfamily, member

-4

Os 181 AF026071 0 0 0 -0.0525 t 25 /// putative NFkB activating protein

182 218085_at chromatin modifying protein 5 NMJ)15961 0 0.0522 0

225385_s_a

183 heterogeneous nuclear ribonucleoprotein L-like AW273811 -0.0519 0 0

222816_s_a

184 zinc finger, CCHC domain containing 2 BE676543 0 0.0516 0 t

206461_x_a

185 metallothionein IH NM_005951 0 0.0512 0 t

186 229194_at poly comb group ring finger 5 AL045882 0 0.0497 0

187 20765 l_at G protein-coupled receptor 171 NM_013308 0 0 0

188 244267_at Special AT-rich sequence binding protein 1 (binds to A AAA223377003399 0.0491 0 0

Table 17: List of 277 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups.

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k nuclear matrix/scaffold-associating DNA 's)

T cell receptor alpha constant /// T cell receptor alpha

3* 189 209670 at M12959 -0.0489 constant

225929_s_a

190 chromosome 17 open reading frame 27 AA233374 0.0489 t guanylate binding protein 1, interferon-inducible, 202269_x_a

191 67kDa /// guanylate binding protein 1 , interferon- BC002666 0 0.0486 0 inducible, 67kDa

192 230590_at Slingshot homolog 2 (Drosophila) BE675486 0 0 0

Solute carrier family 8 (sodium/calcium exchanger),

193 241041 at BF223010 0 0 0 member 1

194 235061_at protein phosphatase IK (PP2C domain containing) AV706522 0 0.0465 0

195 212750_at protein phosphatase 1, regulatory (inhibitor) subunit AB020630 0 0 0

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender Mas by removing male control samples from all disease and healthy control groups.

R ^"

Healthy SLE WG

A RA

AfEy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

16B

196 205241_at SCO cytochrome oxidase deficient homolog 2 (yeast) NM_005138 0 0.0462 0 0

£ 202864 s a

197 nuclear antigen SpIOO NM 003113 0 0.0426 0

198 243489 at BF514098 0.0415 0 0

220998_s_a unc-93 homolog B 1 (C. elegans) /// unc-93 homolog

199 NM_030930 0 0.0412 0

Bl (C. elegans)

200 205098_at chemokine (C-C motif) receptor 1 AI421071 0 0.0396 0

207777 s a 201 SP 140 nuclear body protein NM_007237 0 0.0395 0 t

202 204994_at myxovirus (influenza virus) resistance 2 (mouse) NM_002463 0 0.0387 0

203 222793_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 AK023661 0 0.0383 0

204 206676 at carcinoembryonic antigen-related cell adhesion M33326 0 0 0

Table 17: List of 277 genes of Example 7, which, is a gene list corrected for gender bias by removing male control samples from aE disease and healthy control groups.

R

Healthy SLE WG

A RA

AfEy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k molecule 8

205 231747_at cysteinyl leukotriene receptor 1 NM_006639 0 0.0374 0 0

-4

ATP-binding cassette, sub-family A (ABCl), member

206 203505 at AF285167 0 0.0369 0 1

207 233880_at chromosome 17 open reading frame 27 AL161961 0 0.0368 0

208 223767_at G protein-coupled receptor 84 AF237762 -0.0368 0 0

209 204140_at tyrosylprotein sulfotransferase 1 NM_003596 0 0 0

23533 l_x_a

210 polycomb group ring finger 5 AI341142 0 0.0349 0

Neural precursor cell expressed, developmentally

211 233223 at AK000850 down-regulated 9

208966_x_a 212 interferon, gamma-inducible protein 16 AF208043 0.0342 0

g male control samples from all disease and ^J healthy control groups. J R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

213 240413_at pyrin and HIN domain family, member 1 AI827431 0 0 0 -0.0339

214 229625_at Guanylate binding protein 5 BG545653 0 0.0338 0 0

204890_s_a

215 lymphocyte-specific protein tyrosine kinase U07236 0 0 0 - t

216 243271_at Chromosome 7 open reading frame 6 AI064690 0 0.0336 0 224225 s a

217 ets variant gene 7 (TEL2 oncogene) AF218365 0 0.0335 0

218

AFFX-

AFFX-

HUMISGF3 signal transducer and activator of transcription 1 , 219 HUMISGF3A/M 0 0.033 0

A/M97935_ 9IkDa 97935 3

3 at

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender bias by remo"dng male control samples from all disease and healthy control groups. R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

235256_s_a

220 galactose mutarotase (aldose 1-epimerase) BE788984 0 0.0328 0 t

S! 221 241916_at Phospholipid scramblase 1 AI984040 0 0.0322 0 212185 x a

222 metallothionein 2A NM 005953 0 0.0314 0

tumor necrosis factor (ligand) superfamily, member 10

202687_s_a

223 /// tumor necrosis factor (ligand) superfamily, member U57059 0.0312 0

10

224 225415_at deltex 3-like (Drosophila) AA577672 0 0.0311 0

225 230866_at BE549540 0 0.0297 0

218429_s_a

226 hypothetical protein FLJl 1286 NMJU8381 0 0.0296 0

227 209593_s_a torsin family 1 , member B (torsin B) AF317129 0 0.029 0

Table 17: List of ^"277 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k t

206025_s_a 228 tumor necrosis factor, alpha-induced protein 6 AWl 88198 0.0272 0

S ^t

202307_s_a transporter 1, ATP-binding cassette, sub-family B

229 NM 000593 0.0264 t (MDR/TAP)

211282_x_a tumor necrosis factor receptor superfamily, member

230 U94506 0 -( t 25

206332 s a

231 interferon, gamma-inducible protein 16 NM_005531 0 0.0262 0 t

232 214032_at zeta-chain (TCR) associated protein kinase 7OkDa AI817942 0 0 0 213293 s a

233 tripartite motif-containing 22 AA083478 0 0.0254 0

234 201649_at ubiquitin-conjugating enzyme E2L 6 NM 004223 0 0.0237 0

Table 17: List of 211 genes of Example 7, wMch is a gene list collected for gender bias by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k

0

RRSl ribosome biogenesis regulator homolog (S.

237 227807_at Poly (ADP-ribose) polymerase family, member 9 AI738416 0 0.0215 0

238 202863_at nuclear antigen SpIOO NM_003113 0 0.0204 0

N-ethylmaleimide-sensitive factor attachment protein,

239 20875 l_at BCOOl 165 0 0.0197 0 alpha

240 225897_at Myristoylated alanine-rich protein kinase C substrate AI709406 0 0.0197 0

222986_s_a

241 scotin BC001463 0 0.0193 0 t

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender Has by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs

N score score score score k

242 226925_at acid phosphatase-like 2 AW069729 0 0 0 0.0192

222920 s a

243 ^~ KIAA0748 gene product BG231515 0 0 0 -0 017S

244 209486_at disrupter of silencing 10 BC004546 0 0 0 -(

245 200923_at lectin, galactoside-binding, soluble, 3 binding protein NM_005567 0 0.0166 0

20421 l_x_a

246 eukaryotic translation initiation factor 2-alpha kinase 2 NM_002759 0 0.0158 0 t

247 226548_at hypothetical protein LOCI 12868 AI935915 0 0 0

CD40 ligand (TNF superfamily, member 5, hyper-IgM

248 207892 at NM_000074 0 0 0 syndrome)

249 226905_at hypothetical protein MGC45871 BG036514 0 -0.0149 0

250 205898_at chemokine (C-X3-C motif) receptor 1 U20350 0 0 0

251 204848_x_a hemoglobin, gamma A /// hemoglobin, gamma A NM 000559 0.0137 0 0

Table 17: List of ^"277 genes of Example 7, wMch is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups.

R ^""

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

endoplasmic reticulum-golgi intermediate

-4 252 224576 at AK000752 0 0 0 -4

O compartment 32 kDa protein

211796_s_a 253 T cell receptor beta constant 1 AF043179 0 0 0 -(

UDP-N-acetyl-alpha-D-galactosamineipolypeptide N-

254 219013 at NM_022087 0 0 0 -( acetylgalactosaminyltransferase 11 (GaINAc-Tl 1)

255 236285_at Hypothetical protein BC009980 AI631846 0 0.0111 0

T cell receptor alpha locus /// T cell receptor alpha 209671_x_a

256 locus /// T cell receptor alpha constant /// T cell M12423 0 receptor alpha constant

204285_s_a

257 phorbol- 12-myristate- 13 -acetate-induced protein 1 AI857639 0.0103 0

Table 17: List of 277 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from all disease and , healthy control groups. \

I R

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

212486_s_a

258 FYN oncogene related to SRC, FGR, YES N20923 -0.0101 t

^ 215049 x a

259 CD163 antigen Z22969

260 225525_at KIAAl 671 protein AB051458 0 0 0

261 235157_at Poly (ADP-ribose) polymerase family, member 14 AW297731 0 0.0088 0 AFFX-

AFFX-

HUMISGF3 signal transducer and activator of transcription 1,

262 HUMISGF3A/M 0 0.0081 0

A/M97935_ 9IkDa

97935_5

5_at

263 235175_at guanylate binding protein 4 BG260886 0 0.0076 0

264 232563_at zinc finger protein 684 AW275016 0 0.0072 0

265 221345_at G protein-coupled receptor 43 NM 005306 0 0.0069 0

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups.

R

Healthy SLE WG

A RA

Affy ID Gene Title Ace.No. Donor WBCs WBCs N score score score score k

266 202746_at integral membrane protein 2A AL021786 0 0 0 -0.0061

267 38241_at butyrophilin, subfamily 3, member A3 U90548 0 0.0055 0 -0.0023

;j 208095 s a

^M 268 signal recognition particle 72kDa NM 001222 0 -(

Tumor necrosis factor (ligand) superfamily, member

214329 x a

269 10 /// Tumor necrosis factor (ligand) superfamily, AW474434 0.0046 0 member 10 tumor necrosis factor (ligand) superfamily, member 10 270 202688_at /// tumor necrosis factor (ligand) superfamily, member NM_003810 0.0043

10

Signal transducer and activator of transcription 1,

271 232375 at AI539443 0 0.0028 0

9IkDa 272 235643_at chromosome 7 open reading frame 6 BE886225 0 0.0021 0

Table 17: List of 211 genes of Example 7, which is a gene list corrected for gender bias by removing male control samples from all disease and healthy control groups.

Healthy SLE WG

A RA

Affy ID Gene Title Ace. No. Donor WBCs WBCs N score score score score k

Likely ortholog of mouse acyl-Coenzyme A

273 239277 at AI559696 0 0.002 0 thioesterase 2, mitochondrial

-4 -4

W 229804_x_a COBW domain containing 1 /// COBW domain

274 AWl 69333 0 0.002 0 t containing 2 /// dopamine responsive protein

275 231769_at F-box protein 6 AF129536 0 0.0019 0

8.00E-

276 233072_at netrin G2 AI348745 0 0 04

204419_x_a hemoglobin, gamma A /// hemoglobin, gamma A ///

277 NM 000184 6.00E-04 0 0 t hemoglobin, gamma G /// hemoglobin, gamma G

Table 18: Increases expression of IFN-related genes correlates with increased SLE activity.

Samples comprised the "High IFN-iϊiduced" gene signature group (n=44) vs. the "Low IFN- ttiduced¹" gene signature group (n=28) using a permutation Mann- Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison and the fold change difference (High IFN relative to Low IFN group).

Affy ID Symbol Ace. No. p-value fold change

20241 l_at IFI27 NM_005532 0.002 22.81

204439_at IFI44L NM_006820 0.002 17.62

20241 l_at IFI27 NM_005532 0.002 17.58

213797_at RSAD2 AI337069 0.002 16.23

213797_at RSAD2 AI337069 0.002 15.58

204439_at IFI44L NM_006820 0.002 15.56

21921 l_at USP 18 NM_017414 0.002 13.18

214453_s_at IFI44 NM_006417 0.002 13.10

226702_at LOC 129607 AI742057 0.002 11.40

242625_at RSAD2 AWl 89843 0.002 9.86

218986_s_at FLJ20035 NM_017631 0.002 9.22

218400_at OAS3 NM_006187 0.002 9.03

214453_s_at IFI44 NM_006417 0.002 8.91

203153_at IFITl NMJ)01548 0.002 8.46

205483_s_at G1P2 NM_005101 0.002 8.30

202869_at OASl NM_016816 0.002 8.21

205483_s_at G1P2 NM_005101 0.002 8.14

204972_at OAS2 NM_016817 0.002 7.79

235276_at EPSTIl AA781795 0.002 7.65

218400_at OAS3 NM_006187 0.002 7.51

203153_at IFITl NM_001548 0.002 7.44

218400_at OAS3 NM_006187 0.002 7.25

239979_at EPSTIl BE645480 0.002 7.14

235276_at EPSTIl AA781795 0.002 7.04

228617 at HSXIAPAFl AA142842 0.002 6.93 Table 18: Increases expression of IFN-related genes correlates with increased SLB activity.

Samples comprised the "High IFN-induced" gene signature group (n=44) vs. the '11,Gw IFN- induced" gene signature group (n=28) using a permutation Mann- Whitney test A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-vatae for the comparison and the fold change difference (High DFN relative to Low IFN group).

Affy ID Symbol Ace. No. p-value fold change

202145_at LY6E NM_002346 0.002 6.87

219863_at HERC5 NM_016323 0.002 6.64

21921 l_at USP 18 NM_017414 0.002 6.61

204972_at OAS2 NM_016817 0.002 6.18

235276_at EPSTIl AA781795 0.002 6.17

210797_s_at OASL AF063612 0.002 6.09

228617_at HSXIAPAFl AA142842 0.002 6.06

219684_at IFRG28 NM_022147 0.002 6.03

206133_at HSXIAPAFl NM_017523 0.002 5.97

219352_at HERC6 NM_017912 0.002 5.90

239979_at EPSTIl BE645480 0.002 5.85

202869_at OASl NM_016816 0.002 5.83

202145_at LY6E NM_002346 0.002 5.82

205552_s_at OASl NM_002534 0.002 5.73

219684_at IFRG28 NM_022147 0.002 5.62

203595_s_at IFIT5 N47725 0.002 5.49

44673_at SN N53555 0.002 5.41

218986_s_at FLJ20035 NM_017631 0.002 5.17

210797_s_at OASL AF063612 0.002 5.09

229450_at IFIT3 AI075407 0.002 4.93

242234_at HSXIAPAFl AI859280 0.002 4.87

204415_at G1P3 NM_022873 0.002 4.82

202086 at MXl NM 002462 0.002 4.79

226702_at LOC129607 AI742057 0.002 4.78

219863 at HERC5 NM 016323 0.002 4.54 Table 18: Increases expression of IFN-related genes correlates with increased SLE activity.

Samples comprised the "High IFN-indoced" gene signature group (n=44) vs. the "Low IFN- induced" gene signature group (n=28) using a permutation Mann-Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-v&lue for the comparison and the fold change difference (High IFN relative to Low IFN group).

Affy ID Symbol Ace. No₄ p-value fold change

229450_at IFIT3 AI075407 0.002 4.54

235643_at C7orf6 BE886225 0.002 4.38

204747_at IFIT3 NMJ)Ol 549 0.002 4.35

222816_s_at ZCCHC2 BE676543 0.002 4.32

226603_at C7orf6 BE966604 0.002 4.30

235157_at PARP14 AW297731 0.002 4.28

202269_x_at GBPl BC002666 0.002 4.26

219684_at IFRG28 NM_022147 0.002 4.26

22853 l_at SAMD9 AA741307 0.002 4.25

206133_at HSXIAPAFl NMJH7523 0.002 4.24

217933_s_at LAP3 NM_015907 0.002 4.18

203596_s_at IFIT5 NM_012420 0.002 4.16

205552_s_at OASl NM_002534 0.002 4.07

209417_s_at IFI35 BC001356 0.002 4.04

210797_s_at OASL AF063612 0.002 4.03

233425_at ZCCHC2 AU147903 0.002 3.97

226603_at C7orf6 BE966604 0.002 3.90

235157__at PARP14 AW297731 0.002 3.87

222154_s_at DNAPTP6 AK002064 0.002 3.85

202086_at MXl NM_002462 0.002 3.81

226757_at IFIT2 AA131041 0.002 3.81

222793_at DDX58 AK023661 0.002 3.78

231956_at KIAA1618 AA976354 0.002 3.74

203596 s at IFIT5 NM 012420 0.002 3.72 Table IS: Increases expression, of IFN-related genes correlates with increased SLE activity.

Samples comprised the "High IFN4nduced" gene signature group (n=44) vs. the "Low IFN- induced" gene signature group (&=28) using a permutation Mann- Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison and the fold change difference (High IFN relative to Low IFN group).

Affy ID Symbol Ace. No. p-value fold change

219209_at IFIHl NM_022168 0.002 3.69

200986_at SERPINGl NM_000062 0.002 3.60

219209_at IFIHl NM_022168 0.002 3.55

230314_at — AWO 14557 0.002 3.51

24327 l_at C7orf6 AI064690 0.002 3.50

202430_s_at PLSCRl NM_021105 0.002 3.49

219364_at LGP2 NM_024119 0.002 3.44

210797_s_at OASL AF063612 0.002 3.40

226757_at IFIT2 AA131041 0.002 3.35

205098_at CCRl AI421071 0.002 3.29

217933_s_at LAP3 NM_015907 0.002 3.28

22593 l_s_at C17orf27 AI954660 0.002 3.26

230036_at C7orf6 BE669858 0.002 3.25

225636_at STAT2 H98105 0.002 3.23

218943_s_at DDX58 NMJH4314 0.002 3.21

202446_s_at PLSCRl AI825926 0.002 3.20

231769_at FBXO6 AF129536 0.002 3.19

233880_at C17orf27 AL161961 0.002 3.18

235643_at C7orf6 BE886225 0.002 3.17

211012_s_at PML BC000080 0.002 3.14

202270_at GBPl NM_002053 0.002 3.12

202446_s_at PLSCRl AI825926 0.002 3.12

220492_s_at OTOF NM_004802 0.002 3.11

205098_at CCRl AI421071 0.002 3.09

223501 at TNFSF 13B AW151360 0.002 3.06 Table 18: Increases expression of IFN-related genes correlates with increased SLE activity.

Samples comprised the "High IFN-indueed" gene signature group (n=44) vs. the "Low IFN- induced" gene signature group (n=28) using a permutation Mann-Whitney test. A cutoff of p=0,05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison and the fold change difference (High IFN relative to Low IFN group).

AffyID Symbol Ace. No. p-value fold change

24327 l_at C7orf6 AI064690 0.002 3.04

228230_at PRIC285 AL121829 0.002 3.03

222816_s_at ZCCHC2 BE676543 0.002 3.00

219691_at SAMD9 NM_017654 0.002 2.99

209417_s_at IFI35 BC001356 0.002 2.99

225929_s_at C17orf27 AA233374 0.002 2.99

22593 l_s_at C17orf27 AI954660 0.002 2.94

225929_s_at C17orf27 AA233374 0.002 2.93

222816_s_at ZCCHC2 BE676543 0.002 2.93

233425_at ZCCHC2 AU147903 0.002 2.91

213293_s_at TRIM22 AA083478 0.002 2.89

22470 l_at PARP14 AA056548 0.002 2.88

242234_at HSXIAPAFl AI859280 0.002 2.87

241916_at PLSCRl AI984040 0.002 2.84

22853 l_at SAMD9 AA741307 0.002 2.83

205099_s_at CCRl NM_001295 0.002 2.81

213294_at FLJ38348 AV755522 0.002 2.78

202270_at GBPl NM_002053 0.002 2.76

218429_s_at FLJl 1286 NM_018381 0.002 2.76

218943_s_at DDX58 NM_014314 0.002 2.71

218943_s_at DDX58 NM_014314 0.002 2.70

213293_s_at TRIM22 AA083478 0.002 2.69

231577_s_at GBPl AW014593 0.002 2.67

22350 l_at TNFSF13B AW151360 0.002 2.66

205099 s at CCRl NM 001295 0.002 2.65 Table 18: Increases expression of IFN-related genes correlates with increased SLE activity. Samples comprised the "High IFN-induced" gene signature group (n=44) vs. the "Low IFN- iridueed" gene signature group (n=28) using a permutation Mann-Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison and the fold change difference (High IFN relative to Low IFN group).

AffyID Symbol Ace. No. p-value fold change

223220_s_at PARP9 AF307338 0.002 2.63

218543_s_at ZC3HDC1 NM_022750 0.002 2.62

225636_at STAT2 H98105 0.002 2.62

24296 l_x_at DDX58 AI304317 0.002 2.61

202430_s_at PLSCRl NM_021105 0.002 2.61

202864_s_at SPlOO NM_003113 0.002 2.59

228439_at MGC20410 AW083820 0.002 2.57

2042 l l_x jit EIF2AK2 NM_002759 0.002 2.56

242625_at RSAD2 AWl 89843 0.002 2.54

218085_at CHMP5 NM_015961 0.002 2.53

200923_at LGALS3BP NM_005567 0.002 2.53

204211_x_at EIF2AK2 NM_002759 0.002 2.50

22470 l_at PARP 14 AA056548 0.002 2.48

235276_at EPSTIl AA781795 0.002 2.47

208436_s_at IRF7 NM_004030 0.002 2.45

228152_s_at FLJ31033 AK023743 0.002 2.44

226117_at TIFA AAl 95074 0.002 2.43

222816_s_at ZCCHC2 BE676543 0.002 2.41

219352_at HERC6 NM_017912 0.002 2.40

230036_at C7orf6 BE669858 0.002 2.39

209546_s_at APOLl AF323540 0.002 2.37

232222_at C18orf49 AK000229 0.002 2.35

230405_at LOC441109 AI143416 0.002 2.35

228607_at OAS2 AI651594 0.002 2.34

238581_at GBP5 BG271923 0.004 2.33

228304 at BE674118 0.002 2.33 Table 18: Increases expression, of IFN-related genes correlates with increased SLE activity. Samples comprised the "High IFN-induced" gene signature group (n=44) vs. the *^*Low IFN- indueed" gene signature group (n=28) using a permutation Mann- Whitney test. A cutoff of p^O.OS or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high ΪFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-vatae for the comparison and the fold change difference (High IFN relative to Low IFN group).

Affy ID Symbol Ace, No, p-value fold change

202864_s_at SPlOO NM_003113 0.002 2.32

223434_at GBP3 AL136680 0.002 2.31

202687_s_at TNFSFlO U57059 0.002 2.31

226117_at TIFA AA195074 0.002 2.31

209593_s_at TORlB AF317129 0.002 2.29

211967_at PORIMIN BG538627 0.002 2.28

228230_at PRIC285 AL121829 0.002 2.26

202837_at FLN29 NM_006700 0.002 2.25

225415_at DTX3L AA577672 0.002 2.25

202269_x_at GBPl BC002666 0.004 2.24

201641_at BST2 NM_004335 0.002 2.23

212380_at KIAA0082 D43949 0.002 2.21

235276_at EPSTIl AA781795 0.002 2.20

223952_x_at DHRS9 AF240698 0.004 2.20

23858 l_at GBP5 BG271923 0.002 2.20

241916_at PLSCRl AI984040 0.002 2.19

211967_at PORIMIN BG538627 0.002 2.19

231956_at KIAA1618 AA976354 0.002 2.18

223220_s_at PARP9 AF307338 0.002 2.15

205875_s_at TREXl NM_016381 0.002 2.14

232787_at PRIC285 AK023724 0.002 2.13

211367_s_at CASPl U13699 0.002 2.12

219519_s_at SN NM_023068 0.004 2.12

218085_at CHMP5 NM_015961 0.002 2.11

227458 at PDCDlLGl AI608902 0.002 2.10 Table 18: Increases expression of IFN-reϊated genes correlates with increased SLE activity.

Samples comprised the "High. IFN-induced" gene signature group (n=44) vs. the "Low IFN- taduced" gene signature group (n=28) using a permutation Mann- Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison and the fold change difference (High IFN relative to Low IFN group).

Affy ID Symbol Ace. No. p-value fold change

200986_at SERPINGl NM_000062 0.002 2.08

53720_at FLJl 1286 AI862559 0.002 2.07

212285_s_at AGRN AW008051 0.002 2.06

206026_s_at TNFAIP6 NM_007115 0.012 2.06

222986_s_at SCOTIN BCOO 1463 0.002 2.04

232222_at C18orf49 AK000229 0.002 2.03

229194_at PCGF5 AL045882 0.002 2.02

212185_x_at MT2A NM_005953 0.002 2.02

223952_x_at DHRS9 AF240698 0.002 2.01

209762_x_at SPI lO AF280094 0.002 2.01

206026_s_at TNFAIP6 NM_007115 0.008 2.00

223298_s_at NT5C3 AF312735 0.002 1.99

225973_at TAP2 AA573502 0.002 1.98

212380_at KIAA0082 D43949 0.002 1.98

225973_at TAP2 AA573502 0.002 1.98

203148_s_at TRIM14 NM_014788 0.002 1.97

242907_at GBP2 BF509371 0.002 1.97

211012_s_at PML BC000080 0.002 1.96

218943_s_at DDX58 NM_014314 0.002 1.95

201649_at UBE2L6 NM_004223 0.002 1.92

214329_x_at TNFSFlO AW474434 0.002 1.91

232375_at STATl AI539443 0.002 1.91

203595_s_at IFIT5 N47725 0.002 1.91

206332_s_at IFI16 NM_005531 0.002 1.90

226326 at PCGF5 AI798098 0.002 1.90 Table 18: Increases expression of IFN-related genes correlates with increased. SLE activity. Samples comprised the "High IFN-induced" gene signature group (n=44) vs. the "Low IFN- induced" gene signature group using a permutation Mann- Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison, and the fold change difference (High IFN relative to Low DFN group).

Affy ID Symbol Ace. No. p-value fold change

208436_s_at IRF7 NM_004030 0.002 1.90

225710_at H99792 0.004 1.89

228152_s_at FLJ31033 AK023743 0.002 1.89

220998_s_at UNC93B1 NM_030930 0.002 1.89

209593_s_at TORlB AF317129 0.002 1.89

211367_s_at CASPl U13699 0.002 1.89

235256_s_at GALM BE788984 0.002 1.89

201202_at PCNA NM_002592 0.002 1.88

202863_at SPlOO NM_003113 0.002 1.88

219799_s_at DHRS9 NM_005771 0.002 1.87

222154_s_at DNAPTP6 AK002064 0.002 1.87

229625_at GBP5 BG545653 0.002 1.87

204994_at MX2 NM_002463 0.002 1.86

224009_x_at DHRS9 AF240697 0.002 1.84

224225_s_at ETV7 AF218365 0.002 1.84

203596_s_at IFIT5 NM_012420 0.002 1.84

208966_x_at IFI16 AF208043 0.002 1.84

38241_at BTN3A3 U90548 0.002 1.82

222986_s_at SCOTIN BC001463 0.002 1.81

210705_s_at TRIM5 AF220028 0.002 1.81

231577_s_at GBPl AWO 14593 0.002 1.81

206332_s_at IFI16 NM_OO5531 0.002 1.80

217502_at IFIT2 BE888744 0.002 1.80

204286_s_at PMAIPl NM_021127 0.002 1.80

201649 at UBE2L6 NM 004223 0.002 1.79 Table 18: Increases expression of IFN-related genes correlates with increased SLE activity.

Samples comprised the "High IFN-induced" gene signature group (n=44) vs. the "Low IFN- ittduced^*' gene signature group (n=28) using a permutation Mann- Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-mduced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-vatae for the comparison and the fold change difference (High IFN relative to Low IFN group).

AffyID Symbol Ace. No. p-value fold change

212657_s_at ILlRN U65590 0.002 1.78

228230_at PRIC285 AL121829 0.002 1.78

206025_s_at TNFAIP6 AW188198 0.002 1.77

225897_at MARCKS AI709406 0.01 1.77

202863_at SPlOO NM_003113 0.002 1.77

208966_x_at IFI 16 AF208043 0.002 1.76

219356_s_at CHMP5 NM_016410 0.002 1.76

221827_at C20orfl8 BE788439 0.002 1.76

20309 l_at FUBPl NM_003902 0.002 1.76

209762_x_at SPI lO AF280094 0.002 1.76

20482 l_at BTN3A3 NM_006994 0.002 1.76

225415_at DTX3L AA577672 0.002 1.75

206026_s_at TNFAIP6 NM_007115 0.002 1.74

219799_s_at DHRS9 NM_005771 0.002 1.74

242020_s_at ZBPl AI925506 0.002 1.74

239277_at ACATE2 AI559696 0.004 1.73

20524 l_at SCO2 NM_005138 0.002 1.73

20524 l_at SCO2 NM_OO5138 0.002 1.72

225710_at — H99792 0.006 1.71

208965_s_at IFI 16 BG256677 0.002 1.70

240718_at CASCl AW303384 0.004 1.70

208581_x_at MTlX NM_005952 0.002 1.70

204470_at CXCLl NM_001511 0.002 1.70

214059_at IFI44 BE049439 0.006 1.70

232034 at LOC203274 ALl 17607 0.002 1.69 Table 18: Increases expression of IFN-related genes correlates with increased SLE activity.

Samples comprised the "High IFN-induced" gene signature group (n~44) vs. the "Low IFN- iiiduced'* gene signature group (n=28) using a permutation Mam-Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-vatae for the comparison and the fold change difference (High IFN relative to Low IEN group).

Affy ID Symbol Ace. No. p- value fold change

223298_s_at NT5C3 AF312735 0.002 1.69

229194_at PCGF5 AL045882 0.004 1.69

223502_s_at TNFSF13B AF134715 0.002 1.69

223502_s_at TNFSF13B AF134715 0.002 1.68

224225_s_at ETV7 AF218365 0.006 1.68

204286_s_at PMAIPl NM_021127 0.008 1.68

218543_s_at ZC3HDC1 NM_022750 0.002 1.68

203148_s_at TRIM14 NM_014788 0.002 1.68

227807_at PARP9 AI738416 0.002 1.67

202307_s_at TAPl NM_000593 0.002 1.67

206553_at OAS2 NM_002535 0.002 1.67

234344_at RAP2C AF093744 0.012 1.67

226459_at PIK3AP1 AW575754 0.002 1.66

225897_at MARCKS AI709406 0.006 1.66

202687_s_at TNFSFlO U57059 0.002 1.65

207777_s_at SP140 NM_007237 0.002 1.65

204286_s_at PMAIPl NM_021127 0.002 1.65

223298_s_at NT5C3 AF312735 0.008 1.65

218429_s_at FLJl 1286 NM_018381 0.002 1.64

227458_at PDCDlLGl AI608902 0.022 1.64

202307_s_at TAPl NM_000593 0.002 1.64

207777_s_at SP140 NM_007237 0.002 1.63

201202_at PCNA NM_002592 0.008 1.62

202688_at TNFSFlO NM_003810 0.002 1.62 201641 at BST2 NM 004335 0.002 1.61 Table 18: Increases expression of IFN-related genes correlates with increased SLE activity. Samples comprised the "High IFN-induced" gene signature group (»=44) vs. the "Low IFN- indueed'* gene signature group (n=28) using a permutation Mann- Whitney test, A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were HP/HIGHER in the high IFN-imduced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison and the fold change difference (High DFN relative to Low IFN group).

Affy ID Symbol Ace. No. p-value fold change

219356_s_at CHMP5 NM_016410 0.002 1.61 212657_s_at ILlRN U65590 0.002 1.60 202863_at SPlOO NMJXBl 13 0.002 1.60

202688_at TNFSFlO NM_003810 0.008 1.60

23506 l_at PPMlK AV706522 0.002 1.59

20482 l_at BTN3A3 NM_006994 0.002 1.59

204698_at ISG20 ' NM_002201 0.002 1.59

21451 l_x_at FCGRlA L03419 0.044 1.57

205569_at LAMP3 NMJH4398 0.004 1.57

223298_s_at NT5C3 AF312735 0.002 1.56

209762_x_at SPI lO AF280094 0.002 1.56

206553_at OAS2 NM_002535 0.002 1.56

226459_at PIK3AP1 AW575754 0.002 1.56

204326_x_at MTlX NM_002450 0.004 1.56

211012_s_at PML BC000080 0.002 1.55

231747_at CYSLTRl NM_006639 0.002 1.55

226459_at PIK3AP1 AW575754 0.036 1.55

230405_at LOC441109 AI143416 0.002 1.55

231182_at WASPIP BF446719 0.016 1.53

204285_s_at PMAIPl AI857639 0.002 1.53

239277_at ACATE2 AI559696 0.004 1.53

204698_at ISG20 NM_002201 0.002 1.53

220998_s_at UNC93B1 NM_030930 0.002 1.53

38241_at BTN3A3 U90548 0.004 1.52

232375 at STATl AI539443 0.002 1.52 Table 18: Increases expression of IFN-related genes correlates with increased SLE activity. Samples comprised the "High IFN-induced" gene signature group (n=44) vs. the "Low IFN- induced" gene signature group (n=28) using a permutation Mam-WMtaβy test, A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER, in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison and the fold change difference (High IFN relative to Low IFN group).

Affy ID Symbol Ace. No. p-value fold change

221345_at GPR43 NM_005306 0.018 1.51

204747_at IFIT3 NM_001549 0.002 1.51

202863_at SPlOO NMJXBl 13 0.004 1.51

209498_at CEACAMl X16354 0.05 1.51

205003_at DOCK4 NMJ) 14705 0.024 1.50

223434_at GBP3 AL136680 0.002 1.50

242907_at GBP2 BF509371 0.014 1.49

219691_at SAMD9 NMJ) 17654 0.002 1.49

216565_x_at LOC391020 AL121994 0.008 1.49

20875 l_at NAPA BCOOl 165 0.048 1.48

222498_at AZI2 AI809206 0.044 1.48

235106_at MAML2 AW847318 0.022 1.48

236285_at MGC16635 AI631846 0.002 1.48

216565_x_at LOC391020 AL121994 0.002 1.47

201585_s_at SFPQ BG035151 0.02 1.46

22529 l_at PNPTl AI967971 0.002 1.46

230866_at CYSLTRl BE549540 0.006 1.45

211506_s_at IL8 AF043337 0.006 1.45

22529 l_at PNPTl AI967971 0.004 1.45

241916_at PLSCRl AI984040 0.018 1.44

224589_at — BF223193 0.038 1.44

227807_at PARP9 AI738416 0.024 1.43

215221_at FOXPl AK025064 0.026 1.42

201545 s at PABPNl NM 004643 0.032 1.41 Table 18: Increases expression of IFN-rekted genes correlates with increased SLE activity.

Samples comprised the "High IFN-induced" gene signature group (n=44) vs. the "Low IFN- induced" gene signature group (m=28) using a permutation Maim- Whitney test A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high TFN-mdueed gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison and the fold change difference (High IFN relative to Low IFN group).

AffyID Symbol Ace. No. p-value fold change

235256_s_at GALM BE788984 0.006 1.41

225076_s_at KIAA1404 AAl 50460 0.002 1.40

232563_at ZNF684 AW275016 0.03 1.40

218618_s_at FNDC3B NM_022763 0.048 1.40

226326_at PCGF5 AI798098 0.026 1.40

202659_at PSMBlO NM_002801 0.002 1.39

242020_s_at ZBPl AI925506 0.002 1.39

202837_at FLN29 NMJ3O6700 0.002 1.39

225466_at FLJ36874 BG291961 0.026 1.39

209498_at CEACAMl X16354 0.002 1.38

217502_at IFIT2 BE888744 0.006 1.37

225076_s_at KIAA1404 AAl 50460 0.038 1.36

229625_at GBP5 BG545653 0.014 1.34

242020_s_at ZBPl AI925506 0.018 1.33

225076_s_at KIAA1404 AAl 50460 0.002 1.32

227347_x_at HES4 NM_021170 0.006 1.32

242020_s_at ZBPl AI925506 0.018 1.31

211068_x_at FAM21C BC006456 0.02 1.31

211012_s_at PML BC000080 0.006 1.31

201470_at GSTOl NM_004832 0.002 1.30

207157_s_at GNG5 NM_005274 0.002 1.30

221345_at GPR43 NM_OO5306 0.04 1.30

227354_at FLJ37858 BF589359 0.016 1.30

225076_s_at KIAA1404 AAl 50460 0.002 1.30

202243 s at PSMB4 NM 002796 0.026 1.30 Table 18: Increases expression of IFN-rekted genes correlates with increased SLE activity.

Samples comprised the "High IFN-induced" gene signature group (n=44) vs. the "Low IFN- induced^*' gene signature group (n=28) using a permutation Mann- Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-value for the comparison and the fold change difference (High IFN relative to Low IFN group).

Affy ID Symbol Ace. No. p-value fold change

230645_at FRMD3 BFl 10588 0.032 1.29

223599_at TRIM6 AF220030 0.014 1.28

232034_at LOC203274 ALl 17607 0.002 1.27

233880_at C17orf27 AL161961 0.03 1.26

201930_at MCM6 NM_005915 0.046 1.26

23359 l_at — AK026751 0.01 1.26

202659_at PSMBlO NM_002801 0.038 1.24

225506_at KIAA1468 AA523958 0.02 1.23

201470_at GSTOl NM_004832 0.024 1.23

204170_s_at CKS2 NM_001827 0.02 1.23

209684_at RTN2 AL136924 0.02 1.22

20858 l_x_at MTlX NM_005952 0.018 1.21

223849_s_at MOVlO BC002548 0.042 1.21

244398_x_at ZNF684 BE328243 0.008 1.20

202874_s_at ATP6V1C1 NM_001695 0.022 1.20

22529 l_at PNPTl AI967971 0.038 1.20

224358_s_at MS4A7 AF237916 0.012 1.20

204285_s_at PMAIPl AI857639 0.044 1.18

235175_at GBP4 BG260886 0.034 1.17

202343_x_at COX5B NMJ⁾01862 0.006 1.16

202343_x_at COX5B NM_001862 0.022 1.15

213735_s_at COX5B AI557312 0.028 1.15

232563_at ZNF684 AW275016 0.01 1.15

222036_s_at MCM4 AI859865 0.05 1.14

90610 at LRCH4 AI654857 0.026 1.12 Table 18: Increases expression of IFN-related genes correlates with increased SLE activity.

Samples comprised the "High IFN-indueed" gene signature group (n=44) vs. the "Low IEN- iaduced^*' gene signature group (n~28) using a permutation Mam-Whitney test. A cutoff of p=0.05 or less was used to indicate significant differences. The table only lists the probes that were UP/HIGHER in the high IFN-induced gene group. There were 376 probes identified, from the set of 659 probes, which corresponds to 208 genes. The table lists the p-vatae for the comparison and the fold change difference (High IFN relative to Low IFN group).

AfTy ID Symbol Ace. No. ^* p-value fold change

230314_at — AW014557 0.038 1.11

215338 s at NKTR AI688640 0.002 1.00

EXAMPLE 1 - GENE SELECTION

[00182] Expression of about 22,657 genes and fragments were measured in white blood cell samples from patients suffering from various autoimmune diseases including SLE, Wegener's Granulomatosus, Rheumatoid Arthritis, and Inflammatory Bowel Disease (Crohn's and Ulcerative Colitis); and healthy individuals; and filtered (fold- change > 1.8 and p-value < 0.01). The resulting gene set consisted of about 1645 genes and fragments. The expression values were converted into log values with a floor value of 0, and exported into Avadis 2.0 software for hierarchical clustering. From the clustering, it was noted that one core group of 147 genes were very highly upregulated in SLE patients only. These highly upregulated gene set is shown in Table 1. The hierachical clustering of different samples or a "heat map" was drawn from the analysis. The 147 genes were shown to be highly expressed in all SLE patients (red in the heat map) whereas in non-SLE patients the same genes were expressed at very low level (green in the heat map).

EXAMPLE 2 - EXPRESSION LEVELS AND SLEDAI SCORES CORRELATION

[00183] The expression of the 147 genes was also determined for SLE samples only. The data were then downloaded into the Avadis program for hierarchical clustering. The expression of the genes were separated into two major groups. One group had higher levels of gene expression and associated with a higher SLEDAI scores of ~7.1. The other group had lower levels of expression and associated with a much lower SLEDAI score of

-2.4.

EXAMPLE 3 - IMMUNE CELLS ACTIVATION

[00184] To determine the cell types of the immune system that express the gene set of Table 1, the gene set was used to query all of the cellular biology experiments in the Gene Logic database. It was determined that immune cells that were activated by various means for longer periods of time upregulated practically all of the genes of Table 1. This included 1) CD4+ T-lymphocytes activated with anti-CD3/anti-CD28 or anti- CD3/ICAM1 for 24 hours or 72 hours; 2) Monocytes activated with lipopolysaccharide for 8 hours; or 3) Neutrophils activated with Escherichia coli for 2 hours. We produced a heatmap of the gene expression. 12 samples in the center of the heat map correspond to CD4+ T-lymphocyte activated with anti-CD3/anti-CD28 or anti-CD3/ICAMl for 24 hours or 72 hours. We also noted that stimulation of CD4+ T-lymphocyte for shorter time periods of 2 or 4 hours resulted in no upregulation.

EXAMPLE 4 - DRUG INDUCED SLE

[00185] The gene set of Table 1 was characterized by examining the expression on rheumatoid arthritic patients before and after Remicade treatment. It is known that therapies which block TNF have, in rare cases, resulted in the development of systemic lupus erythematosus (drug induced SLE). More commonly, these patients developed autoantibodies called anti-nuclear antibodies. Applicant has discovered that the gene set of Table 1 is also upregulated in patients treated with drugs known to induce autoantibody expression and some cases SLE. We also constructed a heat map showing the gene set of Table 1 being upregulated in many patients after treatment with Remicade.

EXAMPLE 5 - ACCURACY OF THE GENE SET IN DIAGNOSING SLE

[00186] A Cluster Distribution of the input white blood cell populations consisting of a total of 123 samples in which 52 had been clinically diagnosed as SLE and the remaining 71 consisted of non-SLE samples. The non-SLE samples includes white blood cells from healthy donors, rheumatoid arthritis donors, Wegener's Granulomatosus donors and inflammatory bowel disease donors. Table 2 depicts the cluster distribution.

[00187] AU the 147 genes were used to determine the accuracy of the gene set in determining the accuracy of the gene set in diagnosing lupus. Table 3 shows the ability of all 147 fragments as a whole to distinguish between SLE and non-SLE samples.

[00188] The gene set is about accurate in correctly identifying SLE. Table 3 shows that there is about a 2% false negative rate and about a 2.8% false positive rate.

EXAMPLE 6 - THE ABILITY OF INDIVIDUAL GENE TO DIAGNOSE SLE

[00189] Table 4 gives the results of a Fisher's standardized discriminant function coefficients for a subset of the gene set of Table 1. The standardized discriminant function coefficients may be treated as Beta weights in a multiple regression predicting D from z scores on the X's, D₁ = /J₁Z₁ + P₂Z₂ + ... + β_pZ_p . These coefficients reflect the contribution of one gene in the context of the other genes in the model. High standardized coefficient such as those reported in Table 4, means that the groups do differ a great deal based on that gene expression data. Each single gene in this group has the ability to distinguish between SLE and Non-SLE samples with 100% accuracy as shown in Table 5.

[00190] Table 5 clearly shows that any individual sequence from Table 4 is able to distinguish between SLE and Non-SLE samples with about 100% accuracy. Accordingly, the use of, or a device, or a composition including at least one individual sequence from Table 4 are considered to be preferred embodiments of the invention. The sequences of Table 1 that are not included in Table 4 can also distinguish between SLE and Non-SLE, however, at a lower accuracy than 100%. Detecting more than one, preferably at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more of these sequences can improve the accuracy of the assay.

EXAMPLE 7-SLE ANCA(WG) EXPRESSION PROFILES [00191] Patients : Patients were identified at University of North Carolina, Chapel Hill, hospitals and specialty clinics and enrolled into the study. Healthy volunteer samples were enrolled from both UNC laboratory and Gene Logic facilities. The study was reviewed and approved by the UNC IRB committee and informed consent was obtained from all patients. Study participant demographic information including age, ethnicity, gender, and disease activity as measured either by the Birmingham Vasculitis Activity Score (BVAS) (16) for ANCA patients or SLE Disease Activity Index (SLEDAI) (17) and the BILAG for SLE patients, are summarized in Table 9.

[00192] Patient Blood Sample Preparation: Blood was collected into EDTA containing tubes and red blood cells lysed using a hypotonic solution treatment as previously detailed (18). Isolated total leukocytes were lysed immediately in RNA STAT-60 (TeI- TestB, Friendswood, TX) and RNA was extracted as previously described (19). Contaminating DNA was removed by DNAse treatment and re-purification using RNAEasy Mini Kit (Qiagen, Valencia, CA). RNA quality was spectrophotometrically determined by OD 260/280 nm ratios and by visual inspection of the 28S and 18S ribosomal RNA integrity following agarose gel separation and Sybr Gold staining (Molecular Probes, Eugene OR).

[00193] Sample RNA Processing, Quality Control and Normalization: RNA samples were processed and hybridized to the Ul 33 Genechips A and B (Affymetrix, Santa Clara, CA) exactly as suggested by the manufacturer. Overall chip intensities were standardized and the expression levels of individual genes determined using Affymetrix MAS 5.0 algorithms. Briefly, a scaling factor was determined by comparing the global trimmed mean signal intensity value for each chip to an arbitrary constant of 100. To normalize each array, the signal intensity values on the array were multiplied by this scaling factor.

[00194] Kidney Biopsy Samples: For renal biopsies, archival samples were obtained from residual snap frozen diagnostic renal biopsy specimens stored at -80⁰C. The use and study of the archival tissues were reviewed and approved by the UNC IRB. Only biopsies containing approximately 10-15 glomeruli per section as observed by microscopic examination were chosen for further processing and RNA isolation. RNA was isolated from these samples and recovery was low (<1.0 microgram). The RNA was therefore, subjected to microsample two cycle target-labeling (Affymetrix, Santa Clara, CA).

[00195] Analysis and Patient Sample Microarray Data Parameters: Raw data was initially analyzed using Genesis 2.0 (Gene Logic). The integrity and reliability of the samples and data was validated by examining the 573' expression ratios of the beta-actin and GAPDH probes on each array. AU samples had beta-actin and GAPDH 573' ratios greater than 0.78 or 0.84 respectively. Initially, a separate gene set was identified for each patient population sample set. A gene was included if it was determined to be expressed [noted by a present call calculated by the Affymetrix MAS 5.0 algorithm] in > 10% of the samples in the set and the average expression intensity value was >50. This set of genes was analyzed over the entire sample set and a correlation matrix was plotted. Samples within the same patient population set were generally found to have a Pearson coefficient >0.85.

[00196] The expressed gene set for each patient population was merged and used for relative expression analysis. A cross comparison of all sample sets was performed and genes were considered differentially expressed between the groups if the fold-change difference was >1.8 and the p- value, as determined by a Welch's t-test, was ≤O.Ol. Further analysis of the expression data including principal component analysis, regression analysis, and ANOVA was performed using the AVADIS Prophetic software (Strand Genomics, Bangalore, INDIA).

[00197] For cluster analysis, data was log transformed and then subjected to mean centering and normalization using the Eisen Cluster software (20). Hierarchical clustering was performed using either the Cluster method of Eisen (20) based upon average linkage clustering and uncentered correlation or by using the Avadis Prophetic software (Strand Genomics, Bangalore, INDIA). Clusters were visualized using the program Treeview (20). For identification of unique genes with each cluster, Affymetrix® gene fragment names for the SLE, ANCA and healthy volunteer groups were exported from Treeview, imported into Genesis 2.0, and unique genes identified by comparison of gene names. [00198] Over-represented functional gene ontology classes within each cluster were identified by analysis of the unique genes in each signature using EASE version 2.0 (http://david.niaid.nih.gov/david/ease.htm) based upon the Gene Ontology groupings for cellular components, biologic processes and molecular functions. Over-represented classes were identified based upon an EASE score <0.001.

[00199] Sample Classification Using Gene Expression Profiles: The method of nearest shrunken centroids, implemented in the Prediction Analysis of Microarrays (PAM) software, was used to identify and evaluate the most promising group of classifier genes for each of the sample groups (20B). This method was recently applied successfully to identify expressed gene signatures for the prognosis of patients with acute myeloid leukemia (2OC, 20D).

[00200] Briefly, the centroid for each of the classes was computed using the corresponding gene expression measurements in Iog2 scale. The class centroid of a gene is defined as its average level of gene expression in the class; and the overall centroid corresponds to the average level of gene expression across all samples in the data set(20B). Using a combination of centroid shrinkage (i.e., moving the class centroids to the overall centroid for all classes by a specified threshold value) and cross-validation, an optimal set of genes for discriminating between the classes is identified. The shrunken centroid score for a gene is reflective of the difference between the class and overall centroid; and the larger the relative absolute value, the greater the discriminatory power. Please refer to Tibshirani et al., (2002) for the mathematical derivation of the shrunken centroid score (20B).

[00201] PAM employs a 10-fold cross validation strategy on the sample set to determine the rate of misclassification. In 10-fold cross validation, first -10% of the samples are randomly selected and removed from the sample set (~equal samples/group) and the remaining 90% of the samples are used to fit the classification model. The model is then evaluated on the samples that were removed to determine prediction accuracy. This process is repeated 10 times, such that each sample is used in both model fitting and as a test sample. The overall misclassification error is then computed from the entire cross validation process. [00202] PAM sequentially evaluates increasing levels of centroid shrinking. The cross-validated misclassification error rate at each threshold level is used to identify the best subset of genes for classification (i.e., the smallest gene set with the lowest misclassification error rate for all classes). Genes are eliminated from classification when the shrunken class centroid score reaches zero (i.e., the class and overall centroid are equal) for all classes, making the gene uninformative for classification. The subsequent shrunken centroids are used for classification according to the nearest centroid rules (i.e., a sample gene expression profile is compared to the centroids, and the class centroid it is closest to, in squared distance, is the predicted class) (20B).

[00203] The set of 1,645 genes identified as differentially expressed between each of the four classes (healthy, SLE, ANCA and RA) (n=153) was selected to identify the subset of genes that best discriminated between the four classes using cross-validation in the PAM v2.0 software. An independent test set was not used for this particular classification due to the limited number of samples from the non-SLE groups. As a consequence, splitting this data set into a reference and test set would result in an over fitted classification model that would perform poorly on an independent blinded sample set.

[00204] To identify and validate the gene set that best discriminated between the SLE and non-SLE (i.e., the healthy, ANCA and RA samples combined) patient samples, the set of 153 samples was split into two groups: a reference set for training the classification model and an independent test set for evaluating the classification model (20E). The reference set was comprised of 98 samples (healthy n=18, SLE n=52, RA n=13, ANCA n=15), obtained from 58 patients (healthy n=l 1, SLE n=22, RA n=13, ANCA n=12). The test set was comprised of an additional independent set of 55 samples (healthy n=10, SLE n=20, RA n=13, ANCA n=42). All replicate samples were contained within the reference set.

[00205] All signal intensity data was Iog2 transformed prior to performing any analysis. [00206] In vitro Experiments: In order to determine the expression pattern of the SLE and ANCA signature genes in immune cells we examined purified immune cell subsets activated under a variety of conditions and for a range of time periods. This was done by surveying the immune cell collection that is part of the Immunology and Inflammation DataSuite offered by Gene Logic. This is a database of gene expression data obtained from Affymetrix (Santa Clara, CA) microarray analysis. Cell samples were processed as described above and hybridized to the Affymetrix Ul 33 A and B GeneChips. Results from these microarray experiments were amassed in a searchable database.

[00207] CD4+ T-lymphocytes, CD 19+ B-lymphocytes, and CD 14+ monocytes were obtained by negative selection using magnetic activated cell sorting. The cell preparations were >85% pure based on staining and FACS analysis. CD4+ T- lymphocytes were stimulated for various time periods with: anti-CD3 antibody (Ab) and ICAMl, anti-CD3 Ab and anti-CD28 Ab, tetradecanoylphorbol 13-acetate (TPA) and ionomycin, or TPA and anti-CD3 Ab. CD 19+ B-lymphocytes were stimulated with immunoglobin G (IgG), Lipopolysaccharide (LPS), TPA and ionomycin, or IL4 and LPS. We also examined IgD+ and CD38+ cells isolated from germinal centers. CD 14+ monocytes were stimulated with LPS, E. coli Kl 2, or Borrelia bergdorferi. In addition, we screened macrophages and dendritic cells derived from monocytes in culture. Neutrophils were stimulated with G-CSF, LPS, E. coli Kl 2, Yersinia pestis, or Borrelia burgdorferi.

[00208] RESULTS - Peripheral Blood Leukocyte Expression Profiles: Twenty-six rheumatoid arthritis (RA), 22 WG (ANCA) and 42 systemic lupus erythematosis (lupus) patients were identified, enrolled and blood samples collected at UNC clinics. Samples from 29 healthy volunteer (HC) were collected from donors at local research facilities. For RA and HC, a single leukocyte samples were isolated from each donor while some ANCA and lupus patients donated multiple times, generating 26 and 72 total samples respectively (see Table 9). Our first concern was that the data analysis might be biased by differences in the cell type distribution (percentages of monocytes, neutrophils and lymphocytes in the total count) which may differ depending upon the disease and degree of clinical activity. To address this issue, we examined the distribution of the individual leukocyte cell types as measured in a differential blood cell count in the different disease groups. Principal component analysis of the percentage of each cell type in each disease set was performed and showed slight separation of the ANCA and SLE patient samples as a single group from healthy donor and RA samples, the ANCA and SLE samples could not be distinguished from one another.

[00209] Expression data for patient samples as detailed above was obtained from hybridization of the total leukocyte RNA samples to Affymetrix U133 chips A and B. Data was initially analyzed in the Gene Logic database to uncover genes with Present Calls that fulfilled our set of criteria defined in Material and Methods. This resulted in a final set of 1,645 gene fragments differentially expressed between the four groups (healthy, SLE, ANCA and RA).

[00210] Identification of a Gene Feature Set that Discriminates between Healthy, SLE, RA and ANCA patient samples: From the set of 1,645 genes, shown in Table 6, differentially expressed between the four classes, a subset of 279 genes was identified as the best set for discriminating between the four classes (Figure 2). A list of the 279 genes, along with the corresponding annotation and shrunken centroid scores for each class, is provided in Table 7. The shrunken centroid score is simply the average expression level for a gene in a specific class "shrunk" toward the overall centroid by a fixed amount as determined by the threshold value (20B). A centroid shrinkage threshold of 3.75 was selected to minimize both the total number of selected genes as well as the misclassification rate. The classification probabilities for each sample are indicated in Figure IB. No genes were identified that could provide significant discriminatory power to separate RA from the other three groups. Overall, excluding the RA samples, 83.5% (106 of 127) of the samples were correctly classified.

[00211] Similar results were obtained when samples from male donors were excluded from the analysis (excluding RA samples, the overall classification rate was 77.9% (74 of 95 samples) using 277 genes); or when both replicate samples from the same donor and male donors were excluded (excluding RA samples, the overall classification rate was 80.0% (48 of 60 samples) using 268 genes) (data not shown). The 277 and 268 genes were subsets of the 1645, and mostly, but not completely, overlapped with the 279 gene group.

[00212] Identification and Verification of a Gene Feature Set that Discriminates between SLE and the non-SLE patient samples: The SLE sample group was compared to a second group consisting of a combination of the remaining three non-SLE groups (healthy, ANCA and RA). In this comparison, the 153 samples were divided into two sets: a reference set for training the classification model (n=98) and an independent test set for evaluating the classification model (n=55).

[00213] The reference set was used to identify a subset of the 1 ,645 genes that best discriminated between the two groups. Using PAM, a set of 28 gene features (centroid shrinkage threshold=5.4) was identified that provided strong discriminating power: cross- validation of the reference set correctly classified 88.5% (46 of 52) and 91.3% (42 of 46) of the SLE and "other" non-SLE samples, respectively (Figure 2A). The 28 gene features are listed in Table 4 and are ranked according to the centroid score, which reflects the ability of the gene feature to discriminate between the SLE and non-SLE groups. All 28 genes were also found as part of the 279 gene signature identified for discrimination of SLE in the four group comparison.

[00214] Next, the ability of these genes to correctly classify the two groups was assessed on the set of independent test samples using PAM. This resulted in correctly classifying 80.0% (16 of 20) and 88.6% (31 of 35) of the SLE and other non-SLE test samples, respectively (Figure 2B). A gene feature set as small as six (threshold=6.73) was still able to significantly discriminate between the two groups: 85% of the SLE and 80% of the other test set samples were correctly classified. These six gene features are listed in Table 8, rank positions 1 to 6.

[00215] In addition, when all male samples were removed from both the reference (SLE n=52, Other n=22) and test sample (SLE n=20, Other n=20) sets, similar classification rates were observed: 89.2% (66 of 74) of the reference samples were correctly classified in cross-validation and 85% (34 of 40) of the test sample set was correctly classified (data not shown). [00216] Association of Expression Profile with Disease Severity: A previous study (9) showed that the interferon-induced gene signature characteristic of SLE was also associated with a tendency to develop CNS and/or renal involvement. In our cohort of 42 patients, we had a good sampling of patients who had various levels of severity of kidney disease as defined by the BILAG subscoring for renal severity. Using the SLE gene signature, we subjected the SLE samples alone to hierarchical clustering using the Random Walk method and Euclidean distance metric in the Avadis Prophetic software. We could define 3 separate patient clusters based on this gene expression. Cluster 1 had lower expression of the signature genes than those individuals in Cluster 3 (data not shown). We sought to determine whether there was any statistically significant correlation between gene expression of the three SLE patient clusters and clinical measurement of SLEDAI, BILAG or BILAG clinical subgroup scores. Using univariate analysis of all 72 samples from the 42 patients revealed a correlation between SLEDAI and expression of the SLE gene signature, but when multivariable analysis was performed correcting for age, race and multiple samplings from many of the individuals, the correlation with SLEDAI was lost. This resulted from the fact that many of the patients in our study who had multiple samples taken tended to have very active disease whose clinical activity did not attenuate over the sampling period. For patients with multiple samples, multiple analyses were performed in which the first, last or randomly selected sample for each individual was tested and all revealed no significant correlation between expression levels and SLEDAI or any BILAG subscoring (data not shown). Finally, using regression analysis (both Pearson Correlation Coefficient and Spearman's Coefficient of rank correlation), poor correlation was found between SLEDAI scoring and any individual gene's expression (rθ.38) although with elevated statistical significance. From these data we conclude that while the expression of the SLE signature significantly differentiates the SLE samples from all others, its utility as a predictor of disease activity in our patient population is limited. In addition, going back to the original 1645 differentially expressed gene set we did not see any genes that produced a correlation stronger than was observed with the SLE signature.

[00217] In contrast we evaluated the ANCA patients to determine whether there was a correlation with the entire gene set of 1645 differentially expressed gene set and BVAS. We found quite good correlation of gene expression with BVAS scoring in a subset of the genes. Using a Spearmans correlation coefficient of >0.60 and strong statistical significance, 101 gene fragments representing 95 different genes were identified. The top 33 with correlations > 0.66 are shown (Table 10A). This gene set were not among the best classifiers of ANCA samples. There were many genes which negatively correlated with BVAS scores. The top 61 are shown with scores ≥to -0.66 (Table 10B).

[00218] SLE Signature Gene Expression in Purified Immune Cells: In order to further examine and characterize the key SLE classification genes, we determined how and when these genes were expressed in immune cells from healthy individuals (Figure 3A). We examined expression patterns in CD4+ T-lymphocytes, in monocytes, neutrophils and in B-lymphocytes incubated in vitro over time with a range of cell-type specific stimulants. Expression data of the key SLE classification genes in the SLE signature were determined in the cell samples and then subjected to cluster analysis using the method of Eisen (20) and visualization was performed by using TreeView. Due to size constraints we have summarized the data below.

[00219] We saw little or no expression of the SLE classification genes in B- lymphocytes. We obtained CDl 9+ B-lymphocytes by negative or positive selection. CD 19+ cells obtained by negative selection were stimulated either with TPA with ionomycin for 0, 2, or 8 hr, with LPS alone for 0, 2, or 8 hr, LPS with IL-4 for 0, 3 days or 6 days or IgG for 0, 2, or 8 hr. It may be that the appropriate conditions for expression were not achieved in this survey.

[00220] T-lymphocytes may be activated in a number of ways and we chose to look at CD4+ cells that had been stimulated by the addition of anti-CD3 antibody (Ab) in combination with either anti-CD28 Ab or ICAMl for 0, 2, 8, 24, or 72 hours. We also examined CD4+ lymphocytes that had been stimulated with TPA and ionomycin for 0, 2, or 8 hours, or TPA and anti-CD3 Ab stimulation for 0, 2, or 8 hours. In addition, we examined CD4+ T-lymphocytes that were also CD25+ or of the ThI type or the Th2 type. Results are shown in Figure 3 A. Clearly, the vast majority of genes are tightly co- expressed and up-regulated in activated in immune cells. Figure 3B shows this region magnified and one can see that this gene set is very highly expressed in CD4+ T- lymphocytes undergoing long-term activation by anti-CD3 Ab in combination with either anti-CD28 Ab or in the presence of fixed ICAMl . High levels were not observed in the CD4+ samples that were stimulated for shorter time periods, even with such potent activators as TPA and ionomycin.

[00221] We also observed the expression of this gene set in monocytes. Again we see the same co-regulated genes up-regulated in the monocytes treated with lipopolysaccharide (LPS) for 8 hr (and to a lesser extent the 2 hr time point) as we did in the CD4+ T-lymphocytes treated for the extended period of time with anti-CD3 Ab in combination with either anti-CD28 Ab or ICAMl (Figure 3B). Interestingly, these genes are down regulated in either macrophages or dendritic cells derived from monocytes in culture. No significant expression was observed in neutrophils under any activation conditions which included incubation with LPS, E. coli, and G- or GM-CSF.

[00222] In summary, the SLE signature genes are coordinately induced in activated immune cells, specifically we observed greatest expression in CD4+ T-lymphocytes and in monocytes. Induction is not immediate but this might be explained by the delayed endogenous production of interferons. In the CD4+ experimental set, for example, we found that IFN-γ transcription reached its peak at 24 hours in sample sets treated with anti-CD3 Ab in combination with either anti-CD28 Ab or ICAMl protein (data not shown). The production of IFN-γ would be expected to stimulate the production of most of the genes in this signature. In addition, alpha-interferon is transcribed at earlier time points and the autologous stimulation by such interferons might also give rise to this profile.

[00223] ANCA Signature Gene Expression in individual leukocyte cell types: As noted earlier, we identified genes that were highly correlated with BVAS scores in ANCA patients. The genes that correlated with BVAS scoring, both positively and negatively were examined in the wide panel of in vitro activated immune cell types. A very different profile in activated immune cell sets was observed as compared with the SLE gene signature. We observe two major clusters of genes: those that are expressed predominantly in neutrophils and monocytes, and those that are expressed predominantly in T-lymphocytes and NK cells. The genes that are found highly expressed in the T- lymphocytes and NK cells are negatively correlated with BVAS scores. They predominantly encode T-cell receptors (T-cell receptor alpha, nuclear factor of activated T-cells calcineurin dependent, NFATC2) or are part of T-cell signaling (IL-2 inducible T- cell kinase, ITK). Also present were 2 fragments expressed at high levels in NK cells encoding Killer cell lectin-like receptor subfamily D, member 1 (KLRDl).

[00224] Leukocyte Gene Signature Expression in Renal Biopsies: One of the most common complications of both ANCA and SLE is the development of kidney disease. In SLE this is particularly prevalent in the African- American patients. We had determined that there was a clear gene expression signature correlated with SLE in the peripheral circulating immune cells and also a signature for ANCA that appeared to be shared by a portion of the SLE patient WBCs. Cells from the peripheral blood infiltrate into the kidney during the inflammatory process. We determined whether any of the genes in our initial gene set of 1645 were differentially expressed in kidney biopsies from patients with various types of glomerulonephritis. We obtained kidney biopsies from patients with ANCA glomerulonephritis or SLE glomerulonephritis and control samples from patients with either minimal change disease or no identifiable pathology.

[00225] We examined the expression of all of the 1,645 differentially expressed fragments across the kidney biopsy samples but filtered for a present call of > 50% in any sample set, a fold change >1.8 and ap value < 0.01. The expression of the remaining gene set was then analyzed using hierarchical clustering and visualization using TreeView. Results are given in Figure 4. We found again a core of 27 fragments that were part of the SLE signature in peripheral blood. Many of these genes were among the top SLE classifiers in Table 7 and included RSAD2/CIG5, Corf29, IFITl, IFIT3, GIP2 and LY6E. This similarity of gene expression in blood leukocytes and kidney tissue may be due to the infiltration of immune cells from the peripheral blood into the kidneys of these patients. Yet it is interesting that the SLE gene signature is maintained even though these immune cells have migrated out of the peripheral circulation into the kidney. This was also observed, albeit to a lesser extent, in the ANCA patient kidney samples. In this case a group of 20 fragments were expressed in ANCA biopsies but not in controls. At least 4 of these fragments corresponded to metallothionein genes and interestingly, as in peripheral blood samples, there were a subset of lupus biopsies that also had higher levels of expression of these metallothionein fragments. In fact, it is interesting to note that the genes that distinguish the ANCA kidney biopsies tend to be involved in metal metabolism and include the metallothionein fragments and lactotransferrin. Also found upregulated in the ANCA kidney was olfactomedin, an important ANCA classification gene.

[00226] DISCUSSION - In the past several years, microarray analysis has been utilized extensively in the field of cancer biology, specifically to classify tumors and to predict progression and therapeutic responsiveness (22). Less work has been done in the field of inflammatory diseases. We have utilized gene expression to identify specific patterns of gene expression in peripheral blood samples from patients with ANCA and SLE. No specific signature was observed in RA patient samples.

[00227] While we successfully uncovered distinctive gene signatures characteristic for ANCA and SLE, it is interesting to note that the WBCs from the RA patients did not produce a distinctive gene signature and tended to segregate with either the healthy donor population or in a few cases with either SLE or ANCA samples. Therefore, peripheral blood leukocytes gene expression data may not be the best method for distinguishing this population. Frequently, part of the problem lies in the fact that some of the most potent immune modulators, such as cytokines, chemokines and their receptors may be transcribed either transiently or at very low levels. Even in a database as extensive as Gene Logic's, transcripts encoding IL-2, IL-4 and IL-IO to name a few are exceedingly rare (less than 0.5% of the >12,000 samples, D. Barnes, personal observation.) Better results for RA classification may be obtained with the emerging field of proteomics.

[00228] We, like others investigators (7) (8) (9), found an interferon-inducible gene signature highly expressed in SLE patients. Some of the genes previously identified include PLSCRl, SERPINGl, OASL, MXl, G1P3, LGALS3BP, LY6E (9). However, we see a great many more genes that are known to be induced by type 1 interferons and this may be due to the differences in starting material between this work and those previously published. We utilized this gene set to examine kidney biopsy samples from SLE patients. Both ANCA and SLE patients often develop glomerulonephritis. Interestingly, we found that many of the genes that were diagnostic for SLE in peripheral blood were also elevated in the SLE kidney while the ANCA peripheral blood signature was not as highly represented in the kidney samples from the ANCA patients. The majority of interstitial mononuclear cells in lupus nephritis are CD4+ T-lymphocytes and monocytes/macrophages (23). These are precisely the cell types that we identified when we examined the SLE signature across a purified activated immune cell panel (Figure 3B). Interestingly, the peripheral blood signature might be maintained and expressed by these same cell types after they leave the periphery and migrate into the tissue.

[00229] SLE is a complex disease where activity and flare are hard to assess. Two widely accepted methods are the SLEDAI and the BILAG. The advantage of the BILAG scoring is that it can also be broken down into subcategories allowing the assessment of particular organ or system involvement. We utilized both of these instruments to assess the SLE patients in this study. In contrast to previously published work (8)(9), we did not observe a high degree of correlation between high gene signature expression and disease activity or organ involvement. It should be noted however, that the patients in this study were somewhat more diverse than in previous studies as there was a much larger African American population with greater renal involvement. Nevertheless, while the interferon- inducible genes clearly distinguish SLE from all other patient samples, the relationship between expression of this signature with either disease activity or specific organ system involvement could not be confirmed.

[00230] In the late 1980's, ANCA was shown to be separable into two serotypes and that one of these serotypes reacted with myeloperoxidase (MPO-ANCA) (27). The other major ANCA serotype reacts with proteinase 3 (PR3-ANCA) (27) (28) (29) (30). These autoantibodies are more than serologic markers because they participate in the pathogenesis of ANCA glomerulonephritis (31). ANCA can activate neutrophils and monocytes, resulting in the release of oxygen radicals and toxic granule constituents (14) (15). Here we define a set of genes that classify ANCA patients and a separate gene set that correlated with disease severity in ANCA patients as measured by BVAS. It is worth noting that both MPO and PR3 were identified as differentially expressed and are part of the original 1645 differentially expressed gene set. However, while PR3 is a key classifier of ANCA samples MPO is not (Table 7). Finally, the genes that are positively correlated with higher BVAS scores are found predominantly in neutrophils and those negatively correlated with BVAS are CD4+ lymphocyte or NK cell markers and are differentially expressed at higher levels in healthy donors as compared to ANCA patients. In this instance we cannot rule out the possibility that the tight correlation with BVAS scoring is due to a skewing in the white blood differential cell count. The genes highly correlated to BVAS were not the same genes that are the best classifiers of ANCA patient samples.

[00231] In summary, our data showed for the first time that the patterns of gene expression in circulating blood leukocytes are distinctly different in patients with SLE, ANCA disease (WG) and RA. Furthermore, from the list of differentially expressed genes, we have found a set that may be used to classify with a high degree of accuracy the ANCA and SLE patient samples. These distinctive gene signatures could be of value for both diagnosis and monitoring of disease activity in the case of ANCA patients. With regard to the SLE patients, while the classification gene set identified in Table 7 is good at diffentiating the SLE patients from others, these genes are not particularly tightly correlated to disease activity. This does not necessarily mean, however, that these genes are not important or involved in development of disease activity in SLE patients, since a longitudinal study of SLE patients has not yet been performed using these genes as predictors of disease activity. We have now discovered that a selection of genes presented in Table 13, does classify SLE patients into at least two defined groups: one wherein the patients typically have high anti-ds-DNA antibodies, and higher disease activity, and another, wherein the patients typically have low or no anti-ds-DNA antibodies and have lower SLE disases activity

[00232] References for Example 7

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EXAMPLE 8- Results from BGA SLE Focus Array

[00270] Peripheral blood was collected from 89 human subjects using the PAXGene blood RNA collection system (Qiagen, Valencia, CA). RNA isolated from the peripheral blood of n=72 SLE patients and n=17 healthy patients was profiled on the BGA SLE Focus Array Set. Four SLE patient samples were profiled in duplicate for a total of n=76 profiles. Samples from the 17 healthy patients were profiled in quadruplicate (one set per array) due to limited sample availability; of these, n=44 passed quality control (3 samples in quadruplicate, 8 in triplicate, 2 in duplicate and 4 a single time). The current BGA SLE Focus Array set is comprised of 878 oligo-nucleotide probes (43 control probes and 835 gene probes split across two arrays; all spotted in duplicate), representing 329 unique genes. The BGA SLE Focus Array was generated by spotting the probes on a glass plate in 96 unique sections (1 set of duplicated probes/section) and segmenting the spotted probe sections into a standard 96-well plate format using formed plastic walls. All assays were performed in duplicate on an array (48x2 profiles per array), thus a single probe is assayed four times per sample profiled.

[00271] Following hybridization, probes were quality filtered such that probe spots that had a background corrected signal intensity of < one standard deviation of the local background signal intensity was considered uninformative. All spots were normalized to the median signal intensity of a set of pooled probes representing the housekeeping genes beta-actin and GAPDH. The median signal intensities for the normalized replicate probes were used for the final probe measure. Final probe measures that did not have at least 2 of 4 probe spots pass quality filtering were set to a value of 0 in the respective sample profile. Gene probes were selected for subsequent analysis if at least 10% of the samples had probe spots that passed quality filtering in either the SLE or control group. This resulted in 686 of the 842 probes being selected for subsequent data analysis, which corresponds to 659 gene probes, or 279 unique genes, and 27 controls. Signal intensity values <10 were thresholded to a value of 10. The signal intensity values were Iog2 transformed prior to subsequent analysis.

[00272] Further normalization was performed on the 120 samples X 686 gene probe matrix to account for differences in array batches by centering the median signal intensity for each gene probe across all samples to 0 (by subtracting the median signal intensity value for the gene probe from the measured value for each sample) separately for each of the four batches of array pairs. Subsequent to this, the median signal intensity value for each of the gene probes was re-centered to 0 for the entire set of 120 samples.

[00273] Clustering the Gene Expression Profiles: The 659 gene probes were used to compare the 120 samples using hierarchical clustering. Spearman correlation with average linkage was used to perform hierarchical clustering and a heat map generated to visualize the relationship between the samples. Three major sample clusters resolved from this analysis: 1) Healthy control samples, 2) SLE samples with a relatively high IFN-regulated gene signature and 3) SLE samples with a relatively low IFN-regulated gene signature.

[00274] Gene expression profiles using this set of gene probes clearly demonstrate the ability to distinguish the SLE samples from the healthy control samples, as well as indicates that the SLE samples form two separate groups characterized by the IFN- regulated gene signature.

[00275] To further examine the SLE patient group, the 72 unique sample profiles were clustered using the same parameters; with the exception of using a smaller set of gene probes. A set of 368 gene probes, corresponding to 186 unique genes, was selected from the set of 659 by taking those gene probes whose untransformed signal intensity had a coefficient of variation of at least 0.7 across the 72 samples (i.e., the "most" variable genes). Hierarchical clustering of this 72 SLE sample X 368 gene probe matrix clearly indicates the presence of two distinct SLE groups. Again, these two groups are characterized by the relative level of expression of the IFN-regulated gene signature.

[00276] Statistical analysis was performed on all clinical parameters that were available for comparison (i.e., at least three patients in a group) for the low and high IFN- induced gene signature groups (Table 12). AU statistical analyses were performed in SPSS vl3.0 (SPSS, Chicago, IL). Categorical data was analyzed using a Fishers exact test or a Pearson chi-square test using Monte Carlo simulation (10,000 samples, two- sided). Continuous variables (i.e., age, SLEDAI, SLEDAI-tr) were compared using a Mann- Whitney test with Monte Carlo simulation (10,000 samples, two-tailed). Logistic regression on all clinical parameters was performed using stepwise forward conditional selection with a stepwise entry probability of 0.05 and a removal probability of 0.1; a classification cutoff of 0.5 using a maximum of 100 iterations.

[00277] The detection of the presence of anti-dsDNA antibodies (DNA) and steroid use was significantly increased in the set of patients belonging to the high IFN-regulated gene group; while the mean age was found to be significantly lower in this group. The increased presence of mucosal ulcers (MUC) in the low IFN-regulated gene group approached significance (p=0.055), but more samples are needed in order to be conclusive. Multivariate analysis using logistic regression indicated that only increased anti-dsDNA antibodies was significantly correlated with the high IFN-regulated gene group (Bayesian information criterion = 3.76).

[00278] The association between the expression of the IFN-regulated genes and an increased level of dsDNA binding (as indicated by a Farr assay) is an important one. The detection of α-dsDNA antibodies in blood is highly specific to SLE. The appearance of α-dsDNA antibodies in serum has been shown to occur many years prior to the onset of clinical SLE, indicating the prognostic potential of this test (Swaak & Smeenk, Ann Rheum Dis. 1985 44:245-51 ; Arbuckle et al., NEJM 2003 349: 1526-33). Furthermore, an increase in α-dsDNA antibodies in the sera of SLE patients has been shown to occur prior to, and predictive of, SLE flares (Swaak & Smeenk, Ann Rheum Dis. 1985 44:245- 51; Spronk et al., Lupus 1995 4:86-94; ter Borg et al., Arthritis Rheum. 1990 33:634-43; Ho et al., Arthritis Rheum 2001 44:2342-9; Linnik et al., Arthritis Rheum. 2005 52:1129- 37). Although changes in α-dsDNA antibody titers is often used as part of clinical assessment of SLE patients, there are some studies indicating no association between α- dsDNA antibodie changes and SLE flare (WaIz et al., J Rheumatol. 1994 21:2239-41; Esdaile et al., Arthritis Rheum. 1996 39:370-8). [00279] Thus, the increased expression of IFN-regulated genes is significantly correlated with α-dsDNA antibodies in SLE patients. Without wishing to be bound by a theory, we have therefore demonstrated that these genes as single markers as well as a group are useful, in any combination, as biomarkers for assessing SLE activity as well as predicting SLE flares. Furthermore, only 20 of the 44 patients had a positive α-dsDNA antibody test in the high IFN-regulated gene signature group (while 3 of the 28 were positive in the low IFN-regulated gene signature group). Without wishing to be bound by a theory, this shows that this particular signature is more useful because it is more sensitive and specific than the α-dsDNA antibody test for assessing SLE disease activity.

[00280] Sample Classification Using Gene Expression Profiles: The method of nearest shrunken centroids, implemented in the Prediction Analysis of Microarrays (PAM) software, was used to identify and evaluate the most promising group of classifier genes for each of the sample groups (Tibshirani et al., Proc Natl Acad Sci U S A. 2002 99:6567- 72.).

[00281] Briefly, the centroid for each of the classes is computed using the corresponding gene expression measurements. The class centroid is defined as the average level of gene expression for each gene in each class; and the overall centroid corresponds to the average level of gene expression across all samples in the data set. (Tibshirani et al., Proc Natl Acad Sci U S A. 2002 99:6567-72.). Using a combination of centroid shrinkage (i.e., moving the class centroids to the overall centroid for all classes by a specified threshold value) and cross-validation, an optimal set of genes for discriminating between the classes is identified. The shrunken centroid score for a gene is reflective of the difference between the class and overall centroid; and the larger the relative absolute value, the greater the discriminatory power. Please refer to Tibshirani et al., Proc Natl Acad Sci U S A. 2002 99:6567-72 for the mathematical derivation of the shrunken centroid score.

[00282] PAM employs a 10-fold cross validation strategy on the sample set to determine the rate of misclassification. In 10-fold cross validation, first ~10% of the samples are randomly selected and removed from the sample set (-equal samples/group) and the remaining 90% of the samples are used to fit the classification model. The model is then evaluated on the samples that were removed to determine prediction accuracy. This process is repeated 10 times, such that each sample is used in both model fitting and as a test sample. The overall misclassifϊcation error is then computed from the entire cross validation process.

[00283] PAM sequentially evaluates increasing levels of centroid shrinking. The cross- validated misclassification error rate at each threshold level is used to identify the best subset of genes for classification (i.e., the smallest gene set with the lowest misclassification error rate for all classes). Genes are eliminated from classification when the shrunken class centroid score reaches zero for all classes, making the gene uninformative for classification. The subsequent shrunken centroids are used for classification according to the nearest centroid rules (i.e., a sample gene expression profile is compared to the centroids, and the class centroid it is closest to, in squared distance, is the predicted class) (Tibshirani et al., Proc Natl Acad Sci U S A. 2002 99:6567-72.).

[00284] The set of 659 gene probes that passed filtering were selected to identify the subset of genes that best discriminated between the SLE (n=76) and healthy control (n=44) groups; and between the high and low IFN-induced gene signature groups (72 samples, high IFN group n=44, low IFN group n=28) using cross-validation in the PAM v2.0 software. The ability of each of the 659 gene probes to classify the groups in either of these comparisons is provided in Table 13. The higher the difference (distance) between the scores in the groups, the greater the ability of the gene probe for group separation and sample classification.

[00285] To identify and validate the gene set that best discriminated between the SLE and healthy control patient samples, the set of 120 samples was split into two groups: a reference set for training the classification model and an independent test set for evaluating the classification model. The reference set was comprised of 80 samples (SLE n=51, control n=29), obtained from 57 patients (SLE n=47, control n=10). The test set was comprised of an additional set of 40 samples (SLE n=25, control n=15) from 32 patients (SLE n=25, control n=7). None of the patient samples used in the test set were used in the reference set. [00286] Using PAM, a set of 88 probes was identified that provided strong discriminating power: cross-validation of the reference set correctly classified 92.2% (47 of 51) and 89.7% (26 of 29) of the SLE and healthy control samples, respectively (Figure 5A). The 88 probes are listed in Table 14 and are ranked according to the centroid score, which reflects the ability of the gene feature to discriminate between the two groups.

[00287] Next, the ability of these genes to correctly classify the two groups was assessed on the set of test samples using PAM. This resulted in correctly classifying 96.0% (24 of 25) and 93% (14 of 15) of the SLE and healthy control samples, respectively (Figure 5B).

[00288] To assess whether these 88 gene probes were capable of performing well in a differential diagnostic setting, the original 153 gene expression profiles performed on the Affymetrix Genechips was clustered using this gene set. For this analysis, the 88 gene probes corresponded to a set of 53 Affymetrix probe pairs; which was used in the comparison. This set of gene probes performed reasonably well at separating the SLE sample profiles from the non-SLE sample profiles

EXAMPLE 9- QUANTITATIVE RT-PCT

[00289] We have also measured expression of many of the 1645 genes in SLE and WG patients as well as non-SLE patients using real time quantitative PCR method. These genes include but are not limited to EPSTIl, HERC5, IFIT5, IFRG28, LAMP3, OASl, OTOF, SCO2, SN, TNFAIP6, TRIM6, USP 18, ZCCHC2. The results of these measurements confirmed the test results obtained using the array hybridization technology, thereby confirming the results of the nucleic acid hybridization array analysis. In these analyses the housekeeping gene GAPD was used as a control standard.

[00290] Although certain presently preferred embodiments of the invention have been specifically described herein, it will be apparent to those skilled in the art to which the invention pertains that variations and modifications of the various embodiments shown and described herein may be made without departing from the spirit and scope of the invention. Accordingly, it is intended that the invention be limited only to the extent required by the appended claims and the applicable rules of law.

Claims

CLAIMSWe claim:

1. A method for screening for an individual for an autoimmune disease comprising:

a) testing a biological sample from the individual for expression of at least five genes selected from the groups of genes consisting essentially of groups (a), (b), (c), (d), (e), (f), (g), and (h), wherein

group (a) consists of AI337069; AW189843; NM_006820; NM_001548; NM_005101; AI742057; NM_016323; NM_001549; AA781795; NM_002346; NM_006417; NMJD02534; AL390736; NM_002462; NM_002535; NM__006187; NMJH7631; AA633203; AI075407; BC000080; BE049439; AA142842; NM_017414; NM_016816; AA131041; AK023743; NM_023068; NM_016817; AW337833; AK002064; NM_017523; NM_014314; NM_012420; NM_003733; NM_017742; NM_001972; NM_005532; NM_017654; AI825926; AF307338; NM_007219; BE888744; N47725; NM_017912; NM_005564; AU147903; NM_000045; BE644917; AA167449; NMJ)01925; NM_004030; BC002548; NM_018324; NM_000399; BE645480; NM_002343; NM_021170; M33326; NM_000559; AK000229; NM_022168; AI371550; AF063612; NMJ)00062; BE669858; AV755522; AI925506; NM_021105; BE966604; AA741307; M63310; NM_014398; NM_000184; BC005008; AA761181; NM_024119; AW014593; M18728; AL520984; NM_030776; NM_022147; BC005912; NM_002053; NM_006061; AK000168; AI348745; NM_022750; U65590; NM_002777; NM_016410; BF223193; NM_005091; AU145003; AA056548; AK001844; NM_015907; NM_001700; NM_004126; AL121829; NM_001725; AI859280; AI651594; AF220030; BC001356; NM_015961; NM_004802; NM_005952; BG271923; NM_005605; NMJ302424; AF134715; D86962; AW151360; AF349571; AI967971; AJ240085; NMJ301924; AF177765; AW188198; AA237039; AA768888; AV699347; BE672260; NM_001295; AI984040; NM_004084; M97935; BG236273; AA708470; NM_022873; NM_018961; AI244908; N53555; AB037810; BC002666; AW014557; BF433657; AI709406; NM_004867; AF312735; U94506; NM_004669; J04132; U66065; NM_016381; NM_005531; NM_020152; AW571582; AF105974; R13458; AF208043; AF277174; AF307451; NM_003465; AA035730; V00489; AF182069; AW083820; AF285167; AL045882; NM_007115; AI064690; U57059; BE466274; NM_005965; AI391633; NM_012413; AI341142; AA577672; AI141116; NM_005951; AA628440; NM_025195; AI796169; NM_020406; AI954660; AI091372; BF107565; AI862559; M10943; NM_000240; AW007751; AK023661; NM_003113; AI421071; AK001731L; NMJH2307; BC005931; BG538627; AF333388; NM_005138; U19970; BE788984; BE676543; AI225238; NM_000558; NMJH2329; NM_002759; M97935; AI133353; AW008051; BG545653; AW149270; NM_002532; NM_005764; BE328243; H98105; NM_005384; AL575177; AF317129; NM_006639; AF220028; NM_007237; AW295340; NM_004657; NM_014381; AL566294; NM_004810; X72501; BC001051; AI703476; AI583173; NM_0(b356; AA811138; AL547946; AB020630; AI753104; NM_020415; NM_021127; AF157323; AF218365; AF196976; BE551631; AF026071; BC004998; BC001811; NM_001838; AA083478; NM_002463; AI738416; NM_030930; NM_005567; AA233374; BE549540; NM_003113; X69397; AF294627; NM_000593; BE465037; U94510; AI916948; NM_005178; AL522667; AL136583; M25079; AL161961; BG435404; NM_004221; NM_020995; NM_002199; BC002637; AW474434; M97935; NM_004335; BF905445; M12959; NM_005953; AU154202; AU146285; AL137438; AF129536; X06557; AK026751; M97935; NM_001062; U03858; AI925518; NM_004223; and NM_005306; group (b) consists of AI862559; M10943; NM_006187; AF323540; AF307338; AI738416; NM_004335; NM_001295; AI421071; NM_016323; AW189843; AI337069; BE549540; NMJ306639; NM_005771; AF240697; AF240698; AK002064; AA781795; AA633203; AF218365; AF129536; NM_017631; AA741307; NM_017654; AK023743; BE669858; BE886225; NM_006700; BE788984; BC002666; AW014593; NM_002053; BF509371; AL136680; AW392952; BG545653; BG271923; NM_005306; NM_021170; NM_016410; NM_015961; NM_005531; BG256677; AF208043; NM_005532; BC001356; NM_006417; BE049439; NM_001548; BE888744; AA131041; NM_001549; AI075407; NM_012420; N47725; NM_022147; NM_004030; NM__002201; D43949; AA056548; AL161961; AA233374; NM_014398; NM_015907; NM_024119; AI631846; AW083820; AI742057; AA577672; AK023724; AI709406; NM_022168; AL045882; AI341142; AI798098; AW275016; BE328243; AI809206; BC002548; NMJ305951; NM_005952; NM_002450; NM_002463; AI143416; BCOOl 165; AF312735; NM_002534; NM_016816; NM_016817; NM_002535; NM_004802; BC000080; AI967971; BG538627; AL121829; NM_002759; AK023661; NM_014314; NM_005138; BC001463; NM_023068; N53555; NM_003113; NM_007237; H98105; NM_000593; AW188198; NM_007115; U57059; NM_003810; AW474434; AF134715; AF317129; NM_016381; NM_014788; AA083478; AF220028; AF220030; NM_030930; NM_017414; NM_030776; AI925506; NM_022750; AK000229; BE676543; NM_017742; AI539443; AA768888; AW014557; AI651594; BE674118; AI064690; AI494047; AA708470; BE645480; BG251692; AW297731; AK026751; AU147903; R13458; AW151360; NM_017912; AF333388; BE966604; H99792; and AL121994;

group (c) consist of AI862559; M10943; NM__006187; AF323540; AF307338; AI738416; NM_004335; NM_001295; AI421071; NM_016323; AI337069; NM__005771; AF240697; AF240698; AK002064; AF218365; NM_017631; NM_017654; NM_006700; BC002666; NM_002053; AL136680; NM_005306; NM_021170; NM_016410; NM_015961; NM_005531; BG256677; AF208043; NM_005532; BC001356; NM_006417; BE049439; NM_001548; BE888744; NM_001549; NM_012420; N47725; NM_022147; NM_004030; NM_002201; D43949; AA056548; AA233374; NMJH4398; NM_015907; NM_024119; AI742057; AA577672; AI709406; NM_022168; AI809206; BC002548; NM_005951; NM_005952; NM_002450; NM_002463; BC001165; AF312735; NM_002534; NM_016816; NM_016817; NM_002535; NM_004802; BC000080; AI967971; BG538627; NM_002759; AK023661; NM_014314; NM_005138; BC001463; NM_023068; N53555; NM_003113; NM_003113; NM_007237; H98105; NM_000593; AW188198; NM_007115; U57059; NM_003810; AW474434; AF134715; AF317129; NM_016381; NM_014788; AA083478; AF220028; AF220030; NM_030930; NM_017414; NM_030776; AI925506; NM_022750; BE676543; NM_017742; AA708470; AWl 51360; NM_017912; AF333388; BE966604; H99792; and AL121994;

group (d) consists of AI337069; AW189843; NM_006820; NM_001548; NM_001549; NM_005101; NM_002346; AI742057; AA781795; NM_016323; NM_002534; NM_006417; AA633203; NM_002462; NM_006187; NM_017631; NM_017414; AA131041; AI075407; BC002548; BE049439; NM_017523; BE888744; NM_017654; NM_016817; AA142842; NM_014314; and NM_016816;

group (e) consists of AI337069; AWl 89843; NM_006820; NM_001548; NM_001549; andNM_005101;

group (f) consists of ACATE2; ATF6; BC022357; C20orfl8; C7orf6; C9orf72; CASPl; CCRl; CHMP5; COX5B; DHRS9; DKFZP564F0522; DTX3L; EIF2AK2; EPSTIl; FCGRlA; FLJ31033; FLJ37858; FLJ38348; FLN29; G1P2; G1P3; GSTOl; IFI16; IFI27; IFI44; IFI44L; IFITl; IFIT3; IFIT5; LOC129607; LOC153684; LOC391020; MSRB2; MTlX; MT2A; MX2; NAPA; NT5C3; OSBPLIl; PARP14; PARP9; PLSCRl; PRIC285; PRO1073; RSAD2; SCO2; SCOTIN; SERPINGl; SLC23A2; SPlOO; STK24; TNFAIP6; TNFAIP6; TNFSFlO; TNFSF 13B; TOPORS; and ZCCHC2;

group (g) consists of AA056548; AA577672; AA781795; AF134715; AF208043; AF312735; AI064690; AI075407; AI337069; AI421071; AI559696; AI738416; AI742057; AK023743; AL121829; AL121994; AU147903; AV755522; AW151360; AW188198; AW189843; AW474434; BCOOl 165; BC001463; BE645480; BE676543; BE966604; BF223193; L03419; N47725; NM_000062; NM_001548; NMJXH549; NM_002463; NM_002759; NM_003113; NM_005101; NM_005138; NMJ)05532; NM_005771; NM_005952; NM_005953; NM_006417; NM_006700; NM_006820; NM_007115; NMJU5961; NM_016410; NMJ)21105; NM_022873; U13699; U57059; andX14355; and

group (h) consists of AA035730; AA056548; AA083478; AA131041; AA142842; AA233374; AA237039; AA577672; AA587884; AA633203; AA708470; AA741307; AA761181; AA768888; AA781795; AB020630; AB044805; AB051458; AF026071; AF043179; AF043337; AF063612; AF129536; AF134715; AF208043; AF218365; AF220028; AF220030; AF237762; AF285167; AF295773; AF307338; AF312735; AF317129; AF333388; AFFX-HUMISGF3A/M97935_3; AFFX-HUMISGF3A/M97935_5; AFFX-HUMISGF3A/M97935_MA; AFFX-HUMISGF3A/M97935_MB; AI064690; AI075407; AI225238; AI337069; AI341142; AI348745; AI371550; AI421071; AI539443; AI559696; AI580142; AI583173; AI631846; AI651594; AI709406; AI738416; AI742057; AI796169; AI817942; AI823453; AI825926; AI827431; AI857639; AI859280; AI862559; AI925506; AI935915; AI954660; AI967971; AI983904; AI984040; AJ240085; AK000168; AK000229; AK000752; AK000850; AKOOl 844; AK002064; AK023661; AK023743; AL021786; AL045882; AL049435; AL121829; AL161961; AL390736; AL545921; AL565741; AU145003; AU147903; AV706522; AV755522; AW007751; AW008051; AW014557; AW014593; AW069729; AW083820; AW151360; AW169333; AWl 88198; AWl 89843; AW273811; AW275016; AW297731; AW337833; AW474434; AW514900; BC000080; BC001165; BC001356; BC001463; BC001811; BC002548; BC002666; BC004546; BC004998; BC005008; BC005912; BC006271; BC006271; BE049439; BE328243; BE549540; BE645480; BE669858; BE675486; BE676543; BE788984; BE886225; BE888744; BE966604; BF058422; BF223010; BF509781; BF513244; BF514098; BG036514; BG150085; BG231515; BG236273; BG260886; BG271923; BG538627; BG545653; D43949; D86962; H98105; M10943; M12423; M12959; M15564; M18728; M25532; M33326; M97943; N20923; N47725; N53555; NM_000045; NM_000062; NM_000074; NMJ)OOl 84; NM_000240; NM_000399; NM_000559; NM_000579; NM_000584; NM_000593; NM_001222; NM_001295; NM_001548; NM_001549; NM_001700; NM_001924; NM_001925; NM_001972; NM_002053; NM_002346; NM_002462; NM_002463; NM_002532; NM_002534; NM__002535; NM_002567; NM_002759; NM_002777; NM_003113; NM__003113; NM_003377; NM_003465; NM_003550; NM_003596; NM_003733; NM_003790; NM_003810; NM_004030; NM_004188; NM_004221; NM_004223; NM_004335; NM_004802; NM_004867; NM_005101; NM_005138; NM_005306; NM_005356; NM_005531; NM_005532; NM_005567; NM_005605; NM_005951; NM_005952; NM__005953; NM_006061; NM_006137; NM_006187; NM_006417; NM_006639; NM_006820; NM_007237; NM_012307; NM_012420; NM_013308; NM_014018; NM_014314; NM_014398; NM_015833; NM_015907; NMJ) 15961; NMJH6026; NM_016323; NM_016381; NM_016410; NM_016816; NM_016817; NM_017414; NM_017523; NMJU7631; NM_017654; NM_017718; NM_017742; NM_017912; NM_017933; NM_018324; NM_018381; NM_018961; NM_021105; NM_021127; NM_021170; NM_022087; NM_022147; NM_022168; NM_022750; NM_022873; NM_023068; NM_024119; NM_024693; NM_024699; NM_030776; NM_030930; Rl 3458; T65020; U03858; U07236; U20350; U47924; U57059; U65590; U66065; U87558; U90548; U94506; U94510; W46994; X06557; Y09216; and Z22969;

b) comparing the expression of the genes tested with a control; and

c) determining if the individual has an autoimmune disease by seeing a change in expression of at least five of the tested genes.

2. The method of claim 1 , wherein the change in expression is at least 1.8 fold change.

3. The method of claim 1 or 2, wherein the autoimmune disease is systemic lupus erythematosus (SLE).

4. The method of claim 1 , wherein the autoimmune disease is SLE and the method further comprises:

a) determining SLE disease activity in an individual by testing expression of at least 5 genes selected from the group consisting essentially of AA056548; AA083478; AA083478; AA131041; AA142842; AA150460; AA195074; AA233374; AA523958; AA573502; AA577672; AA741307; AA781795; AA976354; AF043337; AF063612; AF093744; AF129536; AF134715; AF208043; AF218365; AF220028; AF220030; AF237916; AF240697; AF240698; AF280094; AF307338; AF312735; AF312735; AF317129; AF323540; AI064690; AI075407; AI143416; AI304317; AI337069; AI421071; AI539443; AI557312; ^■ AI559696; AI608902; AI631846; AI651594; AI654857; AI688640; AI709406; AI738416; AI742057; AI798098; AI809206; AI825926; AI857639; AI859280; AI859865; AI862559; AI925506; AI954660; AI967971; AI984040; AK000229; AK002064; AK023661; AK023724; AK023743; AK025064; AK026751; AL045882; ALl 17607; AL121829; AL121994; AL136680; AL136924; AL161961; AU147903; AV706522; AV755522; AW008051; AW014557; AW014593; AW083820; AW151360; AW188198; AWl 89843; AW275016; AW297731; AW474434; AW575754; AW847318; BC000080; BCOOl 165; BC001356; BC001463; BC002548; BC002666; BC006456; BE049439; BE328243; BE549540; BE645480; BE669858; BE674118; BE676543; BE788439; BE788984; BE886225; BE888744; BE966604; BFl 10588; BF223193; BF446719; BF509371; BF589359; BG035151; BG256677; BG260886; BG271923; BG291961; BG538627; BG545653; D43949; H98105; H99792; L03419; N47725; N53555; NM_000062; NM_000593; NM_001295; NM_001511; NM_001548; NM_001549; NM_001695; NM_001827; NM_001862; NM_002053; NM_002201; NM_002346; NM_002450; NM_002462; NM_002462; NM_002463; NM_002534; NM_002535; NM_002592; NM_002759; NM_002796; NM_002801; NM_003113; NM_003810; NM_003902; NM_004030; NM_004223; NM_004335; NM_004643; NM_004802; NM_004832; NM_005101; NM_005138; NM_005274; NM_005306; NM_005531; NM_005532; NM_005567; NM_005771; NM_005915; NM_005952; NM_005953; NM_006187; NM_006417; NM_006639; NM_006700; NM_006820; NM_006994; NM_007115; NM_007237; NM_012420; NM_014314; NM_014398; NM_014705; NM_014788; NM_015907; NM_015961; NM_016323; NM_016381; NM_016410; NM_016816; NM_016817; NM_017414; NM_017523; NM_017631; NM_017654; NM_017912; NM_018381; NM_021105; NM_021127; NM_021170; NM_022147; NM_022168; NM_022750; NM_022763; NM_022873; NM_023068; NM_024119; NM_030930; U13699; U57059; U65590; U90548; and X16354; and

b) comparing the expression of the tested genes with a control, wherein highly increased expression of the tested genes is indicative of more active SLE and moderately increased activity of at least 5 of the tested genes is indicative of less active SLE.

5. The method of claim 1, wherein the autoimmune disease is Wegener's granulomatosus ANCA+ vasculitis (WG) and the method further comprises:

a) determining WG disease activity in an individual by testing expression of at least 5 genes selected from the group consisting of groups (i) and (j) wherein

group (i) consists of NM_007219; AL562528; AL575509; AI760166; U41070; NM_001706; AI538394; AW592242; NM_007246; AW264036; NM_001995; NM_003059; AK025534; AI768563; AW295340; L32185; L13974; NM_006931; NM_000717; NM_005384; W60806; AI084056; S67779; AI452715; NM_018324; NM_004668; AI374686; AL136944; AF177765; AI767388; NM_005239; BC004564; and AL049435; and

group (b) consists of BE217880; NM_006159; U30610; NM_024600; NM_000436; BE042354; L34703; AA976536; AI761658; BE218980; NM_020379; NM_006720; NM_021129; AF043899; AW190316; D13720; AI770171; AK025298; AA169780; AW450363; AL578336; NM_021029; NM_015414; BE465433; AA854943; AB051458; BC001051; NM_001767; AA541630; NM_021643; AI745230; T65020; BF223206; AF204231; AA130247; U87558; J04132; AI912976; AF036906; AF288571; AL021786; NM_022898; NM_016337; W60810; AL559122; AB009597; NM_000986; NMJ)Ol 009; N25986; AL121934; BE314601; U90548; NM_005356; NM_002258; U94506; AJ297586; BF217539; AF047448; M12423; X79536; and AF164622; and

b) comparing the expression of the tested genes with a control, wherein increased expression of the tested genes in group (a) and decreased expression of the tested genes in group (b) is indicative of more active WG, and decreased expression of tested genes in group (a) and increased expression of the tested genes in group (b) is indicative of less active WG.

6. The method of any of the preceding claims, wherein the biological sample is whole blood.

7. The method of any of the preceding claims, wherein the biological sample is white blood cells.

8. The method of any of the preceding claims, wherein the biological sample is a kidney biopsy.

9. The method of any of the preceding claims, wherein the biological sample is cells from urine sediment.

10. The method of any of the preceding claims, wherein the control is a biological sample from the same tissue or cell type origin from an individual who is not affected with an autoimmune disease.

11. The method of any of the preceding claims, wherein the control is a database, which has been created from gene expression profiles, as compared to a housekeeping gene standard, of biological samples of same tissue or cell origin from individuals who are not affected with an autoimmune disease.

12. The method of any of the preceding claims, wherein the control is a database, which has been created from gene expression profiles, as compared to a housekeeping gene standard, of biological samples of same tissue or cell origin from individuals who are affected with different autoimmune diseases and/or different disease activity of the same disease, and wherein the expression profile of the measured genes similar to the control is indicative of the individual being affected with the autoimmune disease that the control is created from.

13. A method for screening for an agent capable of normalizing SLE associated gene expression profile comprising exposing cells from an individual affected with SLE to a test agent, and measuring gene expression profile of at least five of the genes selected from the groups a-h of claim 1, before and after exposure to the test agent, wherein change in the expression profile of the measured genes similar to a control gene expression is indicative of the test agent being effective in normalizing SLE associated gene expression profile.

14. A method of predicting or diagnosing drug-induced SLE in an individual comprising analyzing the gene expression profile of a biological sample from an individual exposed to a drug known or suspected of being associated with induction of SLE of at least two of the genes selected from the groups a-h of claim 1, wherein the expression profile of the measured genes similar to an SLE profile is indicative of the individual affected with induced SLE and the expression profile of the measured genes similar to a control is indicative of the individual not being affected with drug-induced SLE.

15. The method of any of the preceding claims, wherein at least 25 genes are tested and a change in expression of at least 25 genes is seen.

16. The method of any of the preceding claims, wherein at least 100 genes are tested and a change in expression of at least 100 genes is seen.

17. The method of claim 4, wherein highly increased expression is at least five (5) times the control level of expression and moderately increased expression is at least two point five (2.5) times the control level of expression.

18. A kit for screening for an autoimmune disease, wherein the kit comprises a plurality of isolated oligonucleotides, the oligonucleotides corresponding to no more than 500 genes, wherein at least 279 of the 500 genes are selected from group (a) of claim 1.

19. A kit for screening for an autoimmune disease, wherein the kit comprises a plurality of isolated oligonucleotides, the oligonucleotides corresponding to no more than 500 genes, wherein at least 147 of the 500 genes are selected from group (b) of claim 1.

20. A kit for screening for an autoimmune disease, wherein the kit comprises a plurality of isolated oligonucleotides, the oligonucleotides corresponding to no more than 500 genes, wherein at least 105 of the 500 genes are selected from group (c) of claim 1.

21. A kit for screening for an autoimmune disease, wherein the kit comprises a plurality of isolated oligonucleotides, the oligonucleotides corresponding to no more than 500 genes, wherein at least 28 of the 500 genes are selected from group (d) of claim 1.

22. A kit for screening for an autoimmune disease, wherein the kit comprises a plurality of isolated oligonucleotides, the oligonucleotides corresponding to no more than 500 genes, wherein at least 6 of the 500 genes are selected from group (e) of claim 1.

23. A kit for screening for an autoimmune disease, wherein the kit comprises a plurality of isolated oligonucleotides, the oligonucleotides corresponding to no more than 500 genes, wherein at least 69 of the 500 genes are selected from group (f) of claim 1.

24. A kit for screening for an autoimmune disease, wherein the kit comprises a plurality of isolated oligonucleotides, the oligonucleotides corresponding to no more than 500 genes, wherein at least 53 of the 500 genes are selected from group (g) of claim 1.

25. A kit for screening for an autoimmune disease, wherein the kit comprises a plurality of isolated oligonucleotides, the oligonucleotides corresponding to no more than 500 genes, wherein at least 277 of the 500 genes are selected from group (h) of claim 1.

26. The kit of any of the preceding claims, wherein the oligonucleotides correspond to no more than 400 genes.

27. The kit of any of the preceding claims, wherein the oligonucleotides correspond to no more than 300 genes.

28. The kit of any of the claims 17-22, wherein the oligonucleotides correspond to no more than 200 genes

29. The kit of any of the claims 19-22, wherein the oligonucleotides correspond to no more than 100 genes.

30. The kit of any of claims 19 or 20, wherein the oligonucleotides correspond to no more than 50 genes.

31. The kit of any of the preceding claims, further comprising a substrate.

32. The kit of any of the preceding claims, wherein is substrate is a glass slide.

33. The kit of any of the preceding claims, wherein the substrate is a bead.