WO2005098448A2 - Method and biomarkers for detecting tumor endothelial cell proliferation - Google Patents

Abstract

Methods, biomarkers and expression signatures are disclosed for assessing the proliferative rate of vascular endothelial cells. More specifically, the invention provides a set of genes which can be used as biomarkers and gene signatures for evaluating the pharmacodynamic effects of cancer therapies designed to regulate the proliferation of endothelial cells in tumor vasculature. In one aspect the invention provides a method of evaluating the efficacy of a compounds designed to inhibit kinase receptor activity, such as a mammalian KDR receptor activity.

Description

TITLE OF THE INVENTION

METHOD AND BIOMARKERS FOR DETECTING TUMOR ENDOTHELIAL CELL

PROLIFERATION

CROSS-REFERENCE TO RELATED APPLICATIONS The present application claims the benefit U.S. Provisional Application No. 60/556,645, filed March 26, 2004, hereby incorporated by reference herein.

FIELD OF THE INVENTION The field of this invention relates to methods, biomarkers, and expression signatures for assessing the proliferative rate of vascular endothelial cells within tumors. More specifically, the invention provides a set of genes which can be used as biomarkers for evaluating the pharmacodynamic effects of cancer therapies designed to regulate the proliferation of endothelial cells in tumor vasculature. In one aspect the invention provides a method of evaluating the efficacy of a compounds designed to inhibit kinase receptor activity, such as a mammalian KDR receptor activity.

BACKGROUND OF THE INVENTION In the description that follows, the teachings of various scientific references are relied on to support particular findings and statements. The numerical citations included at the end of particular sentences refer to the numbered list of references included at the end of the specification. Vascular endothelial cells form a luminal non-thrombogenic monolayer throughout the vascular system. Solid tumors require a vascular system to expand beyond small nodules limited by the diffusion of nutrients and metabolic by products. Although tumor cells can initially colonize existing host capillaries, their growth leads to the collapse of these preexisting normal vessels resulting in hypoxia. Therefore, angiogenesis is critical to the progression of numerous cancers. Subsequent tumor growth requires neovascularization that is achieved by the ingrowth of new host blood vessels, denoted tumor angiogenesis. Tumors induce proliferation, migration and differentiation resulting in neovascularization by secreting growth factors for vascular endothelial cells. Angiogenesis is critical to the progression of numerous cancers. Tumors induce endothelial cell migration, proliferation and differentiation resulting in neovascularization arising from existing blood vessels. Tumor cells induce angiogenesis primarily through the production and secretion of vascular endothelial growth factor (VEGF), a secreted protein that is a potent endothelial cell mitogen and ligand for the kinase insert domain receptor (KDR, FLK-1, or VEGF receptor). Tyrosine kinases are a class of enzymes that catalyze the transfer of the terminal phosphate of adenosine triphosphate to tyrosine residues in protein substrates. Tyrosine kinases are believed, by way of substrate phosphorylation, to play critical roles in signal transduction for a number of cell functions and have been shown to be important contributing factors in cell proliferation, carcinogenesis and cell differentiation. Tyrosine kinases can be categorized as receptor type or non receptor type. Receptor type tyrosine kinases typically have an extracellular, a transmembrane, and an intracellular portion, while non- receptor type tyrosine kinases typically are wholly intracellular, while examples exist of membrane receptors that upon ligand binding recruit intracellular kinases to bind to the intracellular portion of the receptor which, by itself, does not have kinase activity. Both receptor-type and non-receptor type tyrosine kinases are implicated in cellular signaling pathways leading to numerous pathogenic conditions, including cancer, psoriasis and hyperimmune responses. The receptor-type tyrosine kinases are comprised of a large number of transmembrane receptors with diverse biological activity. In fact, about twenty different subfamilies of receptor-type tyrosine kinases have been identified. The kinase insert domain receptor (KDR) belongs to the FLK subfamily of receptor-type tyrosine kinases. KDR is a transmembrane receptor tyrosine kinase expressed primarily in vascular endothelial cells that transduces the majority of physiological functions attributed to VEGF (3, 8-10). Inhibition of KDR catalytic activity blocks tumor neo-angiogenesis, reduces vascular permeability, and, in animal models, inhibits tumor growth and metastasis. Tumor cells induce angiogenesis primarily through the production and secretion of vascular endothelial growth factor (VEGF) a potent endothelial cell mitogen and ligand for the kinase insert domain receptor (KDR, FLK-1, or VEGF receptor 2) (3-7). VEGF binds with high affinity to two transmembrane tyrosine kinase-linked receptors, Flt-1 (VEGFR-1) and KDR (Flk-l/VEGFR-2), that are expressed by vascular endothelial cells. The binding of dimeric VEGF to the extracellular region of KDR promotes receptor dimerization that brings the intracellular tyrosine kinase domains together and promotes phosphorylation of several receptor tyrosine residues, at least some of which are critical for mitogenic signal transduction. Extensive efforts are underway to identify anti-angiogenic therapies for the treatment of human cancers. Since VEGF produced and secreted by tumor cells activates KDR and induces endothelial cell proliferation, inhibition of KDR by a small molecule should lead to a decrease in the proliferation rate of tumor endothelial cells. Currently, several small molecule inhibitors of KDR activity are being evaluated as anti-cancer agents in clinical trials. Once activated, KDR initiates a signal transduction cascade, is internalized and ultimately degraded. Inhibition of the VEGF/KDR system has been shown to inhibit VEGF-dependent tumor angiogenesis and growth in several animal models. Because VEGF produced and secreted by tumor cells activates KDR and induces endothelial cell proliferation, it is acknowledged that inhibition of KDR kinase activity should lead to decreases in the proliferation of tumor endothelial cells. Accordingly, numerous proposed cancer therapeutics target vascular endothelial cell growth factor (VEGF) or the kinase insert domain receptor (KDR/VEGFR-2/FLK-l), the primary VEGF receptor on endothelial cells. Clinically, it is difficult to assess directly the pharmacodynamic effects of KDR inhibitors because KDR protein is not easily detectable in readily available clinical samples. Measurement of changes in vascular permeability within a tumor by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is currently the most common pharmacodynamic assay, but provides an indirect readout and is a complex and expensive procedure. Thus, there is a need in the clinical setting for a rapid, quantitative, reproducible, and inexpensive assay that is compatible with current clinical laboratory instrumentation and which is capable of assessing the efficacy of anti-angiogenic agents.

SUMMARY OF THE INVENTION As the mitogenically and angiogenically competent VEGF receptor, KDR is a particularly attractive target to antagonize VEGF-dependent tumor angiogenesis and growth. Inhibition of KDR catalytic activity blocks tumor neoangiogenesis, reduces vascular permeability, and in animal moldes, inhibits tumor growth and metastasis. However, because KDR protein is not expressed at high levels in readily accessible biological material, such as peripheral blood or bone marrow aspirates, clinical assessment of the in vivo pharmacodynamic efficacy of KDR kinase inhibitors is challenging. Accordingly, current pharmacodynamic assays for KDR inhibition generally rely on surrogate protein kinase markers whose activity is also sensitive to the compound being evaluated (i.e. Fms-related tyrosine kinase-3 (Flt-3) tyrosine phosphorylation in the case of many KDR kinase inhibitors) or on imaging techniques such as DCE-MRI that can assess changes in vascular permeability. These methods have the disadvantage of being indirect measures of KDR function and endothelial cell proliferation. An alternate approach is to assess the pharmacodynamic effects of putative KDR inhibitors on the proliferation rate of tumor endothelial cells. One described method for the in vivo assessment of EC proliferation involves dual immunohistochemical (MC) staining of tumor sections for the endothelial cell marker CD-31 and a nuclear marker of cellular proliferation, Ki-67(11). While an immunohistochemical method such as this can determine the fraction of ECs that are proliferating, the experimental protocol is technically complex and difficult and the analysis required for each stained tumor section is extremely time-consuming. Each of these factors makes clinical use of an MC-based assay unlikely. The methods disclosed and claimed herein are based on the discovery and characterization of biomarkers and gene expression signatures that are specific for proliferating endothelial cells. Gene expression profiling data from cultured primary endothelial cells, cultured tumor cells, and tissue from animal tumor models treated with KDR inhbitors was used to identify a set of genes that are selectively overexpressed in tumor endothelial cells relative to tumor cells, and whose pattern of expression correlates with the rate of tumor endothelial cell proliferation. It is contemplated that the biomarkers and endothelial cell-specific expression signatures which are disclosed and claimed herein will find utility in the context of providing a pharmacodynamic readout for any cancer therapy that aims to inhibit proliferation of endothelial cells in tumor vasculature. As shown herein, the expression levels of these genes serve as the basis of a simple pharmacodynamic assay for the activity of small molecule inhibitors of the KDR receptor tyrosine kinase. The methods disclosed and claimed herein can be used as the basis for a pharmacodynamic assay capable of supporting the clinical development of small molecule inhibitors of the KDR receptor tyrosine kinase. More specifically, the invention provides a method for assessing the in vivo effects of a KDR kinase inhibitor on the proliferative rate of vascular endothelial cells within tumors. In one aspect the invention provides a method for determining the proliferative status (or rate) of endothelial cells. As shown herein, the disclosed method can be used to evaluate the proliferative status of endothelial cells in either an in vitro or in vivo format. One of skill in the art will acknowledge that the disclosed gene expression-based pharmacodynamic assays which can be established based on the disclosure provided herein can be used to support screening assays established to evaluate the efficacy of therapeutic agents intended to regulate the proliferative status of endothelial cells. In a second aspect the invention provides a method for evaluating the proliferative rate of vascular endothelial cells within tumors. In a particular embodiment, the invention provides a gene expression-based pharmacodynamic assay that is suitable for use to support clinical development of cancer therapies designed to regulate the proliferation of endothelial cells in tumor vasculature. For example, it is contemplated that the disclosed methods can be used to establish pharmacodynamic assays that can distinguish tumors containing proliferating endothelial cells from tumors containing mostly quiescent endothelial cells. In a particular embodiment the method may include detecting the expression level of one or more genes selected from a group consisting of Angpt-2, Clu (ApoJ), Cyrόl (CCN1), Endrb (Etb), Ifit-3 (Garg49), Fut-4, Plau (uPA). In a third aspect the invention provides a method for evaluating the activity of anti-angiogenesis therapeutics intended to regulate the proliferative rate of vascular endothelial cells within tumors. In a particular embodiment, the invention provides a method for evaluating the efficacy of small molecule inhibitors of receptor-type kinase inhibitors, such as KDR. For example, this aspect of the invention provides a method which is suitable for use to support clinical development of KDR kinase inhibitors, such as Compound A. Using the information provided herein, particularly the Compound A-and B- induced endothelial cell-specific expression signatures provided in Tables 5. Table 6 provides the summary information describing the changed (suppressed) expression of endothelial cell specific biomarkers (collectively referred to as the proliferation sequence) observed in response to the in vivo administration of KDR Kinase inhibitors (Compounds A and B), provided in Table 6. It is well within the abilities of a skilled artisan to design and validate a gene expression-based assay that is suitable for evaluating the efficacy of anti-angiogenesis agents. It is contemplated that using the disclosure provided herein a skilled artisan can utilize the information provided in the tables summarizing the proliferation signatures disclosed herein to identify compound-specific expression signatures that will facilitate evaluating the efficacy of alternative therapeutic agents intended to regulate endothelial cell proliferation. For example, this aspect of the invention provides a method which is suitable for use to support clinical development of KDR kinase inhibitors, such as Compound A. For example, it is contemplated that the efficacy of Compound A could be evaluated in vivo by establishing an assay which detects changes in the expression of a gene signature comprising the Angpt-2, Clu (ApoJ), Cyrόl (CCN1), Endrb (Etb), Ifit-3 (Garg49), Fut-4, Plau (uPA) genes. In a fourth aspect, the invention provides a composition of genes or biomarkers which are selectively overexpressed in tumor endothelial cells relative to tumor cells, and whose pattern of expression correlates with the rate of tumor endothelial cell proliferation. One embodiment of this aspect of the invention provides compositions comprising at least two oligonucleotides, wherein each of the oligonucleotides comprises a sequence that specifically hybridizes to a gene disclosed in Tables 3 or 4 as well as solid supports comprising at least two probes, wherein each of the probes comprises a sequence that specifically hybridizes to a gene in Tables 3, 4, 5 or 6. In a particular embodiment, the composition will comprise oligonucleotides and/or probes which hybridize with the following genes: Angpt-2, Clu (ApoJ), Cyrόl (CCN1), Endrb (Etb), Ifit-3 (Garg49), Fut-4, Plau (uPA), in combination with other oligonucleotides or probes specific for other genes identified in Tables 3-6. In another aspect the invention provides gene expression signatures, which can be used to establish expression-based pharmacodynamic assays for evaluating the efficacy of therapeutic agents designed to regulate the proliferation of endothelial cells. It is contemplated that one of skill in the art will be able to utilize the information provided in this disclosure, in particular the information contained in the Proliferation Signature Tables, referred to herein as Table 3 (HDMVEC Proliferation Signature), Table 4 (RHMVEC Prolilferation Signature), Table 5 (Compound A-and B-induced Endothelial Cell Specific Sequences) and Table 6 (Changes in EC-specific proliferation signature by KDR Kinase Inhibitor Asministration), to elucidate endothelial cell proliferation signatures that are suitable for monintoring the in efficacy of other anti-angiogenic compounds. As shown herein, the gene expression signature disclosed and claimed herein can be used distinguish tumors containing mostly proliferating ECs from tumors containing mostly quiescent ECs. It is contemplated that the disclosed assay will have the ability to detect inhibition of angiogenesis relatively quickly after initiating therapy, eliminating the longer period of time required to visualize morphological changes in tumor microvasculature. In addition, it is envisioned that the disclosed methods will be particularly useful in circumstances where immunohistochemistry is inappropriate or impractical, such as with small tissue samples from biopsies (i.e. fine needle aspirates) or from tissue samples with poor morphology. In a real time quantitative reverse transcription- polymerase chain reaction (PCR) format, the disclosed assay is predicted to represent an extremely sensitive assay that is readily compatible with existing clinical laboratory instrumentation. Expression profiling-based monitoring of the pharmacodynamic effects of cancer therapy potentially has many benefits. Used in the clinical setting, this technology provides for rapid, quantitative, reproducible, and inexpensive assays that are compatible with current clinical laboratory instrumentation. Carefully designed, gene expression-based asssays, such as the assays disclosed herein, have the potential to make dosing of anti-neoplastic agents more efficient, to identify patient populations most likely to benefit from specific therapies, and to reduce clinical development time of novel therapeutics. Each of these aspects will lead to increased tumor response rates and improved human health.

BRIEF DESCRIPTION OF THE DRAWINGS Figures 1A and IB. Inhibition of Vascular Endothelial Cell (VEC) proliferation in vitro by KDR kinase inhibition. HDMVECs or RHMVECs were trypsinization following the third passage in culture and seeded in fibronectin-coated, six-well tissue culture plates at a density of 10,000 cells/well. Cell growth was arrested for 24h by mitogen withdrawal and then stimulated by the addition of 100 ng/ml VEGF, 100 ng/ml bFGF or 200 μg/ml ENDOGRO. Wells with unstimulated cells and wells containing un-arrested cells were included as controls. At 72 hr following growth factor stimulation, cells were removed from the culture plates by trypsinization and counted on a hemocytometer under bright-field microscopy. Figures 2A and 2B. Identification of a gene expression profile in proliferating vascular endothelial cells in vitro. HDMVECs and RHMVECs were grown in culture and mitogen deprived for 24 hr as described in Figure 1 and Methods. Following a 24 hr stimulation with growth factor, culture media was aspirated quickly and the cells lysed in an RNA stabilizing buffer. Matched control plates that received no supplemental stimulatory growth factor were present for each stimulation condition and RNAs isolated from them served as the reference to which the RNAs from the stimulated cells was compared. Bars corresponding to genes which are regulated (e.g., upregulated or downregulated) are indicated by various shades of gray. Color intensity represents the degree of regulation, not mRNA copy number. Figures 3A-3D. Specific suppression of VEGF-induced gene expression in cultured vascular endothelial cells. EC monolayers were maintained in complete MCDB-131 media until reaching -75% confluence, then induced into a quiescent state by mitogen starvation for 24 hr. Cells were then stimulated to proliferate with 100 ng/ml VEGF for 24 hr in the presence or absence of Compound B. RNA populations isolated from cells exposed to VEGF or VEGF + Compound B were compared to matched control RNAs isolated from quiescent cells exposed to neither VEGF nor Compound B. Each point in the plots represents a gene sequence present on the DNA oligonucleotide microarray and is plotted according to the ratio of the two mRNA levels (experimental sample intensity: control sample intensity, vertical-axis) and the total mRNA quantity (experimental sample intensity + control sample intensity, horizontal-axis) for that gene. Dark-colored points indicate upregulated genes. Light Gray colored points indicate downregulated genes. Figures 4A and 4B. Growth kinetics of established rat tumors following exposure to a KDR kinase inhibitor. Tumor studies were performed as described in Materials and Methods. Figures 4A and 4B illustrate tumor volumes from animals in the C6 profiling study (Fig. 4A) and the Mattlll profiling study (Fig. 4B) as determined by caliper measurements. Tumors were calipered in two dimensions (length and width) and tumor volume was calculated according to the formula (length) x (width) x (V2 width). Figures 5 A-5C. Identification of gene expression changes induced in rat tumors by KDR kinase inhibitors in vivo.Each row represents a distinct tumor from an individual animal. Each column represents a gene. Gray colored points/bars indicate genes that are regulated (e.g., upregulated or downregulated) by KDR kinase. Figure 5A illustrates changes in the expression of genes from rat C6 flank tumors that are regulated following 24, 48, or 72 hrs of systemic exposure to the KDR kinase inhibitor Compound B. Figure 5B illustrates changes in the expression of genes from rat C6 flank tumors regulated following 24, 48, or 72 hrs of systemic exposure to the KDR kinase inhibitor Compound A. Figure 5C illustrates changes in the expression of genes from rat MatBHI mammary tumors regulated following 100 hrs of systemic exposure to the KDR kinase inhibitor Compound A. Figures 6A-6B. Distinct tumor gene expression responses elicited by KDR inhibitors.TheVenn diagram illustrated in figure 6A illustrates the degree of overlap between the tumor gene expression responses to KDR kinase inhibitors in C6 flank tumors and MatBIJI mammary tumors. The Venn diagram provided in Panel B illustrates the degree of overlap between the sets of endothelial cell-specific genes regulated both in vitro by mitogens and in tumor tissue by KDR kinase inhibitors. All of the genes (biomakers) depicted in figure 6B are regulated in vivo by KDR kinase inhibitors in a manner opposite that observed in vitro following exposure to mitogens. Figures 7A-7B. Confirmation of microarray data by real time quantitative real time PCR. Quantitative real time PCR was performed with gene-specific PCR primer pairs and amplicon-specific fluorescent probes (TaqMan). For each RNA sample tested, transcript abundance of GAPDH was determined. In addition, transcript abundance of genes of interest and GAPDH were determined for a calibrator RNA sample (total rat lung RNA). Figure 7A illustrates fold changes in gene expression in tumors from KDR kinase-treated animals relative tumors from vehicle-treated animals were calculated using the ΔΔCT method (see Materials and Methods). Figure 7B illustrates mRNA levels for each gene in the rat tumors relative the calibrator RNA pool. Figure 8. Biomarker protein expression in rat mammary tumors is localized to vasculature. De- waxed, re-hydrated MatBiπ tumor sections were incubated with antibodies against CD31 and one of the following biomarker proteins: CLU, ANGPT2, CYR61, ENDRB, or PLAU. Primary antibodies bound to the biomarker proteins and CD31 were visualized with Alexa488-labeled and Alexa546-labeled secondary antibodies, respectively as described in Materials and Methods. After mounting under coverslips, images were captured with a Zeiss Axiocam through a Zeiss Axiovert 135 fluorescence microscope equipped with a 40x objective and an Axiocam mHR CCD camera.

DETAILED DESCRIPTION OF THE INVENTION In the description that follows, numerous terms and phrases known to those skilled in the art are used. In the interest of clarity and consistency of interpretation, the definitions of certain terms and phrases are provided. The present invention provides compositions and methods to detect the level of expression of genes that may be differentially expressed dependent upon the state of the cell, i.e., proliferating versus quiescent cells. As used herein, the phrase "detecting the level expression" includes methods that quantify expression levels as well as methods that determine whether a gene of interest is expressed at all. Thus, an assay which provides a yes or no result without necessarily providing quantification of an amount of expression is an assay that requires "detecting the level of expression" as that phrase is used herein. The genes identified as being differentially expressed in proliferating endothelial cells 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. For example, traditional Northern blotting, nuclease protection, RT- PCR and differential display methods may be used for detecting gene expression levels. As used herein, oligonucleotide sequences that are complementary to one or more of the genes described herein, refers to oligonucleotides that are capable of hybridizing under stringent conditions to at least part of the nucleotide sequence of said genes. Such hybridizable oligonucleotides will typically exhibit at least about 75% sequence identity at the nucleotide level to said genes, preferably about 80% or 85% sequence identity or more preferably about 90% or 95% or more sequence identity to said genes. "Bind(s) substantially" refers to complementary hybridization between a probe nucleic acid and a target nucleic acid and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target polynucleotide sequence. The phrase "hybridizing specifically to" refers to the binding, duplexing or hybridizing of a molecule substantially to or only to a particular nucleotide sequence or sequences under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA. Assays and methods of the invention may utilize available formats to simultaneously screen at least about 100, preferably about 1000, more preferably about 10,000 and most preferably about 1,000,000 or more different nucleic acid hybridizations. Directly assessing the pharmacodynamics of anti-angiogenesis therapeutics targeted to the VEGF signaling pathway is difficult. Inhibition of the KDR tyrosine protein kinase suppresses endothelial cell proliferation, but it is difficult to assess the rate of proliferation of these cells in vivo. One method that has been used is double immunohistochemical staining of tumor sections for CD31 and Ki67 in order to quantitate proliferating endothelial cells. A second method in use is to assess changes in vascular permeability by magnetic resonance imaging (MRI). Both methods have disadvantages. Immunohistochemistry (MC) is limited to studies where relatively large, intact tumor samples are available. Even then, it is rare to have paired tumor samples taken obtained before and after treatment with a drug candidate for comparison. Fine needle aspiration (FNA) biopsy samples from a clinical setting are not analyzable by this method. Furthermore, to accurately assess microvascular density or the percentage of proliferating endothelial cells throughout the tumor is labor intensive even with semi-automated or automated microscopy equipment. Analyzing MRI images to assess changes in vascular permeability is also labor intensive, requiring highly trained personnel both to operate the imager and to interpret the images. Our strategy in designing a gene expression-based pharmacodynamic assay for endothelial cell proliferation was to employ genome-wide gene expression profiling to first identify a general mitogen- induced proliferation signature in cultured primary microvascular endothelial cells. Expression profiles of genes in particular, tissues, disease states or disease progression stages provide molecular tools for evaluating toxicity, drug efficacy, drug metabolism, development, and disease monitoring. Changes in the expression profile from a baseline profile can be used as an indication of such effects. Those skilled in the art can use any of a variety of known techniques to evaluate the expression of one or more of the genes and/or ESTs identified in the instant application in order to observe changes in the expression profile. Beginning with a large set of genes shown to be regulated in vitro by mitogen-induced proliferation of primary endothelial cells, we identified a subset that was relatively specific to endothelial cells. We then identified the subset of genes from the in vitro proliferation signature that were endothelial cell-specific. Two distinct syngeneic tumor models are used to demonstrate that in vivo exposure to KDR kinase inhibitors mediated robust gene expression changes in a manner consistent with suppression of the proliferative rate of vascular endothelial cells within tumors. Gene expression changes consistent with inhibition of VEGF-signaling and inhibition of endothelial cell proliferation were detected in tumors from each animal model. The endothelial cell specificity of the putative biomarkers was confirmed by immunofluorescence microscopy. The biomakers were further validated by correlating their in vivo gene expression changes to an independent, immunohistochemical measure of endothelial cell proliferation. Genes regulated by systemic exposure to KDR kinase inhibitors in at least two of the three tumor models were selected as endothelial cell proliferation biomarkers. Gene expression changes of these biomarkers (as determined by microarray hybridization) were confirmed by quantitative real time PCR, both in the tumors that were profiled as well as in tumors from an additional, independent animal tumor study. The disclosed set of biomarkers was validated by correlating the compound-induced gene expression changes to compound-induced differences in proliferating tumor endothelial cell number as determined by immunohistochemical staining (again in the same rat tumors that were profiled). The endothelial cell specificity (in the context of our rat tumor models) of the biomarker expression (gene signature) disclosed and claimed herein expression is established by showing that the protein products of the identified genes are restricted to CD31 -expressing cells. Based on the disclosure provided herein it is contemplated that it may be possible to identify a gene expression signature that reflects the proliferation rate of vascular endothelial cells within tumors, thereby allowing a clinician to predict tumor responsiveness to therapy. Based on the data described herein, the instant invention provides a set of genes or biomarkers, collectively referred to herein as a gene signature, that are regulated both in vitro during mitogen-induced proliferation of primary microvascular endothelial cells and in vivo in response to systemic exposure to KDR kinase inhibitors. Changes in expression levels of these biomarkers in response to inhibition of KDR are indicators of change in tumor endothelial cell proliferation rate. It is contemplated that identification of the gene expression signature (or biomarkers) disclosed and claimed herein, the regulation of which indicative of changes in the proliferation rate of tumor vascular endothelial cells provides a non-invasive and inexpensive assay following exposure to anti-angiogenesis therapeutics. While the expectation by random chance of identifying a gene that met all our selection criteria was low, we identified a set of seven potential biomarker genes (Angpt-2, Endrb (Etb), Fut-4, Clu (ApoJ), Cyrόl (CCNl), Plau (uPA), and Ifit-3 (Garg49)). Significantly, each of the seven identified biomarker is known or implicated to be involved in endothelial cell biology. We biased our biomarker selection towards endothelial cell specific genes, but there was no guarantee that genes meeting our multiple criteria would have any known function in endothelial cells. Surprisingly, nearly all the genes identified have been implicated or shown to be directly involved in the regulation of endothelial cell function. The angiopoietin-2 protein (ANGPT2/ANG2) is a well characterized ligand for the Tie-2 receptor tyrosine kinase that functions in concert with VEGF and angiopoietin-1 to regulate vascular remodeling (25). Angiopoietin-2 gene expression has been previously reported to be directly upregulated by VEGF, both in vivo and in vitro, consistent with our results (26). The type B endothelin receptor (EDNRB/ET(B)) is a seven transmembrane G-protein coupled receptor that is mutated in Waardenburg-Hirschsprung disease, a congenital malformation of neuronal ganglia in the hindgut (27). Most published studies of EDNRB describe its role in the neuronal system during neural crest development. However, it does control vasoconstriction and vascular cell proliferation induced by the endothelins and EDNRB has been shown to be overexpressed in primary melanomas(28). EDNRB antagonists have been reported to inhibit vascular cell proliferation and human melanoma cell growth in vitro and in vivo (29, 30). Fucosyltransferase 4 (FUT4) is an alphal, 3-fucosyltransferase involved in the synthesis of myeloglycan, the major physiological binder of E-selectin (31). It is also involved in the synthesis of many other glycosylated proteins, but it is reported to be highly expressed in some tumors with inverse correlation to prognosis (32). Clusterin is a secreted glycoprotein that appears to be overexpressed in apoptotic cells (33-35) but whose function is still largely unknown (33). Clusterin expression has been shown to be anti- proliferative (36) and down-regulated in advanced prostate cancer (37-39). Reduction in serum clusterin levels also correlates with esophageal squamous cell carcinoma tumorigenesis (40). Cysteine rich protein 61 (CYR61) is an extracellular matrix-associated heparin-binding protein with pro-angiogenic properties (41). In vitro CYR61, promotes cell adhesion to extracellular matrix and chemotaxis (42, 43). It stimulates cell motility through interaction with integrin αVβ5, αόβl, αMβ2 and stimulates endothelial cell proliferation through interaction with aVb3 (44-48). Our observations that the Cyrόl gene was upregulated in rat tumor tissue following exposure to KDR kinase inhibitors did not appear to be in agreement with an inhibition of endothelial cell proliferation. However it may be that the upregulation of the Cyrόl gene is a response mechanism the endothelial cell attempting to compensate for the lack of functional KDR. The urokinase type-plasminogen activator (PLAU or uPA) is a proteolytic enzyme that plays a critical role in angiogenesis, tumor invasion, and metastasis by contributing to remodeling of the extracellular matrix (49, 50). It has been characterized as a pro-tumor invasion and pro-metastatic factor. The effect of PLAU activity is the conversion of plasminogen to plasmin. As with Cyrόl, it is unclear why we observe an increase in Plau gene expression in tumors exposed to KDR kinase inhibitors rather than the decrease we would have expected to accompany a decrease in neovascularization. We can surmise that increased Plau expression is a compensatory mechanism elicited by inhibition of the VEGF signaling pathway, but clearly, more investigation is required to determine the mechanism underlying our observations. Ifit3 (interferon-induced protein with tetratricopeptide repeats 3, also known as Garg-49 (glucocorticoid-attenuated response genes) and ERG2 (interferon responsive gene 2) is a gene that as yet has no known function. Cloned from the mouse as part of studies to identify glucocorticoid attenuated response genes induced by lipopolysaccharide or interferon, the highly conserved tetratricopeptide repeat domains of IFIT3 are believed to mediate protein-protein interactions (51-54). No human ortholog of Ifit3 has been identified in human cells, but a homologous gene designated Ift4 is 60% identical and 78% similar by protein sequence (BLASTP, (55)) In practice a gene expression-based pharmacodynamic assay based on a small number of genes can be performed with relatively little effort using existing quantitative real time PCR technology familiar to clinical laboratories. Sufficient RNA for real time PCR can be isolated from low milligram quantities of sample tissue. Quantitative thermal cyclers may now be used with microfluidics cards preloaded with reagents making routine clinical use of multigene expression-based assays a realistic goal. It is to be understood that alternative assay formats, other than the methodologies exemplified herein, may be used to monitor the ability of putative cancer therapeutic agent to modulate the expression of a gene identified in Tables 3-6. For instance, as described above, mRNA expression may be monitored directly by hybridization of probes to the nucleic acids of the invention. However, methods and assays of the invention are most efficiently designed with array or chip hybridization-based methods for detecting the expression of a large number of genes. Any hybridization assay format may be used, including solution-based and solid support-based assay formats. A preferred solid support is a high density array also known as a DNA chip or a gene chip. In one assay format, gene chips containing probes to at least two genes from Tables 5-6 may be used to directly monitor or detect changes in gene expression in biological samples containing endothelial cells prepared from subjects exposed to putative cancer therapeutics designed to regulate the proliferation of endothelial cells in tumor vasculature. Solid supports containing oligonucleotide probes for differentially expressed genes can be any solid or semisolid support material known to those skilled in the art. Suitable examples include, but are not limited to, membranes, filters, tissue culture dishes, polyvinyl chloride dishes, beads, test strips, silicon or glass based chips and the like. Suitable glass wafers and hybridization methods are widely available, for example, those disclosed by Beattie (WO 95/11755). Any solid surface to which oligonucleotides can be bound, either directly or indirectly, either covalently or non-covalently, can be used. In some embodiments, it may be desirable to attach some oligonucleotides covalently and others non-covalently to the same solid support. 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, from 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. 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., Nat. Biotechnol. (1996) 14, 1675-1680; McGall et al., Proc. Nat. Acad. Sci. USA (1996) 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 my also contain oligonucleotides that are complementary or hybridize to at least 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 50, 70 or more the genes described herein. Any hybridization assay format may be used, including solution-based and solid support-based assay formats. 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 Beattie (WO 95/11755). 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. Of the techniques listed above, the most sensitive and most flexible, quantitative method is RT- PCR, which can be used to compare mRNA levels in different sample populations, in normal and tumor tissues, with or without drug treatment, to characterize patterns of gene expression, to discriminate between closely related mRNAs, and to analyze RNA structure. The first step is the isolation of mRNA from a target sample. The starting material is typically total RNA isolated from human tumors or tumor cell lines, and corresponding normal tissues or cell lines, respectively. Thus RNA can be isolated from a variety of primary tumors, including breast, lung, colon, prostate, brain, liver, kidney, pancreas, spleen, thymus, testis, ovary, uterus, etc., tumor, or tumor cell lines, with pooled DNA from healthy donors. If the source of mRNA is a primary tumor, mRNA can be extracted, for example, from frozen or archived paraffin-embedded and fixed (e.g. formalin-fixed) tissue samples. As RNA cannot serve as a template for PCR, the first step in gene expression profiling by RT- PCR is the reverse transcription of the RNA template into cDNA, followed by its exponential amplification in a PCR reaction. The two most commonly used reverse transcriptases are avilo myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT). The reverse transcription step is typically primed using specific primers, random hexamers, or oligo-dT primers, depending on the circumstances and the goal of expression profiling. For example, extracted RNA can be reverse-transcribed using a GeneAmp RNA PCR kit

(Perkin Elmer, California, USA), following the manufacturer's instructions. The derived cDNA can then be used as a template in the subsequent PCR reaction. To minimize errors and the effect of sample-to- sample variation, RT-PCR is usually performed using an internal standard. The ideal internal standard is expressed at a constant level among different tissues, and is unaffected by the experimental treatment. RNAs most frequently used to normalize patterns of gene expression are mRNAs for the housekeeping gene glyceraldehyde-3-phosphate-dehydrogenase (GAPDH), as used herein, or the β-actin gene. Although the PCR step can use a variety of thermostable DNA-dependent DNA polymerases, it typically employs the Taq DNA polymerase, which has a 5'-3' nuclease activity but lacks a 3'-5' proofreading endonuclease activity. Thus, TaqMan.RTM. PCR typically utilizes the 5'-nuclease activity of Taq or Tth polymerase to hydrolyze a hybridization probe bound to its target amplicon, but any enzyme with equivalent 5' nuclease activity can be used. Two oligonucleotide primers are used to generate an amplicon typical of a PCR reaction. A third oligonucleotide, or probe, is designed to detect nucleotide sequence located between the two PCR primers. The probe is non-extendible by Taq DNA polymerase enzyme, and is labeled with a reporter fluorescent dye and a quencher fluorescent dye. Any laser-induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together as they are on the probe. During the amplification reaction, the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner. The resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore. One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data. TaqMan.RTM. RT-PCR can be performed using commercially available equipment, such as, for example, ABI PRISM 7700.TM. Sequence Detection System. TM. (Perkin-Elmer-Applied Biosystems, Foster City, Calif, USA), or Lightcycler (Roche Molecular Biochemicals, Mannheim, Germany). In a preferred embodiment, the 5' nuclease procedure is run on a real-time quantitative PCR device such as the ABI PRISM 7700.TM. Sequence Detection System.TM.. The system consists of a thermocycler, laser, charge-coupled device (CCD), camera and computer. The system amplifies samples in a 96-well format on a thermocycler. During amplification, laser-induced fluorescent signal is collected in real-time through fiber optics cables for all 96 wells, and detected at the CCD. The system includes software for running the instrument and for analyzing the data. A more recent variation of the RT-PCR technique is the real time quantitative PCR, which measures PCR product accumulation through a dual-labeled fluorigenic probe (i.e., TaqMan.RTM. probe). Real time PCR is compatible both with quantitative competitive PCR, where internal competitor for each target sequence is used for normalization, and with quantitative comparative PCR using a normalization gene contained within the sample, or a housekeeping gene for RT-PCR. For further details see, e.g. Held et al., Genome Research 6:986-994 (1996). The genes which are assayed according to the present invention are typically in the form of mRNA or reverse transcribed mRNA. The genes may be cloned or not and the genes may be amplified or not. 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. General methods for mRNA extraction are well known in the art and are disclosed in standard textbooks of molecular biology, including Ausubel et al., Current Protocols of Molecular Biology, John Wiley and Sons (1997). Methods for RNA extraction from paraffin embedded tissues are disclosed, for example, in Rupp and Locker, Lab Invest. 56:A67 (1987), and De Andrs et al., BioTechniques 18:42044 (1995). In particular, RNA isolation can be performed using purification kit, buffer set and protease from commercial manufacturers, such as Qiagen, according to the manufacturer's instructions. Other commercially available RNA isolation kits include MasterPure.TM. Complete DNA and RNA Purification Kit (EPICENTRE.RTM., Madison, Wis.), and Paraffin Block RNA Isolation Kit (Ambion, Inc.). Total RNA from tissue samples can be isolated using RNA Stat-60 (Tel-Test). RNA prepared from tumor can be isolated, for example, by cesium chloride density gradient centrifugation. 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 mRNA 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 may be desirable to inhibit or destroy RNase present in homogenates before homogenates can be used. 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 cells), tissue or fine needle biopsy samples, urine, peritoneal fluid, and pleural fluid, or cells therefrom. Biological samples may also include sections of tissues, such as frozen sections or formalin fixed sections taken for histological purposes. The following non-limiting examples are presented to better illustrate the invention. Methods and Materials The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, and biochemistry, which are within the skill of the art. Such techniques are explained fully in the literature, such as, "Molecular Cloning: A Laboratory Manual", 2.sup.nd edition (Sambrook et al., 1989); "Oligonucleotide Synthesis" (M. J. Gait, ed., 1984); "Animal Cell Culture" (R. I. Freshney, ed., 1987); "Methods in Enzymology" (Academic Press, Inc.); "Handbook of Experimental Immunology", 4.sup.th edition (D. M. Weir & C. C. Blackwell, eds., Blackwell Science Inc., 1987); "Gene Transfer Vectors for Mammalian Cells" (J. M. Miller & M. P. Calos, eds., 1987); "Current Protocols in Molecular Biology" (F. M. Ausubel et al., eds., 1987); and "PCR: The Polymerase Chain Reaction", (Mullis et al., eds., 1994).

Compounds: The structure of the small molecule KDR kinase inhibitors, Compound A and Compound B, used in the exemplification of the present invention are as follows:

Compound A

Compound B

Cell Culture: Primary human dermal microvascular endothelial cells (HDMVEC) and rat heart microvascular endothelial cells (RHMVEC) were purchased from VEC Technologies (Renneslaer, NY) and grown in culture according to the supplier's directions, endothelial cell monolayers were maintained at 37°C in a 5% C02 humidified atmosphere in tissue culture flasks coated with human fibronectin (Sigma, St. Louis, MO) using complete MCDB-131 media (MCDB-131 supplemented with 10% fetal bovine serum (FBS, Invitrogen, Carlsbad, CA) and the growth factor cocktail ENDOGRO, VEC Technologies). For in vitro MVEC proliferation experiments, cells were harvested by trypsinization between passage 3-6 following initiation of culture from frozen stocks, counted, and seeded in fibronectin-coated tissue culture plates at 75% confluence (1.5 x 106 cells/per plate, 100 mm diameter plates). Cell growth was arrested for 24h by mitogen withdrawal and then stimulated by the addition of 100 ng/ml VEGF, 100 ng/ml bFGF or 200 μg ml ENDOGRO. For growth arrest the culture media was changed to pre-warmed DMEM supplemented with 10% FBS. For stimulation of cell growth the growth arrest media was replaced with MDCB-131 supplemented with 10% FBS and the appropriate growth factor. Matched control plates that received no supplemental stimulatory growth factor were made for each stimulation condition. At the desired time following growth factor stimulation, the culture media was removed quickly by aspiration, and the cells were lysed in 1.2 ml RLT buffer (guanidine thiocyanate lysis buffer for RNA stabilization and purification, QIAGEN, Valencia, CA). Cell lysates were homogenized in QIAshredders and total RNA was isolated with RNeasy MINI affinity columns (QIAGEN, Valencia, CA). Gene expression profiles from a total of 8 independent VEGF-stimulated cultures, 7 ENDOGRO- stimulated cultures, and 4 bFGF-stimulated cultures were determined for HDMVECs. Profiles from 4 independent VEGF-stimulated cultures, 4 ENDOGRO-stimulated cultures, and 4 bFGF-stimulated cultures were determined For RHMVECs.

Animal Tumor Models: A rat glial cell line (C6, ATCC CCL-107) and a rat mammary adenocarcinoma (MatBni, ATCC CRL-1666) were used for our animal tumor models. C6 cells were maintained in culture at 37°C in a 5% C02 humidified atmosphere in Ham's F-12 medium supplemented with 2 mM L- glutamine, 1 mg/ml sodium bicarbonate, 15% horse serum, 2.5% fetal bovine serum, 10 U/ml penicillin, and 10 μg/ml streptomycin (all media components from Invitrogen). MatBffl cells were grown in McCoy's 5a medium supplemented with 1.5 mM glutamine, 10% FBS 10 U/ml penicillin, and 10 μg/ml streptomycin. For RNA isolation from C6 or MatBIII cells, 2x106 cells growing in a 100 mm diameter tissue culture plate were lysed directly in 1.2 ml RLT buffer. Following lysate homogenization with a QIAshredder, total RNA was isolated with RNeasy MINI affinity columns. C6 glial cells and MatBHI adenocarcinoma cells were chosen for animal models because they were obtained from Fischer 344 (F344) rats and therefore could be used to create syngeneic tumors in immunocompetent F344 animals. Prior to implantation, cells were collected, washed in phosphate- buffered saline and resuspended in Hanks Balanced Saline Solution (Invitrogen) at a density of 2x107 (C6) or 2x106 (MatBDI) cells/ml. C6 glioma flank tumor model: C6 cells were injected subcutaneously into the right flank of male F344 rats (150-175 g, 107 cells per animal). Following cell injection, animals were randomized according to body weight to receive either vehicle (0.5% methylcellulose) or drug (10 mpk/dose Compound B or 40 mpk/dose Compound A in 0.5% methylcellulose) (12-15). Once-daily oral dosing began 7 days post tumor cell implantation and continued for 1, 2, or 3 days at which point the animals were sacrificed. The tumors were bisected with half preserved for RNA extraction by snap-freezing in liquid nitrogen and half fixed for histology or immunofluorescence microscopy. Five vehicle-treated and five compound-treated animals were sacrificed at each timepoint. RNA was extracted from tumor samples with RNeasy Mini columns according to standard protocols (QIAGEN). Briefly, frozen tumor samples were weighed, placed in sample tubes containing RLT buffer (600 μl RLT per 30 mg tissue), and immediately homogenized for 10-20 seconds using a rotor/stator homogenizer. Total RNA was isolated from homogenized tissue lysate with RNeasy affinity columns, resuspended in DEPC-treated water and frozen at -80°C. RNAs from the five tumors in each vehicle-treated cohort were combined to form three reference RNA pools. RNAs isolated from each of the tumor samples from the five compound-treated rats in each cohort were compared to the appropriate time-matched reference pool of RNA during microarray hybridization. In addition, RNA from individual vehicle treated rats was compared to time matched vehicle treated pool in order to assess inter-animal variability.

MatBiπ Breast Cancer Metastasis Model: MatBIII cells between passage 20-30 were injected on the mammary fat pad around the 4th left nipple (106 cells/animal) of female F344 rats (150-175 g). Prior to dosing, animals were randomized into groups according to tumor size and body weight. Once daily oral dosing of Compound A (40 mpk dose formulated in 0.5% methylcellulose) or vehicle (0.5% methylcellulose) began on day 7 post tumor cell implantation and continued for 4 additional days. Six vehicle-treated and six compound-treated animals were sacrificed on day 11, four hrs after final dosing. At the time of necropsy, tumors were weighed immediately upon removal. Half of each tumor was fixed in Zn-Tris for histology or immunofluorescence microscopy and the other half immediately snap frozen in liquid nitrogen for RNA extraction. Total RNA was isolated in the same manner as with the C6 tumor studies. RNAs from the vehicle-treated cohort were combined to form a control RNA pool. RNAs isolated from each of the tumor samples from the compound-treated rats was compared to the control pool of RNA during microarray hybridization. RNAs from individual vehicle treated animals was compared to the vehicle treated pool in order to assess inter-animal variability.

Gene Expression Profiling: Total RNA isolated from cultured cells or tumor tissue samples was used to make fluorescently-labeled complementary RNA (cRNA) that was hybridized to DNA microarrays as previously described (16, 17). Briefly, 4 μg total RNA from an individual tumor sample or in vitro endothelial cell culture was used to synthesize double-stranded DNA through reverse transcription. cRNA was produced by in vitro transcription and labeled post-synthetically with Cy3 or Cy5. Two populations of labeled cRNA, a reference population and experimental population, were compared to each other by competitive hybridization to oligonucleotide arrays synthesized in situ with inkjet technology. Two hybridizations were performed with each cRNA sample pair using a fluorescent dye reversal strategy. For animal tumor studies, reference cRNA pools were made by pooling equal amounts of cRNA from each tumor in the appropriate vehicle-dosed group. After hybridization, arrays were scanned and fluorescence intensities for each feature were recorded. Ratios of transcript abundance (experimental to control) were obtained following normalization and correction of the array intensity data. Gene expression data analysis was performed with the Rosetta Resolver Client software (v3.2, Rosetta Biosciences, Kirkland, WA). A one-way ANOVA test was used to determine statistically significant changes in gene expression.

Quantitative real time PCR: Quantitative real time polymerase chain reaction was performed with gene- specific PCR primer pairs and amplicon-specific fluorescent probes (TaqMan, Applied Biosystems Inc. (ABI), Foster City, CA) according to published protocols (ABI Assays-on-Demand™ Gene Expression Protocol, Rev A, http://docs.appliedbiosystems.com/pebiodocs/04333458.pdf). One-step quantitative reverse transcription PCR reactions were performed using ABI's TaqMan® One-Step RT-PCR Master Mix Reagents (ABI Product# 4309169) and 25 ng total RNA template on an ABI Prism 7900HT Sequence Detection System. Two-step reverse transcription PCR experiments were initiated by cDNA synthesis from 25 ng total RNA as template using ABI's High Capacity cDNA Archive Kit (ABI Product# 4322171). Second step quantitative real time PCR was performed with standard reagents (TaqMan® Universal PCR Master Mix, ABI Product# 4324018) on the ABI Prism 7900HT Sequence Detection System. Real time PCR reactions were performed in duplicate in a 25 μl reaction volume in 384-well plates. Primer and probe sequences used for each gene are listed below. For every RNA sample, transcript abundance of GAPDH was determined. In addition, transcript abundance of genes of interest and GAPDH were determined for calibrator RNA samples, either total human lung RNA or total rat lung RNA. Fold changes in gene expression were calculated using the ΔΔCT method (ABI User Bulletin #2, Rev B: Relative Quantitation Of Gene Expression, http://docs.appliedbiosystems.com/pebiodocs/04303859.pdf) The teachings of which are incorporated herein by reference. The sequences of the individual biomarker genes which comprise the proliferation and expression signatures disclosed in tables 3-6 are readily available in public databases. The signatures defined in Tables 3 and 4 (HDMVEC and RHMVEC proliferation signatures, respectively) provide the GenBank Accession Number and gene symbol for the included biomarkers, the sequences of which are hereby incorporated by reference. The endothelial cell specific signatures defined in Tables 5 and 6 also provide the GenBank Accession Number and GeneSymbol for the biomarkers comprising the expression signature. The following list provides the name, Accession Number and primer and probes used to detect a subset of the biomarkers: Hs refers to Homo sapiens. Rn refers to Rattus norvegicus. Gene RefSeq Acc# Primer Sequence (or ABI Assay-on-Demand™ ID)

Angpt-2 XM_225004 (Rn)

SEQ ID NO: 1 Forward Primer 5' - GAC AGA GTC CGA ATG CAT GCT - 3' SEQ ID NO: 2 Reverse Primer 5' - TGC GGG TCT GGA GAA ATA CC - 3' SEQ ID NO: 3 TaqMan Probe 5' - CCC TGT GAT TCT AAC CAT GGC CTT CTC A - 3'

NM_001147 (Hs) Hs00169867 ml

Ifit-3 XM_220059 (Rn)

SEQ ID NO: 4 Forward Primer 5' - CGG TTG TTA TCA GGC TCA TAGGAT - 3' SEQ ID NO: 5 Reverse Primer 5' - TGT GGGAGG CAA CAC GAT TT - 3' SEQ ID NO: 6 TaqMan Probe 5' - TCA GGA ATA GGCTGC CTG CAC CCC - 3'

Fut-4 NM_022219 (Rn)

SEQ ID NO: 7 Forward Primer 5' - GAC CGA AAC GTG GCT GTC TAT C - 3' SEQ ID NO: 8 Reverse Primer 5' - GTG ATGTGC ACC GCA TAG CT - 3' SEQ ID NO: 9 TaqMan Probe 5' - CCG CTA CTT CCA CTGGCG TCG G- 3'

NM_002033 (Hs)

SEQ H NO: 10 Forward Primer 5' - AAT TGG GCT CCT GCA CAC -3' SEQ ID NO: 11 Reverse Primer 5' - CCA GGT GCT GCG AGT TCT C - 3' SEQ ID NO: 12 TaqMan Probe 5' - TGG CCC GCT ACA AGT TCT ACC TGG CTT - 3'

Plau NM_013085 (Rn) Rn00565261_ml NM_002658 (Hs) Hs00170182_ml Clu NM_012679 (Rn) Rn00562081_ml NM_001831 (Hs) Hs00156548_ml

Etb NM_017333 (Rn) Rn00569139_ml NM_000115 (Hs) Hs00240752_ml

Cyrόl NM_031327 (Rn) Rn00580055_ml NM_001554 (Hs) Hs00155479_ml

GAPDH NM_017008 (Rn) 4308313

GAPDH NM_002046 (Hs) 402869

Immunohistochemistry: Tumor sam pies were fixed immei by submersion in a Zn-Tris fixative solution for immunohistochemistry (MC Zinc Fixative, BD Biosciences-Pharmingen, San Diego, CA) for 24 hr at room temperature (RT, 22°C) followed by submersion in 70% ethanol at RT for an additional 24 hrs. All subsequent steps were performed at RT. Tumor samples were embedded in paraffin (Tissue-Tek VIP Processing/Embedding Medium, Sakura Finetek, Torrance, CA) and cut into 3 μm sections on a Sakura Accu-Cut SRM microtome (Sakura Finetek). Tissue sections were de-waxed in xylene and re-hydrated through graded ethanol washes. Following washes in deionized H20 (dH20) and tris-buffered saline (TBS), a hydrophobic barrier was placed around the tissue section with a hydrophobic pen (Super Pap Pen, EMS #71310).

CD31 staining: CD31 is a validated endothelial cell-specific protein (18-20). Sections were blocked with Protein Block (Biogenex, San Ramon, CA) for 30 min and incubated with anti-CD31 antibodies (mouse anti-rat, Serotec, Raleigh, NC) diluted 1: 1000 in DAKO Antibody Diluent with Blockers

(DakoCytomation, Carpinteria, CA) for two hours. After several brief washes in TBST (TBS + 0.1% Tween-20), sections were incubated with biotinylated anti-Mouse IgG secondary antibody (DakoCytomation Alkaline Phosphatase Kit Link K-0610) for 10-30 min, washed several times with TBST, and incubated with streptavidin coupled to alkaline phosphatase (DAKO Alkaline Phosphatase Kit K-0610) for 10-30 min. Sections were then washed again with several changes of TBST and CD31 bound antibodies were visualized by incubation with Vulcan Fast Red Substrate (Biocare Medical, Walnut Creek, CA) for lOmin (color development monitored microscopically). Sections were then washed in dH20 stored overnight in TBS. Ki67 Staining: Ki67 is a validated nuclear protein expressed only in proliferating cells (21, 22). To facilitate antibody recognition of Ki67, we used a high temperature antigen retrieval strategy. Sections were submerged in Target Retrieval Solution (lx DakoCytomation S1699 diluted with dH20) in a Decloaking Chamber (Biocare Medical, DC2002) and heated to 195°C for 1 min. Sections were cooled with running dH20 into the retrieval solution and then rinsed in TBS. Residual peroxidase activity was blocked by incubating the sections with 3.0% H202 in TBS for 20 min. Sections were washed several times in TBS, then incubated with anti-Ki67 antibodies (rabbit anti-human, Novacastra, Newcastle upon Tyne, UK) diluted 1:2000 in antibody diluent for 2 hrs. Sections were washed with TBST, and then incubated with undiluted biotinylated anti-rabbit IgG (DakoCytomation, Link K-0609) for 10 min. Sections were washed in TBST, and then incubated with streptavidin coupled to horseradish peroxidase (DakoCytomation, K0609) for 10 min. Sections were washed again in TBST, and antibodies bound to Ki67 were visualized by incubation with diaminobenzidine plus substrate (DakoCytomation, DAB+) for 5 min (color development monitored microscopically). Sections were washed in dH20, incubated with DAB Enhance for 20 min RT, and washed again with dH20. Tumor sections were counterstained with filtered Mayer's Hematoxylin (Lillie's Formulation, DakoCytomation) for two min, and then washed with tap H20 until no color remained in the wash water. Sections were then rinsed in dH20, dehydrated with 100% ethanol, cleared with xylenes and mounted with Permount (Fisher Scientific, Hampton, NH).

Immunohistochemical Analysis of Endothelial Cell Proliferation: Sequential brightfield images of CD31/Ki67 double-labeled tumor sections were obtained with a 3-CCD color video camera (Optronics) attached to an Olympus BX-50 microscope equipped with an automated stage (Prior H128, Watertown, MA) and a 40x objective. The number of images per section varied between 1000 and 4000 depending on total tissue area. CD31 staining and Ki67 staining were quantitated for each image using the ImageProPlus software package (Media Cybernetics, Carlsbad, CA). Proliferating endothelial cells were identified as those cells with cytoplasmic CD31 staining and nuclear Ki67 staining. Cells staining positive for CD31 but without nuclear staining for Ki67 were scored as non-proliferating endothelial cells. The percentage of proliferating endothelial cells was calculated by dividing the Ki67 -positive nuclear area associated with endothelial cells by the total nuclear area associated with endothelial cells (both Ki67+ and Ki67-). Endothelial cell proliferation percentages represent the combined analysis results from at least 100 images with CD31 staining per tumor section.

Immunofluorescence Microscopy: Tumor samples were fixed, embedded, sectioned, de-waxed, and re- hydrated as described for immunohistochemistry above. All subsequent steps were performed at room temperature. After a brief rinse in TBS, tissue sections were blocked by incubation with Sniper Blocking Reagent (Biocare Medical) for 5-10 min, rinsed in TBS and incubated with primary antibodies diluted 1: 1000 in DAKO Antibody Diluent for 2 hrs (Antibodies against ANGPT2, CLU, CYR61, and PLAU were from Santa Cruz Biotechnology, Santa Cruz, CA and were raised in goat or rabbit; antibodies against EDNRB were from Calbiochem, San Diego, CA and raised in sheep, antibodies against CD31 were from Serotec and raised in mouse). Sections were then washed with Tris-buffered saline containing 0.2% Tween-20 (TBST, Sigma) and incubated with appropriate secondary antibodies diluted 1:200 (lOug/ml) in DAKO Antibody Diluent with blocking serum for 45 min (Alexa Fluor 488 donkey anti- goat IgG, Alexa Fluor 488 goat anti-rabbit IgG, Alexa Fluor 488 donkey anti-sheep IgG, Molecular Probes, Eugene, OR; Normal donkey and normal goal blocking serum, Sigma). Following additional washes with TBST, sections were counterstained with DAPI (Molecular Probes, 1:2000 dilution of 1 mg/ml stock in MQH20) for 30 min. Sections were then washed in TBST, dehydrated in 100% EtOH, cleared in xylene, and mounted under coverslips with Permount. Images were captured with a Zeiss Axiocam mHR CCD camera connected to a Zeiss Axiovert 135 inverted fluorescence microscope equipped with a 40x objective. For each fluorophore, all images were captured using equal camera integration times.

EXAMPLE 1 IDENTIFICATION OF GENE EXPRESSION CHANGES IN PROLIFERATING MICROVASCULAR ENDOTHELIAL CELLS In order to identify genes that are regulated in proliferating endothelial cells relative to quiescent endothelial cells, we employed an in vitro angiogenesis model in which primary cultured microvascular endothelial cells were driven to proliferate from a quiescent state by incubation with growth factors. Primary human dermal microvascular endothelial cells (HDMVECs) or rat heart microvascular endothelial cells (RHMVECs) between passage 4 and 7 were grown in monolayers in tissue culture dishes, mitogen-starved for 24 hr, then induced to proliferate by exposure to VEGF, bFGF, or ENDOGRO. HDMVECs or RHMVECs were trypsinization following the third passage in culture and seeded in fibronectin-coated, six-well tissue culture plates at a density of 10,000 cells well. Cell growth was arrested for 24h by mitogen withdrawal and then stimulated by the addition of 100 ng/ml VEGF, 100 ng/ml bFGF or 200 μg/ml ENDOGRO. Wells with unstimulated cells and wells containing un-arrested cells were included as controls. At 72 hr following growth factor stimulation, cells were removed from the culture plates by trypsinization and counted on a hemocytometer under bright-field microscopy. To confirm that VEGF, bFGF, and ENDOGRO (a bFGF-rich bovine brain extract, VEC Technologies) were signaling through different growth factor receptors, we exposed cells to VEGF, bFGF, or ENDOGRO in the presence of Compound A, which is small molecule KDR kinase inhibitor that is 100-fold less active against FGFR1 and FGFR2 (Table 1) (12-15).

A comparison of the gene expression pattern of mitogen-starved, quiescent HDMVECs and RHMVECs to the expression pattern of actively dividing endothelial cells, indicates significant

(p-value <0.01)gene expression changes, that are characteristic of proliferating vascular endothelial cells. Briefly, endothelial cell cultures were grown in culture and mitogen deprived for 24 hr as described above. Following a 24 hr stimulation with growth factor, culture media was aspirated quickly and the cells lysed in an RNA stabilizing buffer. Matched control plates that received no supplemental stimulatory growth factor were present for each stimulation condition and RNAs isolated from them served as the reference to which the RNAs from the stimulated cells was compared. Results: Although growth media supplemented with 10% FBS was not sufficient to drive endothelial cell proliferation, 10% FBS plus additional growth factor induced rapid endothelial cell proliferation. The data provided in Figure 1 demonstrates that exposure of HDMVEC (Figure 1A) and RHMVEC (Figure IB) to Compound A selectively inhibits in vitro microvascular endothelial cell proliferation induced by VEGF as determined by viable cell counting with a hemocytometer. The gene expression profile illustrated in Figure 2 graphically illustrates a gene expression signature that is characteristic of proliferating HDMVEC (panel A) and RHMVEC (panel B) cultures. Color intensity represents the degree of regulation, not mRNA copy number. Table 3 provides a list of genes comprising the HDMVEC Proliferative Signature identified in the expression profiles illustrated in Figure 2. Table 4 provides a list of genes comprising the RHMVEC Proliferative Signature identified in the expression profiles illustrated in Figure 2. Using the information provided in Tables 3 and 4 it is well within the abilities of a skilled artisan to design and validate a gene expression-based assay that is suitable for evaluating the proliferation of vascular endothelial cells in either in vitro or in vivo screening assay format. EXAMPLE 2 SUPPRESSION OF VEGF-INDUCED GENE EXPRESSION SIGNATURES IN PRIMARY ENDOTHELIAL CELLS BY A KDR KINASE INHIBITOR To determine if the growth factor-induced proliferation signatures identified in Example lare sensitive to KDR kinase inhibitors, we stimulated HDMVECs or RHMVECs with VEGF or bFGF for 24 hrs in the presence of 100 nM Compound B. VEGF binds to and activates the fms-like tyrosine kinase (FLT1) and KDR (23, 24). Both FLTl and KDR are inhibited by Compound B (Table 1). bFGF binds to FGFR1 and FGFR2, but not FLTl or KDR. Both FGFR1 and FGFR2 are relatively insensitive to Compound B (see Table 1). Briefly, EC monolayers were maintained in complete MCDB-131 media until reaching -75% confluence, then induced into a quiescent state by mitogen starvation for 24 hr. Cells were then stimulated to proliferate with 100 ng/ml VEGF for 24 hr in the presence or absence of Compound B. RNA populations isolated from cells exposed to VEGF or VEGF + Compound B were compared to matched control RNAs isolated from quiescent cells exposed to neither VEGF nor Compound B. Results: The data provided in Figure 3 demonstrate that the HDMVEC VEGF-induced gene expression signature was effectively suppressed by Compound B while the bFGF-induced signature was unaffected. Parallel experiments were performed with RHMVECs (data not shown). Each point in the plots represents a gene sequence present on the DNA oligonucleotide microarray and is plotted according to the ratio of the two mRNA levels (experimental sample intensity ontrol sample intensity, vertical-axis) and the total mRNA quantity (experimental sample intensity + control sample intensity, horizontal-axis) for that gene.

EXAMPLE 3 IDENTIFICATION OF AN ENDOTHELIAL CELL-SPECIFIC PROLIFERATION SIGNATURE The experimental data provided above identifies gene expression profiles, or expression signatures specific for proliferating endothelial cells. However, the majority of genes regulated during endothelial cell proliferation will also be expressed in other types of proliferating cells (genes that regulate cell cycle and metabolic processes, for example). Tumors contain a complex mixture of cell types, where approximately 1 in 2000 cells (0.05%) are proliferating endothelial cells (Joanne Antanavage, Rosemary McFall, and Ken Thomas, personal communications). Therefore, in attempting to develop a pharmacodynamic assay that specifically measure tumor endothelial cell proliferation, it was acknowledged that there was a need to identify the endothelial cell-specific portion of the HDMVEC and RHMVEC proliferation signatures. Candidate endothelial cell-specific genes were defined as genes characterized by regulated expression during an in vitro proliferative response to mitogens, but expressed at relatively low levels in non-endothelial cells. We used microarray intensity data, which corresponds to the number of labeled cRNAs bound to each array feature and is proportional to mRNA copy number, from previous expression profiling studies and compared it with the microarray intensity data from our HDMVEC proliferation experiments. Existing intensity data from a panel of actively growing tumor-derived cell lines (MOLT-4, HL-60, Raji, SW480, Daudi, G361, A549, K562, MCF7) was used to remove from consideration those genes with EC:tumor microarray intensity ratios less than 3: 1. 702 HDMVEC sequences were selected as endothelial cell-specific in this manner (see, Table 3). We identified many known endothelial cell-specific genes by this method (i.e. ESM-1KDR, FLT-1) as well as numerous novel sequences. In parallel, we obtained a measure of endothelial cell specificity for genes regulated in proliferating RHMVECs by comparing microarray intensity data from the RHMVEC experiments to data from gene expression profiling experiments with rat C6 glioma cells actively growing in culture. We identified 493 genes with RHMVEC:C6 intensity ratios greater than 3:1 (see, Table 4).

EXAMPLE 4 ORALLY-DOSED KDR KINASE INHIBΠΌRS INDUCE SIGNIFICANT GENE EXPRESSION CHANGES IN SYNGENEIC ANIMAL TUMORS Two syngeneic rat tumor models (i.e., C6 glioma flank tumor model and MatBIII Breast Cancer Metastasis Model), were used to assess the effect of the small molecule KDR kinase inhibitors, Compound A and Compound B, on thE genes identified as endothelial cell-specific which were regulated during in vitro endothelial cell proliferation. Tumor studies were performed as described above in

Materials and Methods. The tumor models use C6 glioma and MatBIII mammary carcinoma cell lines, both derived from Fischer 344 rats. These cell lines each secrete VEGF and form highly vascularized tumors that are sensitive to KDR kinase inhibitors. Glioma Flank Tumor Model: C6 cells were injected subcutaneously into the right flank of rats and allowed to form tumors for seven days. At that time, once-daily oral dosing with Compound A,

Compound B, or vehicle commenced and continued for a total of 1, 2 or 3 days (Figure 4, Panel A "C6 Profiling Study). Figure 4 illustrates the growth kinetics of established rat tumors following exposure to a KDR kinase inhibitor. Tumor volumes were determined by caliper measurements. Tumors were calipered in two dimensions (length and width) and tumor volume was calculated according to the formula (length) x (width) x (^lΛ width). Genome-wide gene expression in tumors isolated from compound-treated animals was compared to gene expression from tumors isolated from vehicle-treated animals. In the data provided in Figure 5 each row represents a distinct tumor from an individual animal. Each column represents a gene. Points corresponding to genes which are regulated (upregulated or downregulated) are indicated by various shades of gray. The data presented in Panel A of Figure 5 identifies genes from rat C6 flank tumors that are regulated following 24, 48, or 72 hrs of systemic exposure to the KDR kinase inhibitor Compound B. The data presented in Panel B of Figure 5 identifies genes from rat C6 flank tumors regulated following 24, 48, or 72 hrs of systemic exposure to the KDR kinase inhibitor Compound A. We observed that both Compound A (Figure 5, Panel B) and Compound B (Figure 5, Panel A) induced robust gene expression changes in C6 tumor gene expression, particularly after 48 hrs or more of compound exposure (p-value < 0.05 for individual sequences).

MatBIII Breast Cancer Metastasis Model: MatBIII mammary adenocarcinoma cells were injected into a mammary fat pad of female rats. After allowing tumors to establish for seven days once-daily oral dosing of Compound A began and continued for a total of 5 days (Figure 4B). The data presented in Panel C of Figure 5 identifies genes from rat MatBIII mammary tumors regulated following 100 hrs of systemic exposure to the KDR kinase inhibitor Compound A. When the pattern of tumor gene expression from compound-treated rats was compared to vehicle-treated controls, we again found significant differences (Figure 5, Panel C, p-value < 0.05 for individual sequences). While there was overlap in the gene expression changes induced by the KDR kinase inhibition between the three studies, the majority of gene expression changes were study-specific (data not shown).

EXAMPLE 5 IDENTIFICATION OF GENE EXPRESSION BIOMARKERS OF ENDOTHELIAL CELL PROLIFERATION In each of the three animal studies we performed, we found that we could detect KDR kinase inhibitor-induced changes in expression for a fraction of those genes we had identified as specific to proliferating RHMVECs in culture. Figure 6 provides Venn diagrams which summarize the degree of overlap between the set of genes identified in the various assays formats disclosed herein. More specifically, Figure 6A summarizes the degree of overlap between the tumor gene expression responses to KDR kinase inhibitors in C6 flank tumors and MatBIII mammary tumors. Figure 6B indicates the degree of overlap between the sets of endothelial cell-specific genes determined to be regulated both in vitro by mitogens and in tumor tissue by KDR kinase inhibitors. All genes/sequences represented in Panel B were observed to be regulated in vivo by KDR kinase inhibitors in a manner opposite that observed in vitro following exposure to mitogens. Most interestingly, we found in each study that some of those genes were regulated in a manner consistent with suppression of endothelial cell proliferation. In effect, these genes were oppositely regulated in our in vitro proliferation experiments as compared to our in vivo tumor studies. In both cases the genes were highly expressed when endothelial cells were proliferating and expressed at low levels under non-proliferating conditions. Thus, we identified endothelial cell-specific genes that were "oppositely regulated" in each of the three animal tumor studies and identified genes that were regulated as such in multiple studies (Figure 6B, and Tables 5 and 6). Tables 5 and 6 provide a list of genes which were observed to be regulated by Compound A. Table 5 utilizes the data obtained in the C6 Flank Tumor and MatBill Breast Cancer Metatesis Models to define a Compound induced endothelial cell-specific expression signatures. The table provides the GeneBank Accession number, the gene symbol and summarizes the compound-induced fold change in gene expression that was observed. It is contemplated that the expression signatures provided in Table 5 will find utility in evaluating the in vivo efficacy of anti-angiogenic agents in general and KDR kinase inhibitors in particular. Table 6 provides a summary of the changes (i.e., suppressed expression) observed for individual biomarkers comprising the EC- specific proliferation signatures disclosed herein in response to in vivo KDR inhibitor administration. By imposing a requirement that genes to be considered as biomarkers should have compound- induced in vivo expression changes of at least 1.6 fold, we identified seven genes that were "oppositely regulated" in both Compound A and Compound B studies and two genes that were "oppositely regulated" in all three studies. Based on the data provided in the instant disclosure, the seven genes (Angpt2, Ednrb, Plau, Clu, Fut4, Ifit3, and Cyrόl) identified by both Compound A animal studies were identified as potential biomarkers for tumor endothelial cell proliferation. These genes are identified and described in Table 2.

Table 2

Significantly, each of these genes has been reported to be involved or implicated in endothelial cell function. Table. 3

HDMVEC Proliferation Signature GenBank Accession EC:MCF7 Intensity Growth Number Gene Symbol (Expression) Ratio Fold Change Factor AA013218 FLJ 14079 6.81 1.33 ENDOGRO AA029441 8.22 -1.17 VEGF AA046478 NT5 4.48 1.35 ENDOGRO AA053711 RBM8B 86.86 -1.38 ENDOGRO AA053806 LOC64148 35.28 -1.45 ENDOGRO AA102600 12.51 -1.51 bFGF AA148511 FLJ22724 71.39 -1.18 bFGF AA156672 28.11 1.51 ENDOGRO AA166703 10.11 1.37 VEGF AA173992 4.15 1.42 ENDOGRO AA224245 14.16 -1.22 ENDOGRO AA404374 FLJ21935 21.27 1.40 VEGF AA449120 28.44 2.02 VEGF AA464846 33.20 -1.34 VEGF AA489383 BMP2 5.09 1.66 VEGF AA522536 9.14 -1.55 bFGF AA534774 3.09 -1.38 ENDOGRO AA541787 12.99 -2.77 bFGF AA584310 28.05 -1.36 ENDOGRO AA617813 4.03 -1.35 VEGF AA621714 8.79 -1.38 VEGF AA628517 10.91 1.58 ENDOGRO

AA632012 12.16 -1.37 VEGF

AA707332 6.09 1.27 bFGF

AA740709 8.73 -1.72 ENDOGRO

AA758545 MMP2 93.44 -1.41 ENDOGRO

AA811265 10.22 -1.30 bFGF

AA815048 FLJ 12649 4.37 -1.79 bFGF

AA858297 152.47 1.61 bFGF

AA868377 FLJ22233 3.66 1.45 ENDOGRO

AA868615 3.33 -2.01 bFGF

AA873008 8.82 -2.04 bFGF

AA897516 8.35 1.62 ENDOGRO

AA903334 29.77 1.57 ENDOGRO

AA923461 12.34 -1.30 ENDOGRO

AA932206 11.75 1.94 VEGF

AA946945 14.82 2.11 ENDOGRO

AB007954 KIAA0485 3.69 -1.44 VEGFD

AB011099 KIAA0527 104.01 -1.30 ENDOGRO

AB014538 KIAA0638 6.54 1.31 VEGF

AB014567 KIAA0667 3.53 -1.29 ENDOGRO

AB014604 KIAA0704 23.34 1.33 ENDOGRO

AB018301 KIAA0758 243.54 1.90 VEGF

AB018333 KIAA0790 3.12 1.57 ENDOGRO

AB018339 SYNE-1 B 9.29 -1.44 bFGF

AB028019 LATS2 5.74 -1.43 ENDOGRO

AB028976 KIAA1053 11.78 -1.69 bFGF

AB028981 KIAA1058 6.73 1.24 VEGF

AB032971 KIAA1145 13.30 2.04 bFGF

AB033006 NDRG4 23.14 -1.79 VEGF

AB033035 KIAA1209 12.08 1.68 VEGF

AB033093 DKFZP727C091 4.05 -1.59 VEGFE

AB033100 KIAA1274 32.44 1.41 ENDOGRO

AB033101 KIAA1275 5.36 -1.86 bFGF

AB037722 KIAA1301 4.32 1.80 VEGF

AB037726 KIAA1305 5.96 -1.48 ENDOGRO

AB037751 KIAA1330 8.51 -1.42 ENDOGRO

AB037784 KIAA1363 3.50 1.65 ENDOGRO

AB037820 KIAA1399 289.61 -1.44 ENDOGRO

AB037821 PCDH10 8.07 -1.72 ENDOGRO

AB037857 KIAA1436 3.61 -1.16 ENDOGRO

AF007150 18.82 1.66 ENDOGRO

AF035121 KDR 70.01 1.39 bFGF

AF035306 12.18 -1.34 bFGF

AF035318 47.64 -1.68 bFGF

AF041037 SPRY1 10.05 1.90 VEGF

AF052169 83.10 -1.37 VEGF

AF061034 FIP2 8.51 -1.62 ENDOGRO AF062341 CTNND1 5.61 -1.12 ENDOGRO

AF070569 4.62 -1.41 ENDOGRO

AF070641 8.76 4.19 ENDOGRO

AF091434 PDGFC 67.66 -1.37 ENDOGRO

AF095719 CPA4 19.14 -1.56 ENDOGRO

AF101051 CLDN1 3.73 -2.39 ENDOGRO

AF114264 unknown 35.87 -2.74 ENDOGRO

AF119663 LOC55970 6.47 -1.26 ENDOGRO

AF131762 4.22 1.34 ENDOGRO

AF131817 13.30 -1.49 VEGF

AF134404 FADS3 3.00 -1.58 ENDOGRO

AF181265 EHD4 5.55 1.09 ENDOGRO

AF 186780 KIAA0959 14.14 1.53 VEGF

AF218942 FMN2 6.56 -1.75 bFGF

AF234532 MYO10 6.56 1.26 ENDOGRO

AF238083 SPHK1 4.48 1.37 ENDOGRO

AI005420 4.74 1.48 VEGFE

AI031794 7.72 -1.99 bFGF

AI039171 3.98 -1.33 ENDOGRO

AI051390 3.00 -1.32 ENDOGRO

AI05251 1 12.16 1.52 VEGF

AI073464 PLG 79.09 -1.25 ENDOGRO

AI073669 56.60 1.82 ENDOGRO

AI079944 5.90 1.44 VEGF

AI085787 29.37 3.06 VEGF

AI088104 8.74 -1.40 VEGF

AH 25204 16.83 -2.15 bFGF

AH 25425 7.25 1.68 ENDOGRO

AM 39987 FLJ23056 32.76 -1.69 bFGF

AH 41554 2709.99 -1.59 VEGF

AI141700 LOC63875 6.99 1.30 VEGFE

AM 68436 7.67 -1.40 bFGF

AI188161 109.32 -2.23 bFGF

AI188513 3.42 1.27 ENDOGRO

AI200874 23.78 -1.45 ENDOGRO

AI203531 ART4 3.56 -2.05 ENDOGRO

AI206317 34.47 -1.39 ENDOGRO

AI208788 5.00 -2.02 bFGF

AI218538 20.83 -1.81 ENDOGRO

AI223799 3.29 -1.15 ENDOGRO

AI224533 DKFZp762L0311 3.19 1.70 ENDOGRO

AI275691 13.51 1.18 ENDOGRO

AI277316 4.21 -1.98 bFGF

AI291779 45.84 -1.44 VEGF

AI301312 6.62 -1.97 ENDOGRO

AI338631 11.26 -1.33 VEGFE

AI343000 8.60 -1.36 ENDOGRO AI351898 14.00 1.13 ENDOGRO

AI357650 AD026 4.02 1.87 VEGF

AI375677 8.94 1.47 VEGF

AI376749 SDC2 5.18 -1.89 ENDOGRO

AI378647 6.03 -1.84 ENDOGRO

AI392987 HOXB6 4.40 1.44 ENDOGRO

AI418293 54.98 -1.34 VEGFE

AI418530 4.00 1.37 PIGF

AI418596 10.33 -1.62 bFGF

AI420933 54.00 -2.63 VEGF

AI433789 OS4 3.70 -1.44 ENDOGRO

AI433914 4.47 1.32 VEGF

AI439093 8.40 1.27 ENDOGRO

AI453557 24.20 -1.50 ENDOGRO

AI478770 MYH9 4.94 -1.39 ENDOGRO

AI479854 FLJ20980 46.10 -1.24 VEGF

AI498132 3.84 1.33 ENDOGRO

AI523391 3.67 -1.41 bFGF

AI539275 3.09 -1.22 VEGF

AI569689 3.53 -2.60 ENDOGRO

AI608902 17.83 -1.64 ENDOGRO

AI610727 4.23 -1.21 ENDOGRO

AI633826 5.30 3.89 VEGF

AI633890 48.69 -1.40 VEGF

AI635050 FLJ22252 327.52 -1.79 ENDOGRO

AI652289 31.67 1.32 ENDOGRO

AI652898 30.60 2.98 bFGF

AI652991 13.27 -1.76 ENDOGRO

AI654230 21.37 1.31 ENDOGRO

AI655345 9.29 1.47 ENDOGRO

AI659533 ARGBP2 108.45 -2.15 ENDOGRO

AI659800 4.82 -1.45 ENDOGRO

AI672407 HOXB8 3.72 2.26 bFGF

AI674404 7.93 1.21 bFGF

AI681538 FLJ23403 40.51 -1.48 VEGF

AI681805 15.66 -1.42 ENDOGRO

AI682468 3.07 -1.43 bFGF

AI683621 8.18 -1.77 bFGF

AI684489 CSF2RB 7.89 -1.59 ENDOGRO

AI684705 9.25 -1.29 VEGFE

AI688546 ARHGEF1 35.74 1.25 VEGFE

AI693178 22.73 -1.48 ENDOGRO

AI733194 5.60 -1.26 ENDOGRO

AI733570 FLJ20898 566.31 2.21 VEGF

AI739507 DAB2 1074.51 -1.73 ENDOGRO

AI741128 53.39 2.07 VEGF

AI741880 131.82 1.49 VEGF AI742043 5.43 1.37 ENDOGRO

AI742210 4.99 1.28 ENDOGRO

AI742878 6.05 -1.77 VEGF

AI742936 8.15 1.23 ENDOGRO

AI743880 7.62 -1.36 ENDOGRO

AI743942 6.90 1.84 ENDOGRO

AI744591 31.91 1.34 ENDOGRO

AI745230 7.26 -1.52 VEGF

AI745614 27.20 -1.44 ENDOGRO

AI754423 83.30 -1.58 ENDOGRO

AI760613 6.16 -1.89 VEGF

AI765437 15.10 -1.55 ENDOGRO

AI767993 5.35 1.46 VEGF

AI769801 ALB 4.74 1.87 VEGF

AI803656 5.73 -1.27 ENDOGRO

AI806221 81.13 1.75 VEGF

AI806313 FLJ23091 34.79 -1.15 ENDOGRO

AI807266 6.54 1.46 ENDOGRO

AI810042 FLJ21841 16.31 1.44 ENDOGRO

AI822137 5583.85 -1.44 ENDOGRO

AI823801 SE57-1 5.65 1.35 ENDOGRO

AI825936 KIAA1350 12.43 1.42 ENDOGRO

AI827455 45.22 1.46 VEGF

AI828007 9.30 1.37 ENDOGRO

AI857683 3.74 1.27 VEGF

AI861824 SLC1A1 60.49 1.41 ENDOGRO

AI862120 6.44 -1.33 bFGF

AI887362 3.58 1.48 ENDOGRO

AI889160 5.58 -1.51 ENDOGRO

AI912975 71.62 -1.52 ENDOGRO

AI913402 75.58 -1.34 VEGF

AI924550 4.97 1.54 ENDOGRO

AI926697 6.91 1.67 ENDOGRO

AI927454 8.47 -1.14 ENDOGRO

AI927919 30.58 -1.27 ENDOGRO

AI928427 24.79 1.50 bFGF

AI936034 20.65 -1.58 ENDOGRO

AI949647 18.22 3.10 VEGF

AI949827 10.53 -1.63 bFGF

AI950109 FLJ 12604 37.36 1.35 ENDOGRO

AI968085 WNT5A 3.31 -1.63 ENDOGRO

AI972337 6.36 1.65 ENDOGRO

AI979166 3.20 2.29 ENDOGRO

AI982765 10.21 -1.29 bFGF

AI992251 7.09 -1.36 bFGF

AK000401 4.30 -1.30 ENDOGRO

AK000711 TAX1 BP1 12.69 -1.40 ENDOGRO AK000776 110.22 -1.47 ENDOGRO

AK000884 LRRFIP1 17.73 1.26 VEGF

AK000959 FLJ 10097 3.63 -1.19 ENDOGRO

AK001020 22.23 -1.37 bFGF

AK001362 3.02 -1.45 bFGF

AK001438 FBXL2 8.83 -1.33 VEGF

AK001560 LOC57863 16.74 -1.45 ENDOGRO

AK001630 126.78 1.38 VEGF

AK001872 PDL2 104.85 -1.24 bFGF

AK001903 11.23 -2.25 bFGF

AK001942 25.29 1.33 ENDOGRO

AK002195 6.46 1.31 VEGF

AL035306 STX12 4.35 -1.36 ENDOGRO

AL040051 6.17 -1.76 ENDOGRO

AL043980 PELI1 4.30 -1.28 ENDOGRO

AL049257 69.89 -1.59 ENDOGRO

AL049279 38.68 1.35 VEGF

AL049367 16.98 -1.38 VEGFE

AL049370 4.60 -1.99 ENDOGRO

AL049969 7.15 -1.70 ENDOGRO

AL049998 3.45 -1.17 ENDOGRO

AL050090 DKFZP586F1018 27.49 -1.25 ENDOGRO

AL050166 4.34 -1.37 ENDOGRO

AL110152 10.87 -1.20 ENDOGRO

AL110164 4.96 -1.52 ENDOGRO

AL110171 8.99 -1.30 VEGF

AL110202 4.31 -1.21 VEGF

AL110207 82.49 1.32 ENDOGRO

AL110255 4.30 -1.42 ENDOGRO

AL110280 7.38 -2.19 ENDOGRO

AL117427 4.11 -1.51 VEGF

AL117468 DKFZP586N1922 9.05 -1.51 ENDOGRO

AL117523 KIAA1053 15.24 -1.62 bFGF

AL117525 AKT3 32.46 -1.38 bFGF

AL117604 DLC1 15.23 -1.60 ENDOGRO

AL117615 DKFZP564D0764 257.68 -1.31 ENDOGRO

AL117617 4.04 1.32 bFGF

AL117664 DKFZP586L2024 117.73 -1.61 bFGF

AL122098 FLJ11937 3.98 -1.28 ENDOGRO

AL133118 30.13 1.63 VEGF

AL133596 12.02 -1.47 ENDOGRO

AL133605 PELI2 11.52 -1.71 bFGF

AL133640 DKFZp586C1021 4.67 -1.70 bFGF

AL133706 25.69 -1.39 VEGF

AL137540 NTN4 16.43 -1.86 ENDOGRO

AL137663 4.31 -1.46 bFGF

AL157431 DKFZp762A227 7.70 1.53 ENDOGRO AL157475 DKFZp761 G151 5.36 1.64 ENDOGRO AL157482 FLJ23399 7.50 -1.57 ENDOGRO AL157488 18.63 -1.45 VEGFE AL157502 MSTP032 5.99 1.36 VEGF AL359062 2726.41 -1.58 ENDOGRO AL572015 4.16 -1.81 bFGF AW015537 3.74 1.14 ENDOGRO AW015898 11.49 -1.28 VEGF AW023373 5.60 2.35 VEGF AW024527 3.55 1.44 ENDOGRO AW043571 FLJ20505 46.96 -1.63 ENDOGRO AW069166 CALD1 275.85 -1.68 ENDOGRO AW081929 KIAA1571 3.68 1.20 PIGF AW102613 3.22 1.66 VEGF AW 117242 32.57 1.42 VEGF AW 119059 4.57 -1.60 bFGF AW131552 8.49 2.99 VEGF AW 138207 FLJ22969 6.39 4.22 bFGF AW 139097 95.87 -1.21 ENDOGRO AW 139393 FTH1 37.66 1.63 ENDOGRO AW 139567 32.44 -1.70 ENDOGRO AW 139834 7.44 -1.43 VEGF AW151025 ARHE 7.93 -1.92 ENDOGRO AW 173150 4.05 1.55 ENDOGRO AW183161 42.71 -1.27 ENDOGRO AW 189467 3.79 -1.40 ENDOGRO

AW 190823 LOC58514 4.54 1.57 ENDOGRO

AW 195720 20.83 1.41 VEGF

AW237511 181.16 -2.84 VEGF

AW242009 4.21 1.42 ENDOGRO

AW243046 14.10 1.37 ENDOGRO

AW269515 FLJ20481 13.01 -1.61 ENDOGRO

AW269818 FLJ23144 7.49 -1.40 VEGF

AW271825 45.27 1.33 VEGF

AW274396 3.22 -1.11 ENDOGRO

AW274929 12.68 2.37 ENDOGRO

AW276078 24.62 1.61 bFGF

AW291331 16.15 -1.68 bFGF

AW291988 556.06 1.26 VEGF

AW292303 3.41 1.40 ENDOGRO

AW292755 8.16 1.28 VEGF

AW293366 3.66 -1.32 ENDOGRO

AW293770 1515.01 -1.50 ENDOGRO

AW294011 13.79 -1.41 ENDOGRO

AW294653 MOX2 20.80 1.68 VEGF

AW995919 PRG2 5.74 -1.26 ENDOGRO

BC005133 45.68 1.25 bFGF BM263824 7.39 1.48 ENDOGRO

D38522 KIAA0080 31.39 -1.47 ENDOGRO

D43636 KIAA0096 9.12 1.77 bFGF

D50406 RECK 60.03 -1.30 ENDOGRO

G26403 LOC64148 15.13 -1.30 ENDOGRO

H05089 FLJ 14033 1 1.27 -1.25 ENDOGRO

H09749 8.90 -1.78 bFGF

H11724 8.28 -1.21 ENDOGRO

H 16409 28.49 -1.22 ENDOGRO

H56091 5.97 -1.81 bFGF

H80726 5.53 1.57 VEGF

M 12758 HLA-A 4.93 -1.34 bFGF

M26383 IL8 91.08 1.30 VEGFE

M60721 HLX1 49.44 5.23 VEGFE

M68874 PLA2G4A 176.88 -1.18 ENDOGRO

M80783 TNFAIP1 3.66 -1.41 ENDOGRO

M90657 TM4SF1 17.14 1.26 ENDOGRO

M93718 N0S3 34.51 1.59 ENDOGRO

N36156 31.71 1.63 VEGF

N92500 4.02 1.16 bFGF

N92541 FLJ23462 7.63 -1.46 ENDOGRO

N95435 16.21 -1.73 bFGF

N99256 FLJ 11808 4.58 -1.29 VEGF

NM_000019 ACAT1 3.04 -1.25 PIGF

NM_000024 ADRB2 27.96 1.94 ENDOGRO

NM_000089 C0L1A2 16.78 -2.59 bFGF

NM_000093 C0L5A1 4.58 -1.39 ENDOGRO

NM_000109 DMD 3.44 -1.73 VEGF

NM_000115 EDNRB 5.52 1.43 ENDOGRO

NM_000124 ERCC6 5.51 -1.40 VEGF

NM_000138 FBN1 38.80 -1.48 ENDOGRO

NM_000143 FH 3.13 -1.53 ENDOGRO

NM_000165 GJA1 636.59 -1.50 ENDOGRO

NM_000170 GLDC 3.21 1.60 ENDOGRO

NM_000201 ICAM1 5.70 -2.41 bFGF

NM_000204 IF 3.96 1.42 ENDOGRO

NM_000210 ITGA6 15.87 2.14 VEGF

NM_000237 LPL 9.12 -1.95 bFGF

NM_000240 MAOA 5.87 -2.02 ENDOGRO

NM_000304 PMP22 13.23 1.22 ENDOGRO

NM_000361 THBD 5.73 1.56 bFGF

NM_000393 COL5A2 20.35 -1.51 ENDOGRO

NM_000416 IFNGR1 4.03 -1.30 ENDOGRO

NM_000428 LTBP2 90.66 -1.42 VEGF

NM_000436 OXCT 3.56 -1.46 ENDOGRO

NM_000439 PCSK1 76.58 1.35 ENDOGRO

NM_000441 SLC26A4 5.08 1.89 VEGF NM_000450 SELE 12.46 -3.51 bFGF

NM_000552 VWF 359.59 -1.26 bFGF

NM_000584 IL8 465.02 1.30 VEGFE

NM_000596 IGFBP1 17.07 1.50 bFGF

NM_000627 LTBP1 6.90 -1.14 ENDOGRO

NM_000689 ALDH1A1 133.54 -1.34 PIGF

NM_000784 CYP27A1 5.82 -1.35 ENDOGRO

NM_000793 DI02 5.13 -1.87 VEGF

NM_000820 GAS6 22.28 -1.37 bFGF

NM_000824 GLRB 27.89 -1.41 ENDOGRO

NM_000885 ITGA4 20.27 -2.03 bFGF

NM_000902 MME 7.99 1.44 bFGF

NM_000919 PAM 3.37 -1.29 ENDOGRO

NM_000929 PLA2G5 3.66 -1.78 bFGF

NM_000930 PLAT 15.88 1.87 bFGF

NM_000931 PLAT 17.20 1.90 bFGF

NM_000950 PRRG1 9.96 -1.48 ENDOGRO

NM_000958 PTGER4 4.64 1.54 ENDOGRO

NM_000963 PTGS2 233.39 -2.13 ENDOGRO

NM_001066 TNFRSF1 B 23.17 -1.38 VEGF

NM_001078 VCAM1 61.45 -7.79 ENDOGRO

NM_001122 ADFP 17.09 -1.32 VEGF

NM_001147 ANGPT2 9.05 3.98 VEGF

NM_001159 A0X1 5.24 1.68 ENDOGRO

NM_001165 BIRC3 3.66 -2.59 bFGF

NM_001166 BIRC2 4.58 -1.30 ENDOGRO

NM_001202 BMP4 14.66 -1.92 ENDOGRO

NMJD01223 CASP1 23.83 -1.37 bFGF

NM_001290 LDB2 63.23 1.33 VEGF

NM_001336 CTSZ 41.31 1.63 VEGFE

NM_001343 DAB2 381.87 -1.77 ENDOGRO

NM_001399 ED1 3.60 1.40 ENDOGRO

NM_001430 EPAS1 5.28 -1.25 ENDOGRO

NM_001442 FABP4 7.69 2.05 VEGF

NM_001444 FABP5 9.91 1.50 ENDOGRO

NM_001450 FHL2 4.24 -1.41 VEGF

NM_001457 FLNB 3.39 -1.46 bFGF

NM_001613 ACTA2 11.65 -1.39 VEGF

NM_001627 ALCAM 7.03 -1.98 ENDOGRO

NM_001674 ATF3 4.18 -3.56 ENDOGRO

N _001709 BDNF 357.01 -2.53 bFGF

NM_001711 BGN 3.05 -1.31 ENDOGRO

NM_001718 BMP6 66.96 -1.33 ENDOGRO

NM_001721 BMX 144.68 1.37 ENDOGRO

NM_001724 BPGM 13.36 -1.40 PIGF

NM_001773 CD34 310.68 -1.28 ENDOGRO

NM_001797 CDH11 17.51 1.32 bFGF NM_001839 CNN3 243.45 -1.39 ENDOGRO

NM_001845 COL4A1 20.78 -1.32 ENDOGRO

NM_001850 COL8A1 74.23 -1.60 ENDOGRO

NM_001885 CRYAB 5.53 -1.53 ENDOGRO

NM_001924 GADD45A 3.89 -1.46 bFGF

NM_001945 DTR 38.30 -1.94 bFGF

NM_001946 DUSP6 32.18 2.13 ENDOGRO

NM_001955 EDN1 52.88 -1.74 ENDOGRO

NM_001992 F2R 83.85 -1.62 ENDOGRO

NM_002006 FGF2 34.80 -1.55 ENDOGRO

NM_002019 FLT1 88.72 2.54 VEGF

NM_002053 GBP1 6.07 -1.94 ENDOGRO

NM_002131 HMGIY 5.99 1.70 ENDOGRO

NM_002133 HMOX1 3.75 1.38 ENDOGRO

NM_002153 HSD17B2 32.56 2.49 bFGF

NM_002165 ID1 6.91 1.60 bFGF

NM_002185 IL7R 38.68 -1.31 ENDOGRO

NM_002189 IL15RA 8.70 1.53 ENDOGRO

NM_002192 INHBA 8.93 -2.11 bFGF

NM_002210 ITGAV 4.70 -2.03 ENDOGRO

NM_002223 ITPR2 5.74 -1.46 ENDOGRO

NM_002313 ABLIM 5.35 -1.46 ENDOGRO

NM_002341 LTB 5.48 -1.17 bFGF

NM_002350 LYN 6.10 1.37 VEGF

NM_002397 MEF2C 3.31 2.13 VEGF

NM_002402 MEST 3.13 -1.61 VEGF

NM_002421 MMP1 18.54 2.29 VEGF

NM_002425 MMP10 12.05 1.63 VEGF

NM_002438 MRC1 34.54 -1.35 ENDOGRO

NM_002451 MTAP 40.27 1.48 bFGF

NM_002475 MYL1 3.19 -1.13 ENDOGRO

NM_002526 NT5 5.84 1.73 VEGF

NM_002575 SERPINB2 47.87 3.04 ENDOGRO

NM_002595 PCTK2 4.39 1.28 ENDOGRO

NM_002599 PDE2A 10.28 1.61 ENDOGRO

NM_002600 PDE4B 12.97 1.60 ENDOGRO

NM_002608 PDGFB 11.22 -1.47 bFGF

NM_002659 PLAUR 6.03 2.16 bFGF

NM_002662 PLD1 11.32 -1.42 ENDOGRO

NM_002763 PR0X1 6.17 1.69 ENDOGRO

NM_002837 PTPRB 102.95 -1.47 ENDOGRO

NM_002845 PTPRM 36.50 -1.27 bFGF

NM_002923 RGS2 12.21 2.02 ENDOGRO

NM_002933 RNASE1 25.36 -1.22 ENDOGRO

NM_002937 RNASE4 28.30 -1.49 ENDOGRO

NM_002982 SCYA2 10.53 -3.48 ENDOGRO

NM_002993 SCYB6 5.70 -2.66 bFGF NM_002996 SCYD1 14.41 -5.15 ENDOGRO

NM_003003 SEC14L1 5.78 -1.13 ENDOGRO

NM_003082 SNAPC1 4.43 -1.60 VEGF

NM_ 003113 SP100 4.98 -1.58 ENDOGRO

NM_003115 UAP1 9.18 -1.37 VEGF

NM_003186 TAGLN 36.78 -1.67 VEGF

NM_003199 TCF4 181.64 1.22 VEGFE

NM_003238 TGFB2 9.39 -2.64 bFGF

NM_003246 THBS1 78.99 -1.77 bFGF

NM_003266 TLR4 18.63 -1.44 ENDOGRO

NM_003289 TPM2 7.89 -1.32 ENDOGRO

NM_003330 TXNRD1 5.26 -1.74 bFGF

NMJD03459 SLC30A3 3.97 -1.73 bFGF

NM_003483 HMGIC 55.41 3.05 bFGF

NMJD03494 DYSF 84.07 1.48 VEGF

NM_003603 ARGBP2 11.04 -1.90 ENDOGRO

NM_003607 PK428 3.85 -1.24 ENDOGRO

NM_003633 ENC1 3.48 -1.89 VEGF

NM_003662 PIR 3.05 -1.25 VEGF

NM_003676 DEGS 5.23 1.07 ENDOGRO

NM_003693 SREC 232.16 1.34 ENDOGRO

NM_003706 PLA2G4C 13.06 -2.90 bFGF

NM_003798 CTNNAL1 4.07 -1.23 ENDOGRO

NM_003810 TNFSF10 3.21 -2.50 VEGFE

NM_003812 ADAM23 18.65 -1.34 VEGF

NM_003816 ADAM9 6.16 -1.36 ENDOGRO

NM_003914 CCNA1 10.33 1.31 ENDOGRO

NM_003919 SGCE 8.43 -1.17 ENDOGRO

NM_003947 HAPIP 18.68 1.65 bFGF

NM_003956 CH25H 7.43 -3.03 bFGF

NM_003965 CCRL2 8.41 2.00 bFGF

NM_003975 SH2D2A 3.60 1.33 bFGF

NM_003991 EDNRB 5.28 1.39 ENDOGRO

NM_004010 DMD 5.12 -1.90 bFGF

NM_004024 ATF3 4.83 -4.15 bFGF

NM_004105 EFEMP1 23.60 -1.39 ENDOGRO

NM_004126 GNG11 3428.47 1.47 ENDOGRO

NM_004155 SERPINB9 5.22 1.16 ENDOGRO

NM_004156 PPP2CB 3.27 -1.20 ENDOGRO

NM_004159 PSMB8 10.81 -1.19 bFGF

NM_004184 WARS 4.49 -1.89 bFGF

NM_004267 CHST2 86.99 2.83 bFGF

NM_004289 NFE2L3 6.65 -1.49 VEGF

NM_004334 BST1 165.62 -1.96 bFGF

NM_004342 CALD1 120.74 -1.64 ENDOGRO

NM_004385 CSPG2 14.18 -1.75 VEGF

NM_004414 DSCR1 7.74 2.13 VEGF NM_004417 DUSP1 5.71 1.53 bFGF

NM_004454 ETV5 16.90 2.73 ENDOGRO

NM_004490 GRB14 3.77 1.66 ENDOGRO

NM_004556 NFKBIE 4.86 -1.41 bFGF

NM_004609 TCF15 30.48 1.72 bFGF

NM_004675 ARHI 31.17 -1.47 ENDOGRO

NM_004791 ITGBL1 7.10 -1.40 ENDOGRO

NM_004796 NRXN3 5.25 -1.24 PIGF

NM_004808 NMT2 13.1 1 -1.73 bFGF

NM_004811 LPXN 3.02 1.36 ENDOGRO

NM_004877 GMFG 127.79 1.49 VEGF

NM_004881 PIG3 7.60 -1.15 ENDOGRO

NM_004895 C1 orf7 3.19 1.64 ENDOGRO

NM_005012 R0R1 62.08 -1.64 VEGF

NM_005045 RELN 10.98 -1.42 ENDOGRO

NM_005072 SLC12A4 10.32 -1.48 ENDOGRO

NM_005100 AKAP12 152.34 1.62 VEGF

NM_005118 TNFSF15 3.83 -1.64 VEGF

NM_005127 CLECSF2 16.36 1.73 bFGF

NM_005168 ARHE 6.11 -1.69 ENDOGRO

NM_005203 C0L13A1 3.85 1.31 ENDOGRO

NM_005238 ETS1 3.48 1.49 VEGF

NM_005282 GPR4 8.75 2.25 ENDOGRO

NM_005308 GPRK5 12.51 1.53 bFGF

NM_005360 MAF 5.11 -2.52 bFGF

NM_005420 STE 64.47 -2.17 bFGF

NM_005429 VEGFC 11.68 1.91 VEGF

NM_005438 F0SL1 3.17 1.71 ENDOGRO

NM_005460 SNCAIP 5.44 2.20 VEGF

NM_005541 INPP5D 40.84 1.40 ENDOGRO

NM_005556 KRT7 3.46 -1.17 ENDOGRO

NMJ305574 LM02 14.62 1.35 VEGF

NM_005585 MADH6 3.60 -1.38 VEGF

NM_005627 SGK 27.82 -1.17 ENDOGRO

NM_005630 SLC21A2 102.05 -1.39 ENDOGRO

NM_005711 EDIL3 10.36 -1.35 ENDOGRO

NM_005755 EBI3 3.54 -1.65 ENDOGRO

NM_005795 CALCRL 12.74 1.96 VEGF

NM_005953 MT2A 12.90 1.21 ENDOGRO

NM_005965 MYLK 3.93 -1.37 ENDOGRO

NM_006006 ZNF145 14.58 -2.00 bFGF

NM_006074 STAF50 74.18 -1.43 bFGF

NM_006094 DLC1 9.76 -1.69 ENDOGRO

NM_006100 ST3GALVI 26.24 1.42 VEGF

NM_006102 PGCP 8.16 -1.43 ENDOGRO

NM_006169 NNMT 530.16 -1.79 ENDOGRO

NM_006226 PLCE 13.52 1.64 ENDOGRO NM_006227 PLTP 4.50 -1.33 bFGF

NM_006255 PRKCH 4.77 -1.18 ENDOGRO

NM_006320 PMBP 3.38 -1.33 ENDOGRO

NM_006398 UBD 33.18 -5.18 bFGF

NM_006404 PROCR 52.74 1.20 bFGF

NM_006407 JWA 3.65 -1.19 ENDOGRO

NM_006454 MAD4 3.47 -1.39 ENDOGRO

NM_006457 LIM 6.95 -1.73 ENDOGRO

NM_006474 T1A-2 9.84 1.45 bFGF

NM_006475 OSF-2 870.46 -1.34 bFGF

NM_006509 RELB 4.29 -2.33 bFGF

NM_006528 TFPI2 11.72 3.00 bFGF

NM_006691 XLKD1 5.82 2.91 bFGF

NM_006719 ABLIM 6.08 -1.43 ENDOGRO

NM_006729 DIAPH2 5.11 -1.34 ENDOGRO

NM_006779 CEP2 4.35 1.32 ENDOGRO

NM_006834 RAB32 3.33 -1.38 VEGF

NM_006855 KDELR3 3.47 -1.40 bFGF

NM_006905 PSG1 3.03 -1.49 VEGF

NM_006988 ADAMTS1 24.94 2.05 ENDOGRO

NM_007005 BCE-1 3.54 -1.32 VEGF

NM_007021 DEPP 3.11 1.64 VEGF

NM_007034 DNAJB4 53.46 -1.28 VEGF

NM_007066 PKIG 4.23 1.33 ENDOGRO

NM_007283 HU-K5 14.74 -1.39 bFGF

NM_007288 MME 7.05 1.44 bFGF

NM_007289 MME 5.59 1.41 bFGF

NM_007308 SNCA 120.69 -1.16 ENDOGRO

NM_007361 NID2 22.18 3.23 VEGF

NM_009588 LTB 5.38 -1.19 bFGF

NM_012082 FOG2 10.62 -1.25 ENDOGRO

NM_012250 TC21 9.43 -1.29 VEGF

NM_012269 HYAL4 5.99 -2.44 bFGF

NM_012323 MAFF 3.56 1.25 VEGF

NM_012449 STEAP 301.60 1.45 ENDOGRO

NM_013231 FLRT2 1584.59 -1.71 ENDOGRO

NM_013250 ZNF215 4.12 2.11 ENDOGRO

NM_013352 SART-2 7.17 -1.93 bFGF

NM_013372 CKTSF1 B1 19.71 1.44 bFGF

NM_013423 ARHGAP6 8.68 2.49 VEGF

NM_013956 NRG1 29.07 -1.81 VEGF

NM_013957 NRG1 8.43 -1.74 VEGF

NM_013958 NRG1 13.34 -1.44 VEGF

NM_013961 NRG1 3.70 -1.37 VEGF

NM_013962 NRG1 20.39 -1.38 VEGF

NM_013989 DI02 7.84 -2.07 VEGF

NM_014029 HSPC022 32.99 1.25 ENDOGRO NM_014059 RGC32 28.92 -1.65 ENDOGRO NM_014074 PRO0529 4.39 -1.42 VEGF NM_014143 B7-H1 9.24 -1.30 VEGF NM_014331 SLC7A11 16.15 -1.61 ENDOGRO NM_014344 FJX1 7.64 1.39 ENDOGRO NM_014349 APOL3 11.47 -1.43 bFGF NM_014363 SACS 13.77 -1.44 VEGFE NM_014391 CARP 46.40 -1.80 ENDOGRO NM_014397 NEK6 3.95 -1.28 ENDOGRO NM_014398 LAMP3 15.90 -1.35 ENDOGRO NM_014465 ST1 B2 39.94 -1.84 ENDOGRO NM_014476 ALP 15.82 -1.19 ENDOGRO NM_014521 SH3BP4 3.55 -1.52 ENDOGRO NM_014570 ARFGAP1 3.13 -1.17 ENDOGRO NM_014585 SLC11A3 46.27 -1.41 VEGFE NM_014634 KIAA0015 7.30 1.52 bFGF NM_014686 KIAA0355 3.24 -1.27 ENDOGRO NMJD14705 KIAA0716 87.07 1.36 ENDOGRO NM_014721 KIAA0680 3.70 1.43 VEGF NM_014731 KIAA0552 3.25 -1.79 ENDOGRO NM_014737 RASSF2 23.65 1.40 ENDOGRO NM_014782 KIAA0512 22.06 -1.38 ENDOGRO NM_014795 ZFHX1 B 158.26 -1.36 VEGF NM_014822 SEC24D 3.59 -1.32 ENDOGRO NM_014832 KIAA0603 3.75 1.56 VEGF NM_014840 KIAA0537 7.79 -1.77 ENDOGRO NM_014890 D0C1 12.99 -2.25 ENDOGRO NM_014909 KIAA1036 5.45 1.42 VEGF NM_014933 KIAA0905 3.78 -1.20 ENDOGRO NM_014945 KIAA0843 4.21 1.20 ENDOGRO NM_014959 KIAA0955 7.96 1.84 ENDOGRO NM_014965 KIAA1042 4.04 -1.44 bFGF NM_015376 KIAA0846 9.01 2.98 VEGF NM_015675 GADD45B 3.51 -1.94 ENDOGRO NM_015881 DKK3 286.01 -1.24 ENDOGRO NM_016061 LOC51646 3.01 -1.64 ENDOGRO NM_016109 PGAR 31.81 -1.99 VEGF NM_016134 LOC51670 4.61 -1.36 ENDOGRO NM_016203 PRKAG2 5.09 -1.22 VEGF NM_016232 IL1 RL1 15.56 -1.40 VEGF NM_016235 GPRC5B 5.37 -1.53 bFGF NM_016270 KLF2 5.53 2.17 bFGF NM_016274 LOC51177 5.28 -1.48 ENDOGRO NM_016352 CPA4 54.01 -1.55 ENDOGRO NM_016357 EPLIN 4.98 -1.30 VEGF NM_016385 HSPC057 4.00 -1.40 ENDOGRO NM 016602 GPR2 4.94 -1.29 ENDOGRO NM_016619 LOC51316 5.50 -1.38 ENDOGRO

NM_016848 SHC3 41.19 -1.31 VEGF

NM_016931 NOX4 80.07 1.17 ENDOGRO

NM_017415 KLHL3 40.42 1.72 ENDOGRO

NM_017577 DKFZp434C0328 3.90 -1.35 ENDOGRO

NM_017585 SLC2A6 8.27 -1.47 ENDOGRO

NM_017596 KIAA0449 3.45 1.41 ENDOGRO

NM_017718 FLJ20220 5.02 1.32 ENDOGRO

NM_017734 FLJ20271 124.25 -1.32 ENDOGRO

NM_017752 FLJ20298 6.73 -1.46 ENDOGRO

NM_017805 FLJ20401 41.04 1.27 ENDOGRO

NM_017905 FLJ20623 3.11 -1.30 ENDOGRO

NM_017980 FLJ 10044 125.20 -1.42 ENDOGRO

NM_018004 FLJ10134 17.08 -1.46 bFGF

NM_018012 FLJ 10157 3.96 -1.59 VEGF

NM_018057 FLJ10316 8.37 -1.52 ENDOGRO

NM_018071 FLJ 10357 3.71 -1.59 bFGF

NM_018159 FLJ 10628 6.29 1.17 ENDOGRO

NM_018192 FLJ10718 154.28 -2.02 bFGF

NM_018295 FLJ 11000 4.10 -1.43 ENDOGRO

NM_018324 FLJ11106 5.31 -1.97 bFGF

NM_018326 FLJ11110 64.14 1.66 bFGF

NM_018357 FLJ11196 4.28 -1.34 ENDOGRO

NM_018370 FLJ 11259 6.87 -1.49 ENDOGRO

NM_018384 FLJ 11296 11.26 2.13 bFGF

NM_018401 HSA250839 3.61 1.19 bFGF

NM_018413 C4ST 3.30 1.51 ENDOGRO

NM_018476 HBEX2 106.48 -1.62 VEGF

NM_018482 DDEF1 3.45 -1.19 ENDOGRO

NM_018567 TNS 5.72 1.43 ENDOGRO

NM_018841 LOC55970 12.04 -1.33 ENDOGRO

NM_019858 A 14.27 1.21 ENDOGRO

NM_020130 C8orf4 22.69 -3.60 ENDOGRO

NM_020152 C21orf7 4.33 1.87 VEGF

NM_020163 LOC56920 30.25 -5.28 VEGFE

NM_020186 DC11 25.99 1.58 ENDOGRO

NM_020190 HNOEL-iso 3.76 -1.55 bFGF

NM_020353 LOC57088 426.58 -1.52 VEGF

NM_020651 PELI1 3.43 -1.38 bFGF

NM_021069 ARGBP2 192.99 -2.09 ENDOGRO

NM_021106 RGS3 9.55 -2.34 ENDOGRO

NM_021154 PSA 5.38 1.61 ENDOGRO

NM_021226 LOC58504 6.03 1.38 ENDOGRO

NM_021255 PELI2 6.20 -1.77 bFGF

R49042 16.17 -1.54 bFGF

R92031 6.32 1.33 bFGF

T57773 4.79 -2.27 VEGF T81424 K-ALPHA-1 12.52 1.45 ENDOGRO

T87544 4.04 -1.40 ENDOGRO

T89094 RGS4 1156.70 1.71 ENDOGRO

U10991 G2 205.85 1.46 ENDOGRO

U 17077 BENE 12.42 2.43 VEGF

U27655 RGS3 11.59 -2.23 bFGF

U27768 RGS4 102.15 1.68 ENDOGRO

U50534 13CDNA73 14.49 1.54 bFGF

U61166 ITSN1 4.45 -1.56 ENDOGRO

U79271 SDCCAG8 20.19 -1.33 ENDOGRO

U90908 LOC58504 7.01 1.30 ENDOGRO

W02693 5.01 -1.87 ENDOGRO

W44435 FLJ 12649 6.30 -1.65 ENDOGRO

W46280 5.82 -1.65 ENDOGRO

W46364 630.21 -1.92 ENDOGRO

W60844 6.45 -1.30 ENDOGRO

W69778 32.69 -1.64 bFGF

W87772 472.27 1.26 VEGFE

X04706 H0XD4 38.81 1.55 ENDOGRO

X05610 COL4A2 83.40 -1.35 ENDOGRO

X66945 FGFR1 4.04 1.20 ENDOGRO

X68742 ITGA1 4.63 1.73 VEGF

X93921 DUSP7 6.85 1.34 ENDOGRO

Table. 4

RHMVEC Proliferation Signature

GenBank

Accession EC:MCF7 Intensity Growth

Number Gene Symbol (Expression) Ratio Fold Change Factor

600507553R1 600507553R1 6.40 -1.56 VEGF

600511339R1 600511339R1 10.95 -1.65 ENDOGRO

600513062R1 600513062R1 11.30 -1.84 VEGF

600516127R1 600516127R1 20.18 -1.97 VEGF

600516223R1 600516223R1 3.14 -1.25 bFGF

600518689R1 600518689R1 19.16 -1.92 VEGF

600523987R1 600523987R1 3.36 1.54 VEGF

600524312R1 600524312R1 9.60 -1.78 bFGF

700039220H1 700039220H1 3.64 1.31 bFGF

700067654H1 700067654H1 5.16 1.33 VEGF

700588837H1 700588837H1 3.28 -1.58 ENDOGRO

700690490H1 700690490H1 5.36 1.29 VEGF

701347738H1 701347738H1 4.31 -1.55 ENDOGRO

701349191 H1 701349191 H1 5.30 -1.50 bFGF

701350288H1 701350288H1 8.43 1.20 ENDOGRO

701353618H1 701353618H1 5.33 1.28 VEGF

701354577H1 701354577H1 5.05 1.49 VEGF

701354657H1 701354657H1 3.71 1.27 VEGF

701417958H1 701417958H1 3.13 1.20 bFGF

701419627H1 701419627H1 15.42 -1.76 ENDOGRO

AA799503 g2862458 4.90 -1.23 ENDOGRO

AA799750 Erg 482.85 -1.31 bFGF

AA800192 g2863147 4.60 -1.49 bFGF

AA800293 g2863248 104.39 -1.37 bFGF

AA800550 g2863505 39.16 1.20 VEGF

AA801220 g2864175 222.44 1.25 ENDOGRO

AA848714 g2936254 9.08 -1.26 bFGF

AA850055 g2937595 4.18 -1.26 bFGF

AA850311 g2937851 3.44 1.22 VEGF

AA851637 Lu 42.24 -1.51 ENDOGRO

AA859260 g2948611 3.32 -1.34 VEGF

AA859278 g2948629 4.10 1.36 bFGF

AA859444 g2947975 10.74 -1.73 bFGF

AA874964 g2979912 5.37 -1.33 VEGF

AA875261 g2980209 8.23 1.41 bFGF

AA891911 g3018790 9.75 1.35 bFGF

AA899923 g3035277 3.48 -1.44 bFGF

AA925057 g3072193 25.13 -1.36 VEGF AA926129 74.21 -1.32 bFGF

AA944413 g3104329 3.96 1.21 VEGF

AA944542 g4132423 3.97 -1.23 bFGF

AA944936 g3104852 6.51 1.72 bFGF

AA945463 g3105379 3.61 -1.45 VEGF

AA945677 g3105593 29.07 -1.25 ENDOGRO

AA945788 g3105704 5.63 -1.20 VEGF

AA946190 g3106106 14.83 -1.28 VEGF

AA946201 g3106117 102.57 -1.25 ENDOGRO

AA946350 g3106266 80.11 1.45 bFGF

AA955134 g3513034 3.01 1.30 ENDOGRO

AA956085 g3119780 3.61 -1.23 bFGF

AA957335 g3121030 158.89 -1.55 bFGF

AA957776 g2936580 38.11 -1.18 bFGF

AA963106 g3136598 7.68 1.47 bFGF

AA964004 Pter 4.69 1.35 ENDOGRO

AA964264 g3137756 14.05 -1.20 bFGF

AA996897 g3187452 23.71 -1.24 ENDOGRO

AA997073 g3187934 5.63 -1.21 VEGF

AA998510 g3189161 26.21 -1.78 ENDOGRO

AA998516 g3189167 5.07 1.19 VEGF

AA998618 g3189269 3.48 -1.48 VEGF

AA999079 g3189670 3.67 -1.18 VEGF

AB000199 cca2 3.23 -1.31 VEGF

AB005540 PCTAIRE2 3.66 1.20 bFGF

AB010467 Abcc3 4.40 -1.28 VEGF

AB015308 Gna15 19.47 1.21 bFGF

AB015746 Il4r 22.40 -1.17 bFGF

AB019120 AB019120 67.88 -1.55 bFGF

AB020978 GADD45gamma 3.19 1.27 bFGF

AB032085 RM3 4.60 -1.28 bFGF

AB032087 g3730102 3.17 -1.18 ENDOGRO

AB060092 Scyb2 7.67 -1.76 ENDOGRO

AF003835 Idi1 3.42 1.32 ENDOGRO

AF021350 NKG2A 3.04 1.64 bFGF

AF029241 RT1.S3 5.62 -1.32 bFGF

AF047707 Ugcg 3.82 -1.65 VEGF

AF072816 mrp3 5.04 -1.30 bFGF

AF102262 beta1 -4GT 3.91 -1.25 VEGF

AF154245 chemotactic protein-3 5.09 -1.32 bFGF

AF164039 AF164039 18.79 -1.31 bFGF

AF189709 collagen XVIII 14.86 -1.25 ENDOGRO interferon-gamma

AF201901 receptor 4.50 -1.50 bFGF AF205717 LRTM4 8.60 1.20 VEGF AF244366 FLIP short form 16.14 1.32 bFGF AF254801 AF254801 69.37 1.29 bFGF AF259504 Bak 4.27 -1.27 VEGF

AF259898 E3karp 10.92 -1.69 VEGF

AF271786 Fgf13 11.13 1.31 VEGF

AF314657 clusterin 10.00 -1.43 ENDOGRO

AF324255 Erol l 3.40 -1.66 bFGF

AF368269 Cyp2t1 19.99 -1.38 ENDOGRO

AI008035 700068780H1 9.35 1.32 bFGF

AI008526 g3222358 16.48 2.48 bFGF

AI009368 g3223200 8.25 -1.34 VEGF

AI009736 g3223568 6.35 1.32 bFGF

AI009780 g3223612 3.02 1.23 bFGF

AI009783 g3223615 3.33 -1.32 ENDOGRO

AI010312 g4133226 31.15 -1.34 bFGF

AI011501 g3225333 17.92 -1.20 bFGF

AI012580 g3226412 10.77 -1.22 bFGF

AI012597 g3226429 13.23 1.19 bFGF

AI013470 g4133876 3.54 -1.48 ENDOGRO

AI013562 g3227618 7.03 -3.34 VEGF

AI029460 g3247286 5.84 -1.40 bFGF

AI031004 g3248830 80.92 -1.39 bFGF

AI043630 g3290365 13.96 1.23 bFGF

AI043724 g3290459 4.08 1.22 ENDOGRO

AI043851 g3290586 210.09 -1.35 bFGF

AI043958 g3290693 4.08 -1.20 VEGF

AI044026 g3290761 6.81 -1.34 bFGF

AI044530 g3291391 8.51 -2.18 bFGF

AI044674 g3291535 5.62 -1.49 VEGF

AI044760 g3291621 26.81 1.43 VEGF

AI044802 g3290865 4.52 -2.03 ENDOGRO

AI044912 g3291731 33.22 1.40 ENDOGRO

AI044948 g3291767 10.36 1.36 bFGF

AI045186 g3292005 21.40 -1.52 ENDOGRO

AI045920 g3292739 5.07 1.24 ENDOGRO

AI058759 g3332536 25.51 1.23 bFGF

AI059060 g3332837 3.24 -1.62 VEGF

AI059103 g3332880 14.45 -1.36 VEGF

AI059204 g3332981 55.91 -1.44 VEGF

AI059363 g3333140 124.38 1.40 bFGF

AI059449 g3333226 7.39 -1.34 bFGF

AI059450 g3333227 8.45 -1.69 VEGF

AI060115 g3333892 66.25 -1.25 VEGF

AI070068 g3396319 6.13 -2.29 bFGF

AI070370 g3396621 3.50 -1.23 ENDOGRO

AI072357 g3398551 7.13 1.22 ENDOGRO

AH 01062 g3706050 4.44 -1.91 VEGF

AH 01250 g4133997 4.27 1.45 bFGF

AH 01270 g4134000 87.91 -1.28 bFGF AH 01402 g3706309 3.52 1.18 bFGF AI101757 g3706619 6.05 -1.20 bFGF AI101945 g3706786 6.82 -1.26 VEGF AH 02248 g4134070 13.24 -1.22 VEGF AH 02320 g3707114 3.90 -1.25 bFGF AH 03007 g3704802 3.47 -1.29 bFGF AH03106 g3704827 3.90 1.47 bFGF AH03618 g3708145 3.01 -1.36 VEGF AH03939 g3704876 4.41 1.22 ENDOGRO AH 04128 g3708534 3.38 -1.36 VEGF AH05417 g3709501 45.14 -1.30 VEGF AH05452 g3709529 3.95 -1.44 VEGF AH 12636 g3512585 5.56 -1.25 bFGF AH 37629 g3638406 18.18 1.41 bFGF AH 37826 g3638603 3.28 -1.33 ENDOGRO AH37944 g3638721 222.74 -1.76 bFGF AH45002 g3666801 23.08 1.23 VEGF AH45832 g3667631 6.35 -1.23 bFGF AH68952 g3705260 5.36 1.21 VEGF AH69422 g3705730 10.92 -1.37 VEGF AH69635 g3709675 15.87 -1.21 ENDOGRO AI171908 g3711948 3.49 -1.23 ENDOGRO AH72056 g4134696 16.18 1.34 VEGF AH 72117 g4134703 10.06 -1.32 ENDOGRO AH 75466 g3726104 6.20 -1.45 bFGF AH 76486 g3727124 146.17 1.31 bFGF AH76965 g4133497 82.43 -1.88 bFGF AH76983 g3727621 3.19 1.26 bFGF AH77055 g3727693 19.15 1.29 VEGF AI177120 g3829605 4.30 -1.39 bFGF AI177198 g3727836 4.37 1.16 VEGF AH77396 g3728034 3.05 -1.62 bFGF AH77621 g3728259 264.10 -1.28 bFGF AH77939 g4135031 36.48 -1.32 VEGF AH78222 g3728860 7.21 1.23 ENDOGRO AH 78718 g4135092 114.85 1.41 bFGF AH78978 g3729616 7.39 -1.25 ENDOGRO AH79786 g3730424 6.81 -1.33 VEGF AH80386 g3731024 21.30 -1.50 VEGF AI230758 g3814645 89.23 -1.24 ENDOGRO AI230762 g3814649 3.23 -1.25 VEGF AI230918 g3814805 3.00 -1.24 bFGF AI231805 g3815685 43.95 -1.18 ENDOGRO AI231999 g3815879 22.28 1.31 ENDOGRO AI233099 g3816979 3.19 1.31 VEGF AI233773 Mawbp 68.74 -1.27 bFGF AI235721 g3829227 3.22 -1.32 VEGF AI235960 g3829466 229.73 -1.23 VEGF

AI236381 g3829887 4.52 -2.09 bFGF

AI236799 g4136246 25.50 1.32 bFGF

AI236912 Nab1 7.23 1.24 bFGF

AI237544 g3831050 4.46 -1.28 bFGF

AI407547 g3727827 3.84 -1.17 bFGF

AI409186 g2938420 31.41 1.29 ENDOGRO

AI409841 g3706639 3.36 -1.26 VEGF

AI411054 g3812200 3.37 1.46 bFGF

AI711100 g3224246 385.26 -1.29 VEGF

AJ000696 KIF1D 4.52 -2.61 bFGF

AJ011116 nos3 58.27 -1.31 VEGF

AW140657 600510887R1 6.53 -1.44 ENDOGRO

AW142011 g3333577 3.20 -1.35 bFGF

AW142194 g2864225 41.07 1.23 VEGF

AW142519 g3071124 3.12 -1.39 bFGF

AW523549 g3224204 17.12 -1.22 bFGF

AW914004 g3224058 306.81 1.35 VEGF

AW916926 Slc22a7 13.17 -1.37 ENDOGRO

AW917188 Dpyd 9.05 1.63 VEGF

AW920825 701222534H1 32.82 1.57 VEGF

AY024364 GATA-3 4.64 -1.24 bFGF

BE098266 g3071239 323.96 -1.21 bFGF

BE108269 g3246659 6.26 1.34 ENDOGRO

BE121287 700032038H1 4.23 -1.16 ENDOGRO

BF283084 600520366R1 5.93 1.27 VEGF

BF398271 g3292264 7.25 -1.36 bFGF

BF416417 g3707631 4.83 -1.27 bFGF

BF548232 g3828538 3.62 -1.58 VEGF

BF551997 BF551997 21.20 1.33 bFGF

BG381698 g2672938 4.40 1.20 bFGF

BG664717 701222952H1 12.84 1.54 VEGF

BI275290 g3020546 3.50 -1.26 bFGF

BI277635 g3728852 9.73 -1.39 VEGF

BI283830 g3817681 9.65 -1.28 ENDOGRO

BI284263 g3137012 511.46 -1.25 bFGF

BI285246 g3830698 61.06 1.22 ENDOGRO

BI287221 g3705125 32.89 -1.24 VEGF

BI294910 g3705813 43.33 -1.51 ENDOGRO

BI296015 g3711886 5.26 -1.37 VEGF

BM384585 g2862699 6.07 -1.31 ENDOGRO

BM384701 g3224341 20.20 -1.42 VEGF

BM388598 g3187570 6.05 -1.56 bFGF

BM388852 g3106350 28.05 -1.19 bFGF

BM391182 600518660R1 4.10 -1.28 VEGF

BQ190671 g4132974 3.42 1.21 VEGF

BQ192029 g4133216 376.26 -1.31 bFGF BQ198730 g3224083 39.70 1.24 VEGF

BQ199612 g3727571 29.44 -1.43 bFGF

BQ199678 g3818042 3.96 -1.35 bFGF

BQ200399 g3727330 128.03 1.21 bFGF

BQ203036 g2937343 10.46 1.20 VEGF

BQ203060 g3221834 19.92 -1.27 bFGF

BQ203246 g3102732 188.91 1.28 bFGF

BQ204980 g3222960 4.72 1.37 VEGF

BQ205927 g3103480 7.39 -1.25 bFGF

BQ779673 700052535F1 3.36 -1.43 bFGF

BQ780778 g2937314 29.44 -1.23 bFGF

BQ781420 g2936107 3.31 1.36 bFGF

BU671151 3.04 1.28 VEGF

BU671574 701216766H1 3.51 1.44 VEGF

CA333942 600524307R1 6.48 -1.57 VEGF

CA503512 g4134955 3.09 -1.30 VEGF

CA504040 g3709254 3.01 1.29 VEGF

CA506715 g2938431 102.56 1.24 bFGF

CA507008 g976837 3.86 -1.36 ENDOGRO

CA508330 g3813525 3.00 -1.25 VEGF

CA509105 600513095R1 3.10 -1.21 bFGF

CA509955 g3730145 37.61 1.42 bFGF

CA513003 701353736H1 3.92 1.23 bFGF

D00636 b5R 3.13 -1.26 bFGF

D11444 gro 3.41 -2.00 bFGF

D16339 g6981681 10.14 1.33 ENDOGRO

D16339 Ttpa 15.43 1.53 bFGF

D28860 D28860 3.78 -3.13 VEGF

D31838 weel 4.16 1.34 VEGF

D42148 600520458R1 94.76 -1.47. bFGF

D86086 Abcc2 5.88 1.21 bFGF

G2887744 9.40 -1.24 VEGF

G2887885 3.21 -1.58 ENDOGRO

G2888124 16.17 -1.70 ENDOGRO

G2937254 3.04 -1.36 bFGF

G2937336 3.11 -1.48 ENDOGRO

G2938797 6.83 1.24 bFGF

G2938805 3.65 -1.21 bFGF

G2938831 3.04 -1.33 bFGF

G2939578 6.47 -1.68 ENDOGRO

G3019428 39.84 1.20 VEGF

G3020059 7.27 -1.29 bFGF

G3021176 6.67 -1.33 bFGF

G3035644 5.53 1.32 bFGF

G3071714 3.04 -1.46 ENDOGRO

G3071902 167.52 -1.28 bFGF

G3072603 8.46 -1.26 bFGF G3072712 56.89 1.22 ENDOGRO

G3073258 7.51 1.54 bFGF

G3102686 9.14 -1.38 bFGF

G3103279 34.67 1.38 ENDOGRO

G3137338 5.03 -1.53 VEGF

G3137782 22.69 1.33 VEGF

G3137957 273.68 -1.34 bFGF

G3137994 8.42 -1.34 bFGF

G3138006 6.05 -1.25 bFGF

G3189628 3.21 1.35 bFGF

G3224642 3.55 -1.69 VEGF

G3225906 14.76 1.21 bFGF

G3226018 5.47 -1.21 bFGF

G3226140 98.14 -1.31 bFGF

G3227787 13.27 -1.25 VEGF

G3246847 3.40 -1.48 bFGF

G3246942 135.33 -1.52 ENDOGRO

G3247784 14.84 -1.31 VEGF

G3247854 199.84 -1.30 bFGF

G3248097 26.74 1.35 bFGF

G3248367 21.02 -1.88 bFGF

G3291935 5.77 -1.46 ENDOGRO

G3291949 3.22 -1.16 VEGF

G3292531 18.79 -1.34 ENDOGRO

G3292629 3.80 -1.27 VEGF

G3333900 8.95 -1.34 ENDOGRO

G3333935 5.10 -1.21 bFGF

G3396358 3.87 -1.40 bFGF

G3396493 3.05 -1.32 VEGF

G3396557 26.97 -1.36 bFGF

G3396633 8.07 -1.45 bFGF

G3397437 304.78 -1.22 VEGF

G3397680 3.38 1.24 ENDOGRO

G3397969 9.69 -1.63 VEGF

G3398076 61.74 -1.60 bFGF

G3398171 4.81 -1.20 ENDOGRO

G3399145 22.81 -1.58 bFGF

G3399177 4.24 1.34 VEGF

G3399284 11.67 1.21 VEGF

G3399406 13.82 1.54 bFGF

G3511710 5.60 -1.27 VEGF

G3512937 31.87 -1.40 VEGF

G3513230 4.55 -1.21 bFGF

G3636910 5.68 1.20 VEGF

G3637432 14.94 -1.28 VEGF

G3637746 6.69 1.20 bFGF

G3638675 36.35 -1.27 VEGF G3666728 3.09 -1.26 bFGF G3666899 64.34 -1.48 bFGF G3667173 8.07 -1.28 bFGF

G3707946 3.06 -1.27 bFGF

G3708389 17.55 -2.00 bFGF

G3708633 4.16 -1.35 VEGF

G3708986 95.05 -1.44 bFGF

G3709440 3.09 1.18 bFGF

G3710527 6.48 1.22 bFGF

G3710770 5.18 -1.19 bFGF

G3711240 8.06 -2.85 ENDOGRO

G3711421 22.68 -1.76 bFGF

G3711520 26.51 1.39 VEGF

G3711533 5.04 -1.39 bFGF

G3711566 31.85 1.34 ENDOGRO

G3712171 4.18 1.37 VEGF

G3725993 3.63 -1.22 ENDOGRO

G3726061 3.64 -1.16 ENDOGRO

G3727230 14.55 -1.37 VEGF

G3729898 1566.10 1.38 bFGF

G3730814 6.28 -2.55 bFGF

G3811611 6.82 -1.27 bFGF

G3812445 3.50 -1.28 bFGF

G3813207 398.22 -1.31 VEGF

G3813483 8.65 -1.50 ENDOGRO

G3829163 3.61 -1.32 bFGF

G4131670 3.34 1.24 VEGF

G4131679 5.44 -1.24 bFGF

G4131762 4.42 -1.46 ENDOGRO

G4132317 47.79 1.22 VEGF

G4132471 3.75 -1.22 bFGF

G915019 3.97 -1.30 VEGF

G976993 11.77 1.50 VEGF

G977252 3.56 -1.74 bFGF

G977371 9.43 -1.28 ENDOGRO

G977384 3.01 1.66 VEGF

G977468 3.82 -1.41 bFGF

G977854 5.07 -1.42 bFGF

G977919 5.12 -1.31 bFGF

G979053 10.84 -1.41 bFGF

H32317 g977734 3.08 1.32 VEGF

H32799 g978216 3.31 -1.65 VEGF

H34328 g979745 17.72 1.76 bFGF

H34385 g979802 7.34 -1.19 bFGF

H34603 g980020 4.26 1.43 VEGF

H34681 g980098 5.73 1.38 VEGF

J03637 AD mRNA 4.24 -2.80 bFGF J03819 erb62 7.20 1.86 VEGF

L11995 cyclin B 3.64 1.22 VEGF

L20468 cerebroglycan 31.80 1.30 ENDOGRO

L22294 PDH 4.81 -1.47 ENDOGRO

L23128 L23128 3.23 1.20 bFGF

L27651 Slc22a7 7.71 -1.34 ENDOGRO

L34049 megalin 4.23 1.27 bFGF

M17412 LOC60380 4.02 -1.73 ENDOGRO

M26125 XEH mRNA 223.02 -1.53 ENDOGRO

M58040 transferrin receptor 3.87 1.28 bFGF

M80367 Gbp2 9.84 -1.62 bFGF

M81855 Abcbl 9.60 -1.79 bFGF

M83143 M83143 3.03 1.31 bFGF

M91235 M91235 11.54 -1.94 ENDOGRO

NM_012502 Ar 8.93 2.18 bFGF

NM_012528 Chrnbl 25.35 -1.31 bFGF

NM_012548 Edn1 392.42 -2.23 bFGF

NM_012566 Gfi1 14.50 1.39 bFGF

NM_012620 Serpinel 54.90 -2.51 ENDOGRO

NM_012679 Clu 3.34 -1.30 ENDOGRO

NM_012715 Adm 9.14 -1.97 ENDOGRO

NM_012762 Caspl 5.76 -1.26 bFGF

NM_012827 Bmp4 80.49 -1.44 bFGF

NM_012912 Atf3 4.89 -1.43 bFGF

NM_013000 Pam 7.26 1.40 bFGF

NM_013062 Kdr 405.26 1.34 bFGF

NM_013085 Plau 9.54 2.20 bFGF

NM_013130 Madhl 6.04 -1.20 ENDOGRO

NM_013145 Gnail 14.79 1.48 bFGF

NM_013151 Plat 5.26 -1.38 ENDOGRO

NM_016987 Acly 3.21 -1.28 VEGF

NM_017028 Mx1 14.33 -1.79 bFGF

NM_017076 Tage4 10.54 1.78 bFGF

NM_017079 Cd1 d 26.25 -1.30 bFGF

NM_017105 Bmp3 19.82 -2.20 ENDOGRO

NM_017112 Hpn 3.02 -1.91 VEGF

NM_017225 Pctp 5.87 1.30 bFGF

NM_017259 Btg2 26.14 -1.27 ENDOGRO

NM_017317 ram 4.89 -1.51 bFGF

NM_017350 Plaur 7.45 1.31 bFGF

NM_019144 Acp5 223.88 -1.54 ENDOGRO

NM_019147 Jag1 65.16 -1.46 VEGF

NM_019234 Dncid 32.61 -1.51 bFGF

NM_019249 Ptprf 22.72 -1.20 ENDOGRO

NM_019261 Klrc2 11.07 1.78 bFGF

NM_019285 Adcy4 15.84 -1.18 bFGF

NM_019370 LOC54410 34.00 1.25 VEGF NM_019371 SM-20 7.13 -1.61 ENDOGRO

NM_020072 Ppal 3.37 1.51 VEGF

NM_020082 Rnase4 25.93 1.41 VEGF

NM_021655 Chga 3.64 1.28 VEGF

NM_021679 Nxph3 6.16 1.28 ENDOGRO

NM_021751 LOC60357 140.84 -1.40 bFGF

NM_021846 Mcl1 8.92 1.36 VEGF

NM_022005 Fxyd6 812.43 -1.31 bFGF

NM_022177 Sdf1 9.97 -1.68 VEGF

NM_022224 Rpr1 3.40 1.38 bFGF

NM_022297 Ddahl 4.46 -1.28 VEGF

NM_022441 AcvrH 61.21 -1.34 bFGF

NM_022528 Hif3a 3.50 -1.47 bFGF

NM_022705 Mch 12.79 -1.27 bFGF

NM_022715 Mvp 3.80 1.29 VEGF

NM_022856 Nab1 4.04 1.23 bFGF

NM_023103 Mug1 3.24 1.26 ENDOGRO

NM_023960 Kcnmb4 5.42 1.43 VEGF

NM_024160 Cyba 44.10 -1.34 bFGF

NM_030834 Mct3 27.50 -1.81 ENDOGRO

NM_030868 Nov 193.60 1.20 ENDOGRO

NM_030985 Agtrla 33.27 2.02 VEGF

NM_031059 Msx1 4.48 -1.40 bFGF

NM_031100 RpHO 4.31 -1.32 VEGF

NM_031242 Cds1 10.30 -1.37 bFGF

NM_031321 Slit3 5.51 -1.58 ENDOGRO

NM_031327 Cyr61 24.10 -1.65 ENDOGRO

NM_031544 Ampd3 24.58 -1.42 bFGF

NM_031550 Cdkn2a 7.80 1.40 bFGF

NM_031645 Rampl 4.16 -1.47 ENDOGRO

NM_031646 Ramp2 14.25 -1.50 VEGF

NM_031771 Thbd 14.40 1.38 bFGF

NM_031807 Tpbg 66.41 -1.25 bFGF

NM_031970 Hspbl 52.18 -1.36 bFGF

NM_033237 Gal 546.73 -4.46 ENDOGRO

S68135 GLUT1 5.83 -1.52 ENDOGRO

S70011 g3137721 3.01 1.41 VEGF

S70011 tricarboxylate carrier 4.01 1.23 ENDOGRO

U03388 cyclooxygenase 1 22.47 -1.42 bFGF

U05989 Pawr 45.60 1.29 VEGF

U 16858 testin 4.35 -1.47 ENDOGRO

U 17604 rS-Rex-b 4.23 1.61 bFGF

U 18060 PGHS-1 11.82 1.59 bFGF

U22830 P2Y purinoceptor 3.89 1.30 bFGF

U24174 WAF1 3.08 -1.32 ENDOGRO

U38376 Pla2g4a 10.63 1.23 bFGF

U39208 CYP4F6 8.18 -1.40 bFGF U44948 SmLIM 33.23 1.19 VEGF chemokine receptor U54791 LCR1 20.18 1.41 ENDOGRO

U60085 CYP3A9 18.44 1.40 bFGF

U65656 gelatinase A 21.42 -1.33 bFGF U72353 lamin B1 4.02 1.20 VEGF

U94330 OPG 3.13 -1.89 bFGF

U94709 EP4 prostanoid receptor 3.47 -2.55 VEGF X00469 Cyp1 a1 15.35 -2.04 bFGF X00722 g3727098 3.04 -1.37 bFGF X02601 Mmp3 8.70 1.55 bFGF X13016 OX-45 mRNA 3.55 1.19 VEGF

X14264 CaMII 3.33 1.36 VEGF

X14977 Aldh2 3.11 -1.20 bFGF

X54862 Mgmt 23.74 -1.28 bFGF X58830 vgr 22.26 -1.34 ENDOGRO

X63515 phosphorylase 3.93 -1.91 ENDOGRO X63744 Slc1 a3 7.36 -1.38 VEGF X66539 TNF-alpha 3.97 -1.48 ENDOGRO X68101 trg 4.28 1.19 VEGF

X70706 T-plastin 4.40 1.50 bFGF X84004 CI100 20.03 -1.20 ENDOGRO

Y17328 CDK108 7.15 -1.45 bFGF

Z18877 Oas1 9.02 -3.11 bFGF

Table. 5

C6 Flank Tumor Model, Compound A-induced Signature, EC-specific Sequences Compound-induced Fold Changes in Gene Expression

GenBank

Accession 1 2 3

Number Gene Symbol Dose Doses Doses

M 10934 Rbp4 2.54 1.59 1.45

600519878R1 600519878R1 1.02 -1.94 -1.46

AA925717 1.09 1.34 1.62

AB028461 AB028461 1.36 2.08 1.51

AF056034 AF056034 -1.91 1.34 -2.03

AF058786 JE/MCP-1 1.47 1.58 1.38

AF058786 JE/MCP-1 1.44 1.62 1.36 chemotactic

AF154245 protein-3 1.26 1.63 1.22

AF158385 ATP1 B4 -2.03 1.40 -1.71

AF276998 Jam 1.07 -1.42 -1.84

AF295535 Ata3 -1.79 -1.30 -2.23

AJ299016 Ret 1.05 -1.65 -1.71

BF564460 BF564460 -1.08 -1.49 -1.78

D13871 glut 5 coding -1.54 -1.65 -1.19

AA800146 g2863101 1.08 1.85 1.60

AA818658 g2888244 1.23 2.07 1.57

AA818845 g2888431 -2.40 1.13 -1.63

BG378083 g2888538 -1.80 1.42 -1.84

AA819832 g2889019 -1.26 -1.74 -1.75

AA848809 g2936349 1.28 1.85 1.59

G2937470 g2937470 -1.76 1.09 -2.73

BI282277 g2939494 -1.73 1.30 -1.66

BM390487 g2948168 -1.13 -1.81 -2.19

G3019978 g3019978 1.06 -1.39 -1.68

G3020570 g3020570 -1.01 -1.50 -1.65

AA900587 g3035941 -2.36 1.58 -2.63

AC091752 g3071324 1.22 1.79 1.46

G3073040 g3073040 1.02 -1.31 -1.69

G3103294 g3103294 -1.11 -1.70 -1.46

AA943790 g3103706 -2.49 1.33 -4.44

AA944827 g3104743 1.20 1.91 1.56

AA946094 Mb -2.04 1.18 -2.31

AA946201 g3106117 1.47 2.25 1.31

AW251703 g3120965 1.20 1.73 1.51

G3136659 g3136659 -1.57 1.33 -1.70

G3136765 g3136765 -1.67 -1.54 -1.19

AA963444 g3137002 -1.68 -1.58 -1.27

AA996414 g3186969 1.01 -1.50 -1.66

AA996581 g3187136 -1.85 -1.23 -1.49

AI008203 g3222035 -1.72 -1.52 -1.32

CA503524 g3222465 1.24 1.95 1.60

AI009946 g3223778 -1.82 -1.59 -1.25

AI044213 g3291116 1.05 -1.44 -1.65

AI044263 g3291166 1.23 1.78 1.58 AI044643 g3291504 -1.01 -1.52 -1.66

AI059122 g3332899 1.14 1.70 1.26

BF558524 g3333166 -2.26 1.24 -2.52

AI059446 g3333223 -1.19 -1.77 -1.87

AI059511 g3333288 -1.66 -1.65 -1.30

G3398050 g3398050 -1.15 -2.01 -1.68

AI072733 g3398927 -1.47 1.16 -1.61

AH 13026 g3512975 -1.19 -1.29 -1.71

G3637152 g3637152 -1.02 -1.36 -1.63

G3637289 g3637289 -1.02 -1.66 -1.96

AH 37249 g3638026 -1.56 1.38 -1.78

AH 37425 g3638202 -1.06 -1.91 -1.28

M31591 g3704673 1.44 2.24 1.90

G3708698 g3708698 -2.63 1.39 -2.88

AH 04620 g3708949 -1.96 1.40 -1.71

AH 05417 g3709501 -1.15 -1.85 -1.91

AH 70840 g3710880 -2.23 1.43 -2.16

BQ211970 g3711814 -2.26 1.52 -2.37

G3725683 g3725683 -2.15 1.08 -3.22

CA503625 g3726615 -1.15 -1.66 -1.98

G3727000 g3727000 -1.19 -1.25 -1.64

AA924506 g3728041 1.17 -1.60 -1.35

AH78585 g3729223 1.03 -1.53 -1.77

G3811945 g3811945 1.15 1.89 1.53

G3813551 g3813551 1.10 -1.78 -1.47

AI231826 g3815706 -1.12 -1.72 -2.24

AI232784 g3816664 1.06 -1.36 -1.62

CA509598 g3817191 1.22 2.30 1.38

AI233962 g3817842 -1.81 1.19 -1.90

G977684 g977684 -1.61 -1.42 -1.20

K02111 MYHC mRNA -1.70 -1.36 -1.50

L19998 Sult1a1 1.10 -1.80 -1.48

M11596 Caleb 1.03 1.41 1.59

M26125 XEH mRNA 1.06 -1.76 -1.48

M26744 IL6 1.37 1.71 1.02 alpha(B)-

M55534 crystallin 1.04 1.65 1.41

M81785 syndecan 1.22 1.59 1.35

NM 012561 Fst 1.41 2.01 1.92

NM 012945 Dtr 1.27 1.95 1.28

NM 012949 Eno3 -2.30 1.36 -2.24

NM 013012 Prkg2 1.06 1.62 1.51

NM 013153 Has2 1.27 1.59 1.42

NM 017099 Kcnjδ 1.06 -1.33 -1.63

NM 017117 Capn3 -2.03 1.43 -2.17

NM 017123 Areg 1.22 1.61 1.54

NM 017178 Bmp2 1.46 1.71 1.40

NM 017210 Dio3 1.21 3.37 1.69

NM 019156 Vtn 1.01 -1.53 -1.71

NM 019341 Rgs5 -1.11 -1.62 -2.01

NM 021588 Mb -1.85 1.44 -1.99

NM 021666 Trdn -1.55 1.43 -1.72

NM 022235 Kcne3 -1.58 -2.05 -2.07

NM 022604 Pg25 -1.66 -2.21 -2.73

NM 024483 Adrald 1.25 1.61 1.29

NM 031327 Cyr61 1.13 1.65 1.29 NM 031345 Gilz -1.29 -1.59 -1.60

NM 031970 Hspbl -1.42 1.10 -1.77

U05341 p55CDC -1.59 -1.42 -1.29

U23407 CRABP II 1.29 1.74 1.25

U53855 ratpgis 1.89 1.71 1.31

U94330 OPG 1.28 1.65 1.24

U94330 OPG 1.30 1.65 1.22

U94330 OPG 1.32 1.68 1.30

X15679 X15679 -1.37 -1.67 1.05

X52883 SulH al 1.11 -1.76 -1.54

Y13275 D6.1A protein -1.24 -1.60 -2.50

C6 Flank Tumor Model, Compound B- induced Signature, EC-specific Sequences Compound-induced Fold Changes in Gene Expression

GenBank Accession 1 2 3

Number Gene Symbol Dose Doses Doses

600507547R1 600507547R1 1.33 2.22 1.53

AW 140657 600510887R1 1.23 2.48 1.54

600522244R1 600522244R1 1.17 1.62 1.38

AI454872 700031879H1 -1.05 2.01 1.64

BQ206769 700064878H1 1.34 1.68 1.44

700510178H1 700510178H1 1.10 1.85 1.30

701216526H1 701216526H1 -1.04 -1.81 -1.43

AW920825 701222534H1 1.10 1.90 1.48

701347825H1 701347825H1 -1.70 -1.84 -1.99

701348620H1 701348620H1 -1.12 -1.62 -1.27

701350232H1 701350232H1 -1.10 -1.63 -1.23 fatty acid

AB005743 transporter 1.35 1.87 1.45 PPAR- gamma

AB011365 protein 1.16 1.83 1.36 PPAR- gamma

AB011365 protein 1.17 1.95 1.45 AB032828 AB032828 -1.08 1.72 1.40 AB036792 ficolin-B -1.77 -2.44 -2.34 AB060092 Scyb2 1.43 2.31 1.92 AF016387 RXRgamma -1.09 -1.76 -1.41 AF058786 JE/MCP-1 1.18 1.78 1.61 AF058786 JE/MCP-1 1.22 1.78 1.56 AF081582 Kpl1 1.01 -1.81 -1.34 AF084934 RT1.D(u) -1.39 -1.81 -1.41 AF087946 Gpr37 -1.07 -1.71 -1.36 AF131294 Abcd2 1.09 -1.65 -1.26 AF131294 Abcd2 1.06 -1.62 -1.25 AF146518 Enpep 1.15 2.35 1.75 chemotactic

AF154245 protein-3 -1.05 1.78 1.45

AF314657 clusterin -1.41 -1.61 -1.42

AW914760 AW914760 -1.23 -1.63 -1.42

AW914760 AW914760 -1.24 -1.60 -1.45

AW914760 AW914760 -1.23 -1.59 -1.36

AW920598 AW920598 1.21 1.61 1.50

D14839 rat FGF-9 1.10 1.74 1.66

D28560 NPH-type III -1.20 -2.11 -1.37

D85509 MT3-MMP -1.07 -2.11 -1.40

D89730 g2429082 1.21 4.18 1.82

BG381698 g2672938 1.01 1.66 1.42

AA799278 g2862233 -1.03 -1.89 -1.31

AA799657 g2862612 1.18 1.60 1.35

AA800145 g2863100 -1.03 1.68 1.30 AA800146 g2863101 1.20 1.75 1.49

BE115875 g2864040 1.12 1.67 1.40

G2888594 g2888594 1.07 2.38 1.65

G2888948 g2888948 -1.16 -1.62 -1.50

AA818607 g2889346 1.25 1.65 1.54

AA848639 g2936179 -1.20 2.23 1.52

AA848993 g2936533 1.39 1.70 1.46

AA849479 g2937019 -1.15 -1.68 -1.26

G2938081 g2938081 -1.06 1.67 1.29

G2939209 g2939209 1.17 1.82 1.41

AA858479 g2948819 1.12 -1.70 -1.28

AA875261 g2980209 1.08 1.67 1.37

BU758985 g3019743 1.02 1.76 1.26

G3019865 g3019865 -1.06 2.11 1.32

AA893022 g3019901 1.08 2.19 1.57

AA899521 g3034875 -1.26 -1.98 -1.41

AA925019 g3072155 -1.01 1.98 1.48

G3073258 g3073258 1.07 1.62 1.35

G3103279 g3103279 -1.15 2.14 1.61

AA943907 g3103823 -1.02 -1.62 -1.29

BQ204813 g3104100 1.16 2.06 1.45

BG375318 g3104739 -1.01 -1.79 -1.24

AA944827 g3104743 1.24 1.69 1.52

AA945643 g3105559 -1.92 -1.34 -1.71

G3105912 g3105912 1.10 2.31 1.38

AA946201 g3106117 1.11 2.01 1.41

AA946355 g3106271 -1.18 -1.61 -1.15

BQ201957 g3106396 -1.34 -1.99 -1.57

G3137782 g3137782 -1.06 1.77 1.33

G3137957 g3137957 -1.02 1.82 1.41

AA996727 g3187282 -1.41 -1.72 -1.63

BM391207 g3188195 -1.10 2.11 1.65

AA998510 g3189161 1.63 3.15 1.81

BQ202244 g3189311 -1.06 -1.83 -1.36

AA998953 g3189544 1.01 2.07 1.58

BQ203060 g3221834 -1.01 1.70 1.39

AI008526 g3222358 -1.04 1.70 1.33

CA503524 g3222465 1.18 2.02 1.38

AI009946 g3223778 1.03 -2.08 -1.39

BQ198730 g3224083 -1.00 1.76 1.37

AI010304 g3224136 1.23 1.72 1.40

AI502256 g3226632 -1.55 -2.23 -1.54

BI290624 g3227931 -1.06 -1.73 -1.35

AI029379 g3247205 1.17 1.64 1.31

G3247660 g3247660 -1.00 1.65 1.43

BQ196623 g3248862 1.43 2.17 1.43

AI411352 g3290939 -1.10 1.61 1.46

AI044052 g3290955 -1.32 -1.95 -1.44

AI044556 g3291417 1.04 2.21 1.51

AI044912 g3291731 1.06 1.89 1.53

AI044948 g3291767 1.29 1.80 1.29

AI045191 g3292010 1.01 3.41 1.60

G3292531 g3292531 1.12 2.03 1.65

AI058759 g3332536 1.35 1.80 1.54

AH03652 g3332682 1.22 1.91 1.36

AI059735 g3333512 -1.27 -1.47 -1.59 AF327511 Smhsl .06 1.66 1.35

BG377159 g3397026 .03 1.71 1.22

BE099056 g3397110 .02 1.61 1.31

G3397860 g3397860 .13 1.64 1.42

AI072959 Mgll .00 2.03 1.37

G3512385 g3512385 .05 -1.85 -1.34

G3513248 g3513248 .05 1.98 1.38

AH36855 g3637632 .20 1.79 1.36

G3637836 g3637836 .06 1.70 1.29

BI289488 g3638183 .06 1.70 1.34

G3638417 g3638417 .30 -2.15 -1.25

G3638675 g3638675 .27 2.08 1.53

G3638748 g3638748 .18 1.67 1.36

G3666553 g3666553 .05 1.71 1.48

G3666899 g3666899 .09 1.72 1.31

G3667679 g3667679 .11 -2.68 -1.59

G3667962 g3667962 .12 -2.02 -1.45

G3668045 g3668045 .24 1.63 1.34

M31591 g3704673 .13 1.97 1.67

BI294910 g3705813 .04 1.83 1.36

AH 01330 g3706248 .13 -1.66 -1.28

AH 02081 g3706915 .08 -1.76 -1.35

G3708538 g3708538 .29 1.87 1.71

G3708830 g3708830 .26 2.40 1.54

G3710429 g3710429 .04 2.10 1.48

G3711566 g3711566 .12 1.62 1.32

AH72274 g3712314 .09 1.92 1.42

G3727230 g3727230 .09 1.63 1.35

G3727318 g3727318 .14 1.79 1.38

AH76957 g3727595 .05 2.12 1.51

AH78367 g3729005 .12 -1.61 -1.49

AH79184 g3729822 .23 -1.96 -1.40

G3729898 g3729898 .36 2.21 1.47

BE117878 g3730830 .07 2.04 1.41

BF282318 g3730930 .90 -1.47 -2.02

G3811572 g3811572 .07 2.42 1.58

BQ206905 g3812156 .02 1.62 1.24

G3812233 g3812233 .13 -1.68 -1.23

G3813551 g3813551 .50 1.87 1.28

BI283128 g3815073 .16 1.93 1.45

NM_175582 g3816235 .45 -2.46 -1.96

AI232356 g3816236 .16 1.77 1.34

AI232402 g3816282 .07 1.70 1.25

CA509598 g3817191 .10 1.68 1.25

AI407821 g3817623 .01 1.93 1.29

G3817759 g3817759 .08 -1.88 -1.35

G3828430 g3828430 .01 1.99 1.40

G3828465 g3828465 .16 2.40 1.71

BI278601 g3829380 .03 1.64 1.32

AI236212 g3829718 .11 1.72 1.33

AI317824 g4033091 .37 -2.14 -1.88

AA800480 g4131501 .35 2.36 1.41

G4132436 g4132436 .00 2.43 1.94

BQ192029 g4133216 .06 1.64 1.27

AH 01250 g4133997 .02 1.73 1.36

AH72271 g4134732 .17 2.01 1.48 AH 77939 g4135031 1.06 1.74 1.30 G807364 g807364 -1.15 1.63 1.28 H32476 g977893 -1.01 1.92 1.34 J03637 AD mRNA -1.14 3.17 1.42 platelet factor

M 15254 4 1.67 2.18 1.39 M 18847 M 18847 1.05 -1.68 -1.30 M23601 Maobf3 -1.06 1.74 1.32 potassium

M26161 channel 1.03 -1.96 -1.34

M26744 IL6 1.14 1.92 1.50

M81785 syndecan 1.06 1.72 1.32

NM_012561 Fst 1.10 1.84 1.65

NMJ312733 Rbp1 -1.00 1.83 1.54

NM_012771 Lyz -1.49 -1.53 -1.69

NM_012908 Tnfsfδ 1.04 -1.64 -1.39

NM_012908 Tnfsfδ 1.02 -1.61 -1.39

NM_013012 Prkg2 1.31 2.03 1.48

NM_013057 F3 1.06 1.65 1.46

NM_013080 Ptprzl -1.11 -1.61 -1.30

NM_013191 S100b 1.04 -1.86 -1.37

NM_016994 C3 -1.74 -1.94 -2.10

NM_017061 Lox -1.22 2.17 1.63

NM_017083 Myo5b 1.82 3.00 1.62

NM_017161 Adora2b 1.07 2.13 1.45

NM_017173 Serpinhl 1.03 1.83 1.32

NM_017210 Dio3 1.97 1.69 2.45

NM_017354 RNU16845 1.05 -2.04 -1.33

NM_019343 Rgs7 1.09 1.87 1.43

NM_019355 CPG2 -1.22 -2.12 -1.24

NM_019358 Gp38 1.05 1.94 1.25

NM_019370 LOC54410 1.02 2.31 1.70

NM_020082 Rnase4 -1.03 1.86 1.43

NM_020542 LOC57301 1.22 1.64 1.39

NM_021698 F13a 1.21 1.64 1.31

NM_022182 Fgf7 1.00 1.79 1.41

NM_022226 Prsd 1.03 1.65 1.24

NM_022230 Stc2 1.07 1.59 1.45

NM_022236 Pde10a -1.02 1.59 1.17

NMJ522849 Crpd -1.07 1.70 1.39

NM_022925 Ptprq 1.29 1.71 1.13

NM_024142 LOC79110 -1.06 -1.60 -1.49

NM_024159 Dab2 1.03 1.82 1.29

NM_030656 Agxt 1.18 1.61 1.24

NM_030832 Fabp7 1.17 2.32 1.70

NM_030990 Plp1 -1.05 -2.33 -1.53

NM_031012 An pep -1.14 1.67 1.35

NM_031022 Cspg4 -1.14 -1.70 -1.23

NM_031050 Lum -1.17 1.97 1.52

NM_031334 Cdh1 -1.32 -2.12 -1.39

NM_031645 Rampl 1.07 1.63 1.21

NM_031712 Pdzkl -1.43 -1.86 -1.62

NM_031713 Pirb -1.68 -1.37 -1.59

NM_031716 Wispl -1.03 1.88 1.43

NM_031736 Slc27a2 -1.07 -1.72 -1.71

NM 031761 Figf -1.03 1.84 1.39 NM_031807 Tpbg 1.04 1.77 1.44 NM_032060 C3ar1 1.20 1.68 1.29 glutathione S- transferase

S72505 Yd subunit 1.72 2.68 1.39 glutathione S- transferase

S72505 Yd subunit 2.01 2.79 1.50 glutathione S- transferase

S72505 Yd subunit 2.02 2.92 1.65 S82820 GSTA5 1.91 2.60 1.46 U04808 Rbs11 -1.18 -1.61 -1.33 cytochrome

U36992 P450 Cyp7b1 -1.22 1.78 1.49 cytochrome

U36992 P450 Cyp7b1 -1.20 1.82 1.57 cytochrome

U36992 P450 Cyp7b1 -1.22 1.84 1.63 U39943 CYP2J3 -1.12 -1.72 -1.40 U53855 ratpgis 1.33 2.53 1.59 U57062 RNKP-4 -2.10 -1.70 -2.07 U65217 U65217 -1.50 -2.21 -1.55 U65656 gelatinase A -1.01 2.05 1.43 U66470 U66470 1.16 2.05 1.41 U75581 A-FABP 1.55 2.22 1.69 U75581 A-FABP 1.60 2.46 1.73 U75581 A-FABP 1.60 2.48 1.79 U81037 NrCAM 1.24 2.20 1.43 U85512 Gchfr 1.41 1.74 1.64 U94330 OPG 1.01 1.66 1.34 X15679 X15679 1.07 -2.00 -1.33 X59859 DCN -1.02 2.43 1.60 X68312 igM -1.19 -2.16 -1.50 X78997 cadherin -1.21 -1.79 -1.35 Z30663 Z30663 1.06 -1.74 -1.36

MatBIII Tumor Model, Compound A-induced Signature, EC-specific Sequences Compound-induced Fold Change in Gene

GenBank Accession Number Gene Symbol Expression

600511261 R1 600511261 R1 1.61

600512030R1 600512030R1 -2.01

600516277R1 600516277R1 1.70

600521787R1 600521787R1 2.45

600521928R1 600521928R1 -1.72

600522339R1 600522339R1 1.72

700031150H1 Hbb -2.93

700031292H1 Hbb -2.95

700033761 H1 700033761 H1 -1.69

700035711H1 700035711H1 -1.77

700036014H1 Hbb -3.21

700037874H1 700037874H1 -2.14

700040546H1 700040546H1 -2.36

700041049H1 700041049H1 -2.47

700509540H1 700509540H1 1.59

701217088H1 701217088H1 1.80

701347811H1 701347811H1 -1.74

AA012768 g1473830 1.72

AA799471 g2862426 3.28

AA799964 g2862919 1.62

AA800145 g2863100 -1.75

AA800690 700036377H1 -3.01

AA800790 g2863745 -2.53

AA801013 g2863968 2.88

AA818163 g2888043 1.78

AA818207 700035764H1 -3.04

AA818804 g2888390 1.81

AA818845 g2888431 2.74

AA819500 -1.68

AA848265 g2935805 1.88

AA848809 g2936349 1.60

AA858479 g2948819 1.65

AA859373 g2948724 2.23

AA874889 g2979837 -2.20

AA874924 g2979872 -1.69

AA892298 g3019177 -1.61

AA900587 g3035941 1.99

AA924082 g3071218 1.59

AA943742 g3103658 -1.76

AA943743 g3103659 -2.53

AA944410 g3104326 -1.74

AA945100 g3105016 -1.60 AA9451 19 Hbb -3.64

AA945677 g3105593 1 .95

AA945951 g4132652 5.93

AA946094 Mb 2.83

AA946457 g4132801 -2.19

AA956834 g3120529 -2.23

AA963068 g3136560 -2.08

AA963366 g3136858 2.43

AA996698 g3187253 -1.67

AA997375 g3187690 1.71

AB011533 MEGF7 -1.70

AC091752 g3071324 1.78

AF009329 SHARP-1 1 .83

AF015304 Slc29a1 1 .69

AF037272 ps20 1 .75

AF055286 3-Oct 1 .80

AF056034 AF056034 2.30

AF058786 JE/MCP-1 -1 .80

AF058786 JE/MCP-1 -1 .76

AF058786 JE/MCP-1 -1 .69

AF063102 CIRL-2 -1 .80

AF109393 podocalyxin -2.34

AF109674 Lgl1 1 .61

AF134409 Rhes protein 2.29

AF146518 Enpep -2.03

AF150082 DDP1 -1.66

AF157005 MYHC 6.94

AF158385 ATP1 B4 2.57

AF159103 Tnfip6 -1.67

AF160978 C1qRp -2.02

AF173834 calpain isoform Rt88' 1.96

AF269251 mob-5 1.97

AF271786 Fgf13 2.06

AF314657 clusterin 2.13

AF323174 Clicδ 2.57

AF364071 Smpx 2.64

AF372834 g4135229 1.63

AF404762 g3704880 1.67

AF450248 Actn3 3.96

AI008526 g3222358 -2.88

AI009020 600518256R1 1.61

AI009669 g3223501 -1.61

AI01 1757 g3225589 -1.62

AI013912 g3227968 -1.72

AI029383 g3247209 3.23

AI030556 g3248382 1.77

AI043880 g3290615 1.76 AI044257 g3291160 1.99 AI044658 g3291519 2.38 AI044948 g3291767 -1.94 AI045276 g3292095 -2.89 AI058243 700034477H1 -1.69 AI059662 g3333439 1.98 AI070419 g3396670 -1.65 AI071230 g3397445 1.80 AI071570 600520320R1 2.07 AI072669 g3398863 1.78 AI072687 g3398881 1.64 AI072733 g3398927 1.68 AI072751 g3398945 -1.70 AH02560 g3707304 -2.36 AH04898 g3708043 2.57 AH04955 g3709178 2.22 AH 13026 g3512975 -2.36 AH 37425 g3638202 -2.48 AH37674 g3638451 1.79 AH44943 g3666742 1.87 AH 69239 g3705547 -3.08 AH 69311 g3705619 1.78 AH 70840 g3710880 2.19 AH 70948 g3710988 -1.77 AH71466 g3711506 1.87 AH72271 g4134732 -2.04 AH75988 g3726626 3.28 AH76957 g3727595 -2.20 AH77013 g3727651 1.65 AH77057 g4134951 -3.44 AH77392 g3728030 -1.67 AH77951 g3728589 -1.82 AH78376 g4135065 1.60 AH78585 g3729223 -2.30 AH 78996 g3729634 1.59 AI231053 g3814933 -1.91 AI231438 g3815318 1.61 AI233773 Mawbp 1.77 AI235210 g4136063 -4.17 AI235960 g3829466 -1.66 AI236229 g4136175 3.67 AI409186 g2938420 -2.62 AI411737 Hbb -3.37 AI412460 g3704629 -1.65 AI603145 g3707784 2.62 AJ242926 irl685 2.05 AJ426426 600524449R1 1.68 AW253240 700039226H1 -3.10

AW915763 600523193R1 1.65

AW916287 g2980074 -1.71

AY027527 NADPH oxidase 4 -1.66

AY1 15564 g3712131 2.68

BE109616 g2862726 2.56

BE117010 g2949577 -2.03

BF287821 700065626H1 -1.63

BF393825 g3814029 -1.59

BF395396 g3187656 2.88

BF401710 g2863152 1.63

BF419896 600508357R1 -1.67

BF558524 g3333166 1.94

BG373503 g3138384 -1.65

BG374556 700510594H1 1.61

BG378083 g2888538 2.54

BG670348 g3332207 -1.62

BI274062 Trela 2.08

BI277462 g3729596 -1.96

BI279373 g3814946 1.70

BI282277 g2939494 2.23

BI283128 g3815073 -2.27

BI285246 g3830698 -1.81

BI291451 g2889589 -1.78

BI294910 g3705813 -1.88

BI296277 g3705123 -1.67

BM386121 g2862284 -2.23

BM390441 g3707901 -1.67

BQ190196 g3831151 -1.78

BQ191387 g3512957 1.72

BQ194973 g3118966 -1.93

BQ 196248 g2938644 -1.65

BQ 199466 g3712138 -1.67

BQ 199747 g3707262 -1.65

BQ204163 g3291004 4.70

BQ206937 g3816206 1.59

BQ208795 LOC85383 1.75

BQ211970 g3711814 1.84

BQ779790 g3709350 2.08

BU758944 g3729204 -1.62

CA503430 g3818031 -2.01

CA503625 g3726615 -1.97

CA505509 g3020114 2.75

CA507161 g3226571 -1.77

CA508003 g3707933 -1.89

CA509083 g3397522 1.59

CA509145 g3727217 1.93 CA509211 g3704741 -1.60

CA509598 g3817191 2.15

CA509955 g3730145 -1.74

D12520 nitric oxide synthase 1.63

D14051 nitric oxide synthase 1.62

D28561 glucose transporter 2.60

D63164 cyclin E -1.66

D86800 D86800 -1.92

D86800 D86800 -1.85

G2863860 3.31

G2889725 2.55

G2939329 -1.67

G3018718 -1.64

G3018906 -2.03

G3020570 -1.63

G3036209 -1.61

G3072525 3.27

G3072678 2.28

G3073004 -1.77

G3105912 -1.63

G3136659 2.50

G3138335 -2.07

G3187018 -1.69

G3225225 -1.92

G3226067 -2.21

G3226140 5.03

G3226701 2.48

G3227787 -2.28

G3291802 -1.77

G3292543 2.04

G3396388 1.91

G3396690 -1.99

G3396723 1.77

G3397083 1.59

G3397437 -1.72

G3397917 -1.62

G3397969 -2.39

G3398441 -2.39

G3399406 -2.47

G3513002 1.96

G3513248 -2.52

G3636896 -1.94

G3637290 1.97

G3637649 1.60

G3637836 1.69

G3638063 -1.64

G3638106 -1.60 G3638248 -1 .86

G 3666834 -1 .75

G3667558 -1 .64

G3667798 -1 .59

G3708538 -1 .59

G3708698 3.29

G3708830 1 .72

G3708934 1 .61

G3709332 1 .78

G3709581 -1.76

G3710109 -1.87

G3710353 -1.89

G3710419 -1.60

G3710427 -1 .67

G3710782 1.72

G3712041 -1.70

G3712094 3.52

G3712205 1.79

G3712229 1 .68

G3725978 3.71

G3726013 2.02

G3726093 1 .91

G3726475 -3.16

G3727000 1 .91

G3727318 -1 .61

G3811492 -2.18

G3812333 -1.88

G3813207 -1.60

G3817985 -1.66

G4131487 1.95

G4131762 1.84

G4135671 2.78

G977371 1.70

G978154 -1.86

H35065 g980482 3.04

J02582 apoE 1.64

J02585 s-CoA d mRNA 2.04

K00781 g3247405 1.94

L00381 L00381 2.50

L16764 HSP70 1.60

L16764 HSP70 1.70

L16764 HSP70 1.79

L20681 Ets-1 -1.59

M11670 cat mRNA 1.60

M11851 MLC2 mRNA 2.69

M26744 IL6 -2.45

M26744 IL6 -2.38 M26744 IL6 -2.35

M29853 P-450 mRNA 2.02

M29853 P-450 mRNA 2.03

M34097 -1.64

M55149 pap 2.08

M58040 transferrin receptor -1.81

M60616 UMRCase 1.81

NM_012491 Add2 -1.78

NM_012497 Aldoc 1.60

NM_012505 Atp1 a2 3.08

NM_012530 Ckm 2.64

NM_012588 Igfbp3 -3.62

NM_012604 Myh3 2.35

NM_012605 Myl2 2.36

NM_012771 Lyz -1.74

NM_012786 Coxδh 3.99

NM_012812 Cox6a2 2.55

NM_012864 Mmp7 2.08

NM_012949 Eno3 3.06

NM_012966 Hspel -1 .71

NM_013037 111 rl1 -1 .79

NM_013044 Tmod 2.36

NM_013062 Kdr -3.79

NM_013153 Has2 -1 .82

NM_013186 Kcnbl 2.96

NM_013197 Alas2 -2.48

NM_017049 Slc4a3 1 .67

NM_017066 Ptn -1.97

NM_017104 Csf3 1.85

NMJ317115 Myog 2.53

NM_017117 Capn3 2.47

NM_017131 Casq2 1.66

NM_017184 Tnnil 1 .96

NM_017185 Tnni2 3.43

NM_017328 Pgam2 3.97

NM_017333 Etb -2.74

NM_019131 Tpm1 1.97

NM_019212 Actal 3.55

NM_019278 Resp18 1.69

NM_019282 Cktsf1b1 -1.82

NM_019292 Ca3 2.82

NM_019334 Pitx2 2.84

NM_019341 Rgs5 -1.83

NM_021588 Mb 2.44

NM_021593 Kmo -1.62

NM_021666 Trdn 1.64

NM 021693 LOC59329 1.61 NM_022235 Kcne3 -1 1.33

NM_022396 Gng11 -1.80

NM_022604 Pg25 -6.48

NM_022631 Wntδa -1.74

NM_022674 H2afz -1.74

NM_023991 Prkaa2 3.17

NM_024141 Thox2 2.32

NM_030856 Lrrn3 -1.87

NM_031007 Adcy2 1.94

NM_031022 Cspg4 -1 .77

NM_031039 Gpt 1 .70

NM_031511 Igf2 3.83

NM_031531 Spin2c 2.18

NM_031612 Apel -2.36

NM_031715 Pfkm 1 .68

NM_031813 Mybph 1 .84

NM_032063 DII1 -1 .76

NMJD32072 Appbpl -1.71

U22520 IP-10 -2.40

U25281 CR16 1 .60

U25684 U25684 -1 .60

U31935 CAP2 2.53

U94330 OPG -1.68 glutathione

X67654 transferase 1 .69 X81449 g587519 1 .68 X82152 fibromodulin, unnamed 1 .92 X92069 P2X5 1 .86 X98517 Mmp12 1.66

Table. 6

C6 Flank Tumor Model, Compound A

GenBank Accession Number Gene Symbol

600520 86R1

701217994H1

AA945677 g3105593

AA957449 g3121144

AA964264 g3137756

AB015308 Gna15 chemotactic

AF154245 protein-3

AF244366 FLIP short form

AF314657 clusterin

AI010322 g3224154

AI012597 g3226429

AI059363 g3333140

AH 36847 g3637624

AI236799 g4136246

AI454865 g3103424

AW142194 g2864225

BI285246 g3830698

BQ207019 g3730060

G2938456

G2938797

G3021176

G3137780

G3138247

G3225906

G3396115

H32810 g978227

H34187 g979604

L20468 cerebroglycan

NM_012922 Casp3

NM_013085 Plau

NM_017105 Bmp3

NM_031327 Cyr61

NM_080783 600519254R1

U 17604 rS-Rex-b

U 18060 PGHS-1

Y15685 g2648067 C6 Flank Tumor Model, Compound B

GenBank Accession Number Gene Symbol

600520186R1

700510178H1

701217994H1

701419627H1

AA964264 g3137756

AB015308 Gna15

AF075704 Ata1

AF140232 S100A6

AF154245 chemotactic protein-3

AI008035 700068780H1

AI009736 g3223568

AI010322 g3224154

AI012085 g4133563

AI012597 g3226429

AI059363 g3333140

AH 36847 g3637624

AH77939 g4135031

AI228076 g4135309

AI454865 g3103424

AW140657 600510887R1

BE115875 g2864040

BI278601 g3829380

BI285246 g3830698

BI294910 g3705813

BQ192029 g4133216

BQ196623 g3248862

BQ203060 g3221834

D89730 g2429082

G2938081

G2946933

G3072603

G3137780

G3137957

G3138247

G3292531

G3396115

G3397675

G3512937

G3638675

G3666553

G3666899

G3710770

G3726475

G3813551 G3814512

G977854

M81855 Abcbl

NM_012566 Gfi1

NM_019261 Klrc2

NM_022925 Ptprq

NM_031518 Mox2

N M_080783 600519254R 1

U36992 cytochrome P450 Cyp7b1

U60085 CYP3A9

U60085 CYP3A9

U65656 gelatinase A

Y15685 g2648067

MatBIII Tumor Model, Compound A

GenBank Accession Number Gene Symbol

600520186R1

701219674H1

AA800293 g2863248

AA848602 g2936142

AA859467 g2948987

AA945677 g3105593

AA957449 g3121144

AA963106 g3136598

AA996897 g3187452

AF022774 Rph3al

AF248543 iGb3 synthase

AF314657 clusterin

AF368269 Cyp2t1

AI008526 g3222358

AI010322 g3224154

AI012085 g4133563

AI012597 g3226429

AI044404 g3291307

AI044948 g3291767

AI045276 g3292095

AH 69311 g3705619

AH70948 g3710988

AH 76957 g3727595

AI228076 g4135309

AI233773 Mawbp

AI409186 g2938420

AI454865 g3103424

AW142194 g2864225

BI278601 g3829380

BI285246 g3830698

BM388852 g3106350

BM390441 g3707901

BQ196557 g3729556

D16339 g6981681

D16339 Ttpa

D88666 PS-PLA1

G2938797

G3034536

G3226140

G3396115

G3398076

G3399406

G3513248 G3638802

G3666553

G3666899

G3667173

G371 1240

G3725764

G3730626

G3813079

G977371

H32810 g978227

H35065 g980482

NM_012715 Adm

NM_013062 Kdr

NM_021676 Shank3

NM_021751 LOC60357

NM_022242 Niban

NM_022959 P-cip1

NM_031327 Cyr61

NM_031544 Ampd3

NM_031658 Msln

U03388 cyclooxygenase 1

U18771 Rab26

U38419 LOC64305

X63515 phosphorylase

EXAMPLE 6 BIOMARKER VALIDATION In order to confirm that the seven genes we identified as potential biomarkers of tumor endothelial cell proliferation were specifically expressed in tumor vasculature and whose expression levels reflected endothelial cell proliferation rates, we performed several validation experiments. First, we independently assessed gene expression levels in the animal tumor RNA samples by quantitative realtime PCR to confirm the microarray hybridization results. The biomarker data obtained from the microarray experiments described above was validated by real time quantitative real time PCR. Results: Quantitative real time PCR was performed with gene-specific PCR primer pairs and amplicon- specific fluorescent probes (TaqMan). For each RNA sample tested, transcript abundance of GAPDH was determined. In addition, transcript abundance of genes of interest and GAPDH were determined for a calibrator RNA sample (total rat lung RNA). (A) Fold changes in gene expression in tumors from KDR kinase-treated animals relative tumors from vehicle-treated animals were calculated using the ΔΔCT method (see Materials and Methods). mRNA levels for each gene in the rat tumors are also shown relative the calibrator RNA pool (B). As shown in Figure 7, the results obtained from the real time PCR studies closely matched those from the DNA microarrays (Figure 7). We also measured the expression levels of the biomarker genes in an additional set of rat MatBIII tumors from a fourth animal study for which no gene expression profiling was performed. In this independent study, animals with established MatBIII breast tumors (seven days post cell implantation) were dosed orally once per day with Compound A or vehicle for a total of eight days. Half of each tumor from our animal tumor studies was fixed and preserved for sectioning and immunohistochemistry as described in Materials and Methods. In order to determine if expression of the biomarker genes was specific to the endothelial cells within tumors, we visualized their protein products in rat tumor tissue sections by immunofluorescence microscopy. Antibodies are available commercially for five of the seven biomarker protein products and we were able determine optimal conditions for immunofluorescence staining. Individual tumor sections approximately 3-5 um thick were de-waxed, rehydrated and incubated with antibodies against one of the biomarker proteins and also with antibodies against the endothelial cell surface protein CD31 (to label the tumor vasculature). De-waxed, re-hydrated MatBIII tumor sections were incubated with antibodies against CD31 and one of the following biomarker proteins: CLU, ANGPT2, CYR61, ENDRB, or PLAU. Primary antibodies bound to the biomarker proteins and CD31 were visualized with Alexa488-labeled and Alexa546-labeled secondary antibodies, respectively as described in Materials and Methods. After mounting under coverslips, images were captured with a Zeiss Axiocam through a Zeiss Axiovert 135 fluorescence microscope equipped with a 40x objective. Results: We found that the five proteins we examined (ANGPT2, CLU, CYR61, EDNRB, and PLAU) were each localized specifically to the tumor vasculature in MatBIII tumors (Figure 8). Indicating that biomarker protein expression in rat mammary tumors is localized to vasculature. The expression levels of all genes with the exception of Cyrόl changed as expected in response to exposure to the KDR kinase inhibitor. Finally, we correlated the confirmed expression changes of the biomarker genes in Compound A- treated tumors with an independent measure of tumor endothelial cell proliferation. Using a modification of the method described by Mundhenke, et al. (Mundhenke, 2001), we measured endothelial cell proliferation rates by double immunohistochemical staining of tumor sections for the endothelial cell marker CD31 and the nuclear proliferation marker Ki67. We analyzed C6 flank tumors from five vehicle- treated animals and five Compound A-treated animals (3 doses vehicle or compound over 72 hrs). Results: We determined the endothelial cell proliferation rate in tumors from vehicle treated animals to be 34% +/- 5%. In contrast, we determined that the endothelial cell proliferation rate was only 19 % +/- 5% in tumors from animals treated with Compound A. While the present invention has been described with reference to what are considered to be the specific embodiments, it is to be understood that the invention is not limited to such embodiments. To the contrary, the invention is intended to cover various modifications and equivalents included within the spirit and scope of the appended claims. 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Claims

WHAT IS CLAIMED IS:

1. A method for determining the proliferative status of a population of endothelial cells comprising: a) providing an array comprising a substrate having a plurality of addresses, wherein each address has disposed thereon a capture probe or oligonucleotide that can specifically bind an endothelial cell proliferative biomarker; b) preparing a nucleic acid test sample from a population of endothelial cells; c) contacting the nucleic acid sample with the array; and d) determining an expression profile by detecting binding of the nucleic acids in the test sample to each address of the plurarity of addresses present on the array, thereby determining the proliferative rate of the endothelial cells.

2. The method of claim 1 wherein the array comprises oligonucleotides that specifically binds one or more genes selected from the gene sequences set forth in Table 3 or Table 4.

3. The method of claim 2 wherein the array comprises oligonucleotides that specifically binds to Angpt-2, Clu (ApoJ), Cyrόl (CCNl), Endrb (Etb), Ifit-3 (Garg49), Fut-4, Plau (uPA) genes in combination with other biomarkers selected from the genes identified in Tables 3 through 6.

4. The method of claim 1 wherein the nucleic acid sample is prepared from a population of vascular endothelial cells obtained from a tumor biopsy.

5. The method of claim 4 wherein the sample is prepared from a cancer patient receiving treatmentwith a therapeutic agent intended to inhibit the proliferation of endothelial cells in tumor vasculature.

6. The method of claim 5 wherein the patient is being treated with a KDR kinase inhibitor.

7. The method of claim 6 wherein the patient is being treated with Compound A.

8. A method for screening a plurality of therapeutic agents for anti-angiogenic activity comprising: contacting a compound with a population of cells containing a polynucleotide comprising a nucleic acid sequence selected from the group consisting of the biomarkers identified in Tables 4 and Table 5 under conditions wherein said polynucleotide is being expressed, and determining a change in expression of an endothelial cell proliferation signature, wherein a change in expression is indicative of anti-angiogenic activity.

9. The method of claim 8 wherein the population of cells is isolated from a tumor biopsy of a cancer patient who is being treated with a therapeutic agent intended to inhibit the proliferation of endothelial cells in tumor vasculature.

10. The method according to claim 10 wherein the therapeutic agent is a receptor-type kinase inhibitor.

11. The method of claim 8 wherein the change in of the endothelial cell expression signature is determined by hybridization to a microarray comprising oligonucleotide that can specifically bind an endothelial cell proliferative biomarker or by RT-PCR.

12. The method of claim 11 wherein the endothelial cell proliferation signature comprises capture probes or oligonucleotides that specifically binds to Angpt-2, Clu (ApoJ), Cyrόl (CCNl), Endrb (Etb), Ifit-3 (Garg49), Fut-4, Plau (uPA) genes in combination with other biomarkers selected from the genes identified in Table 5 or Table 6.

13. An array comprising a substrate having a plurality of addresses, wherein each address has disposed thereon a capture probe or oligonucleotide that can specifically bind a polynucleotide sequence of a biomarker gene seleceted from the group consisting of the genes comprising a proliferation signature defined in Table 3 and 4.

14. A composition comprising the biomarker genes comprising the proliferation signatures set forth in Table 3 or Table 4.

15. A composition comprising the biomarker genes comprising the expression signatures set forth in Table 5 or Table 6.

16. An endothelial cell proliferation signature comprising Angpt-2, Clu (ApoJ), Cyrόl (CCNl), Endrb (Etb), Ifit-3 (Garg49), Fut-4, and Plau (uPA) genes.