AU2014200166B2 - Differentiation of human embryonic stem cells - Google Patents

Abstract

The present invention provides methods to promote the differentiation of pluripotent stem cells. In particular, the present invention provides an improved method for the formation of pancreatic endoderm, pancreatic hormone expressing cells and pancreatic hormone secreting cells. The present invention also provides methods to promote the differentiation of pluripotent stem cells without the use of a feeder cell layer.

Description

DIFFERENTIATION OF HUMAN EMBRYONIC STEM CELLS FIELD OF THE INVENTION [0001] The present invention provides methods to promote the differentiation of pluripotent stem cells. In particular, the present invention provides an improved method for the formation of pancreatic endoderm, pancreatic hormone expressing cells and pancreatic hormone secreting cells. The present invention also provides methods to promote the differentiation of pluripotent stem cells without the use of a feeder cell layer. BACKGROUND [0002] Advances in cell-replacement therapy for Type I diabetes mellitus and a shortage of transplantable islets of Langerhans have focused interest on developing sources of insulin-producing cells, or P cells, appropriate for engraftment. One approach is the generation of functional p cells from pluripotent stem cells, such as, for example, embryonic stem cells. 100031 In vertebrate embryonic development, a pluripotent cell gives rise to a group of cells comprising three germ layers (ectoderm, mesoderm, and endoderm) in a process known as gastrulation. Tissues such as, for example, thyroid, thymus, pancreas, gut, and liver, will develop from the endoderm, via an intermediate stage. The intermediate stage in this process is the formation of definitive endoderm. Definitive endoderm cells express a number of markers, such as, HNF-3beta, GATA4, Mixll, CXCR4 and Sox-17. [00041 Formation of the pancreas arises from the differentiation of definitive endoderm into pancreatic endoderm. Cells of the pancreatic endoderm express the pancreatic-duodenal homeobox gene, Pdxl. In the absence of Pdx 1, the pancreas fails to develop beyond the formation of ventral and dorsal buds. Thus, Pdx 1 expression marks a critical step in pancreatic organogenesis. The mature pancreas contains, among other cell types, exocrine tissue and

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endocrine tissue. Exocrine and endocrine tissues arise from the differentiation of pancreatic endoderm. [00051 Cells bearing the features of islet cells have reportedly been derived from embryonic cells of the mouse. For example, Lumelsky et al. (Science 292:1389, 2001) report differentiation of mouse embryonic stem cells to insulin-secreting structures similar to pancreatic islets. Soria et al. (Diabetes 49:157, 2000) report that insulin-secreting cells derived from mouse embryonic stem cells normalize glycemia in streptozotocin-induced diabetic mice. [00061 In one example, Hori et al. (PNAS 99: 16105, 2002) disclose that treatment of mouse embryonic stem cells with inhibitors of phosphoinositide 3-kinase (LY294002) produced cells that resembled P cells. 100071 In another example, Blyszczuk et al. (PNAS 100:998, 2003) reports the generation of insulin-producing cells from mouse embryonic stem cells constitutively expressing Pax4. 100081 Micallef et al. reports that retinoic acid can regulate the commitment of embryonic stem cells to form Pdx 1 positive pancreatic endoderm. Retinoic acid is most effective at inducing Pdx I expression when added to cultures at day 4 of embryonic stem cell differentiation during a period corresponding to the end of gastrulation in the embryo (Diabetes 54:301, 2005). 100091 Miyazaki et al. reports a mouse embryonic stem cell line over-expressing Pdx 1. Their results show that exogenous Pdx I expression clearly enhanced the expression of insulin, somatostatin, glucokinase, neurogenin3, P48, Pax6, and HNF6 genes in the resulting differentiated cells (Diabetes 53: 1030, 2004). [0010] Skoudy et al. reports that activin A (a member of the TGFO superfamily) up regulates the expression of exocrine pancreatic genes (p48 and amylase) and endocrine genes (Pdx 1, insulin, and glucagon) in mouse embryonic stem cells. 2 The maximal effect was observed using InM activin A. They also observed that the expression level of insulin and Pdxl mRNA was not affected by retinoic acid; however, 3nM FGF7 treatment resulted in an increased level of the transcript for PdxI (Biochem. J. 379: 749, 2004). [00111 Shiraki et al. studied the effects of growth factors that specifically enhance differentiation of embryonic stem cells into Pdxl positive cells. They observed that TGFP2 reproducibly yielded a higher proportion of PdxI positive cells (Genes Cells. 2005 Jun; 10(6): 503-16.). [00121 Gordon et al. demonstrated the induction of brachyury+/HNF-3beta+ endoderm cells from mouse embryonic stem cells in the absence of serum and in the presence of activin along with an inhibitor of Wnt signaling (US 2006/0003446A 1). 100131 Gordon et al. (PNAS, Vol 103, page 16806, 2006) states "Wnt and TGF-beta/ nodal/ activin signaling simultaneously were required for the generation of the anterior primitive streak". [00141 However, the mouse model of embryonic stem cell development may not exactly mimic the developmental program in higher mammals, such as, for example, humans. [00151 Thomson el al. isolated embryonic stem cells from human blastocysts (Science 282:114, 1998). Concurrently, Gearhart and coworkers derived human embryonic germ (hEG) cell lines from fetal gonadal tissue (Shamblott et al., Proc. Natl. Acad. Sci. USA 95:13726, 1998). Unlike mouse embryonic stem cells, which can be prevented from differentiating simply by culturing with Leukemia Inhibitory Factor (LIF), human embryonic stem cells must be maintained under very special conditions (U.S. Pat. No. 6,200,806; WO 99/20741; WO 01/51616). [00161 D'Amour et al. describes the production of enriched cultures of human embryonic stem cell-derived definitive endoderm in the presence of a high 3 concentration of activin and low serum (D'Arnour KA et a. 2005). Transplanting these cells under the kidney capsule of mice resulted in differentiation into more mature cells with characteristics of some endodermal organs. Human embryonic stem cell-derived definitive endoderm cells can be further differentiated into Pdxl positive cells after addition of FGF-10 (US 2005/0266554A1), [0017] D'Amour et aL. (Nature Biotechnology - 24, 1392 - 1401 (2006)) states "We have developed a differentiation process that converts human embryonic stem (hES) cells to endocrine cells capable of synthesizing the pancreatic hormones insulin, glucagon, somatostatin, pancreatic polypeptide and ghrelin. This process mimics in vivo pancreatic organogenesis by directing cells through stages resembling definitive endoderm, gut-tube endoderm, pancreatic endoderm and endocrine precursor en route to cells that express endocrine hormones". [0018] In another example, Fisk et al reports a system for producing pancreatic islet cells from human embryonic stem cells (US2006/0040387A 1). In this case, the differentiation pathway was divided into three stages. Human embryonic stem cells were lust differentiated to endoderm using a combination of n butyrate and activin A. The cells were then cultured with TGFP antagonists such as Noggin in combination with EGF or betacellulin to generate Pdxl positive cells. The terminal differentiation was induced by nicotinamide. [0019] In one example, Benvenistry et al. states: "We conclude that over-expression of Pdxl enhanced expression of pancreatic enriched genes, induction of insulin expression may require additional signals that are only present in vivo" (Benvenistry et a, Stem Cells 2006; 24:1923-1930). [0020] Therefore, there still remains a significant need to develop conditions for establishing pluripotent stem cell lines that can be expanded to address the current clinical needs, while retaining the potential to differentiate into pancreatic endocrine cells, pancreatic hormone expressing cells, or pancreatic hormone secreting cells. An alternative approach to improve 4 2566195vi the efficiency of differentiating human embryonic stem cells toward pancreatic endocrine cells was taken. 5 2566195vi SUMMARY [00211 In one embodiment, the present invention provides a method for differentiating pluripotent stem cells, comprising the steps of: a. Culturing the pluripotent stem cells, and b. Differentiating the pluripotent stem cells into cells expressing markers characteristics of the definitive endoderm lineage, c. Differentiating the cells expressing markers characteristics of the definitive endoderm lineage into cells expressing markers characteristics of the pancreatic endoderm lineage, and d. Differentiating the cells expressing markers characteristics of the pancreatic endoderm lineage into cells expressing markers characteristics of the pancreatic endocrine lineage. [00221 In one embodiment, cells expressing markers characteristic of the definitive endoderm lineage are differentiated from pluripotent stem cells by treating pluripotent stem cells by any one of the following methods: a. Culturing the pluripotent stem cells in medium containing activin A in the absence of serum, then culturing the cells with activin A and serum, and then culturing the cells with activin A and serum of a different concentration, or b. Culturing the pluripotent stem cells in medium containing activin A in the absence of serum, then culturing the cells with activin A with serum of another concentration, or c. Culturing the pluripotent stem cells in medium containing activin A and a Wnt ligand in the absence of serum, then removing the Wnt ligand and culturing the cells with activin A with serum, or d. Culturing the pluripotent stem cells on a tissue culture substrate coated with an extracellular matrix, and culturing the pluripotent stem cells with activin A and a Wnt ligand, or 6 e. Culturing the pluripotent stem cells on a tissue culture substrate coated with an extracellular matrix, then culturing the pluripotent stem cells with activin A and a Wnt ligand in a first culture medium containing serum, then culturing the pluripotent stem cells with activin A in a second culture medium containing serum, or f. Culturing the pluripotent stem cells on a tissue culture substrate coated with an extracellular matrix, then culturing the pluripotent stem cells with activin A and a Wnt ligand in a first culture medium containing serum, then culturing the pluripotent stem cells with activin A and a Wnt ligand in a second culture medium containing serum of a different concentration. [0023] In one embodiment, cells expressing markers characteristic of the pancreatic endoderm lineage are differentiated from cells expressing markers characteristic of the definitive endoderm lineage by treating cells expressing markers characteristic of the definitive endoderm lineage by any one of the following methods: a. Treating the cells expressing markers characteristic of the definitive endoderm lineage with a fibroblast growth factor and a hedgehog signaling pathway inhibitor, then removing the medium containing the fibroblast growth factor and the hedgehog signaling pathway inhibitor and subsequently culturing the cells in medium containing retinoic acid, a fibroblast growth factor and the hedgehog signaling pathway inhibitor, or b. Treating the cells expressing markers characteristic of the definitive endoderm lineage with retinoic acid and at least one fibroblast growth factor, or c. Treating the cells expressing markers characteristic of the definitive endoderm lineage with retinoic acid, then removing the retinoic acid and subsequently treating the cells with at least one fibroblast growth factor. 7 [00241 In one embodiment, cells expressing markers characteristic of the pancreatic endocrine lineage are differentiated from cells expressing markers characteristic of the pancreatic endoderm lineage by treating cells expressing markers characteristic of the pancreatic endoderm lineage by any one of the following methods: a. Culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing DAPT and exendin 4, then removing the medium containing DAPT and exendin 4 and subsequently culturing the cells in medium containing exendin 1, IGF-1 and HGF, or b. Culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing exendin 4, then removing the medium containing exendin 4 and subsequently culturing the cells in medium containing exendin 1, IGF- I and HGF, or c. Culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing DAPT and exendin 4, or d. Culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing exendin 4, or e. Treating the cells expressing markers characteristic of the pancreatic endoderm lineage with a factor that inhibits the Notch signaling pathway. 100251 In one embodiment, the present invention provides a method for treating a patient suffering from diabetes, comprising the steps of: a. Culturing pluripotent stem cells, b. Differentiating the pluripotent stem cells into cells expressing markers characteristics of the definitive endoderm lineage, 8 c. Differentiating the cells expressing markers characteristics of the definitive endoderm lineage into cells expressing markers characteristics of the pancreatic endoderm lineage, d. Differentiating the cells expressing markers characteristics of the pancreatic endoderm lineage into cells of a p-cell lineage, and e. Implanting the cells of a p-cell lineage into the patient. BRIEF DESCRIPTION OF THE DRAWINGS [0026] Figure 1 panel a shows the expression of the definitive endoderm markers CXCR4, GATA4, HNF-3beta, Mixl1, Sox-17 in the human embryonic stem cell line H9 following treatment with 1OOng/ml activin A for two, five and eight days. Expression of definitive endoderm markers was assayed at the mRNA level and normalized to expression levels in untreated human embryonic stem cells. Panel b shows the expression of the anterior endoderm markers Cerberus, Otx-I and Hex genes in the human embryonic stem cell line H9 following treatment with with 1OOng/ml activin A for three and five days. [0027] Figure 2 shows the expression of definitive endoderm markers in the human embryonic stem cell line H.9 following treatment with 100ng/mil activin A for five days. Expression of the definitive endoderm markers was detected by immunohistochemistiy. Panel (a) shows Sox-17 expression. Panel (b) shows HNF-3beta expression. Panel (c) shows Oct3/4 expression. 100281 Figure 3 shows the expression of definitive endoderm markers in the human embryonic stem cell line H9 following a step-wise differentiation protocol. Expression of the definitive endoderm markers was assayed at the mRNA level and normalized to expression levels in untreated human embryonic stem cells. Panel (a) shows GATA4 expression. Panel (b) shows Sox-17 expression. Panel (c) shows HNF-3beta expression. Panel (d) shows Mixll expression. Data points marked 'AA' denote activin A treatment for one (1d), 9 three (3d), five (5d), or seven days (7d). Data points marked 'UT' denote untreated controls cultured for one (ld), three (3d), five (5d), or seven days (7d). [00291 Figure 4 shows the expression of extra-embryonic endoderm markers in the human embryonic stem cell line H9 following a step-wise differentiation protocol. Expression of the extraembryonic endoderm markers was assayed at the mRNA level and normalized to expression levels in untreated human embryonic stem cells. Panel (a) shows the effect of 100 ng/ml activin A on AFP expression. Panel (b) shows the effect of 100 ng/ml activin A on Sox7 expression. Data points marked 'AA' denote activin A treatment for one (Id), three (3d), five (5d), or seven days (7d). Data points marked 'UT' denote untreated controls cultured for one (ld), three (3d), five (5d), or seven days (7d). [00301 Figure 5 shows the expression of mesoderm and ectoderm markers in the human embryonic stem cell line H9 following a step-wise differentiation protocol. Expression of the mesoderm and ectoderm markers was assayed at the mRNA level and normalized to expression levels in untreated human embryonic stem cells. Panel (a) shows the effect of 100 ng/ml activin A on Brachyury expression. Panel (b) shows the effect of 100 ng/ml activin A on Zic 1 expression. Data points marked 'AA' denote activin A treatment for one (1d), three (3d), five (5d), or seven days (7d). Data points marked 'UT' denote untreated controls cultured for one (ld), three (3d), five (5d), or seven days (7d). [00311 Figure 6 shows the expression of the definitive endoderm markers Brachyury (panel a) CXCR4 (panel b), Mixil (panel c), Sox17 (panel d), HNF-3beta (panel e), Oct4 (panel f) in the human embryonic stem cell line H7 following treatment with 1OOng/mI activin A for one, three, five and seven days. Expression of definitive endoderm markers was assayed at the mRNA level and normalized to expression levels in untreated human embryonic stem cells. 10 [00321 Figure 7 shows the expression of definitive endoderm markers in the human embryonic stem cell line H9 following application of a differentiation protocol. Expression of the definitive endoderm markers was detected by immunohistochemistry. Panels (a) and (b) show Sox-17 expression. Panels (c) and (d) show HNF-3beta expression. Panels (e) and (f) show GATA4 expression. Panels (b), (d) and (f) show counter staining of the nuclei with DAPI. The columns marked 'treated' denote activin A treatment (100ng/ml) for five days. The columns marked 'untreated' denote untreated controls. [00331 Figure 8 shows the expression of pancreatic endoderm markers in the human embryonic stem cell line H9 following application of a second differentiation protocol. Expression of the pancreatic endoderm markers was assayed by PCR and normalized to expression levels in activin A treated human embryonic stem cells. Panel (a) shows Pdxl expression. Panel (b) shows GLUT-2 expression. Panel (c) shows PTF 1 a expression. 100341 Figure 9 shows the expression of pancreatic endoderm markers in the human embryonic stem cell line H9 following application of a second differentiation protocol. Expression of the pancreatic endoderm markers was detected by immunohistochemistry. Panel (a) shows Pdx1 expression in the untreated control, and panel (b) shows Pdxl expression in the culture treated by the step wise differentiation protocol. [00351 Figure 10 shows the expression of pancreatic endocrine markers in the human embryonic stem cell line H9 following application of a third differentiation protocol. Expression of the pancreatic endocrine markers was assayed by PCR and normalized to expression levels in activin A treated human embryonic stem cells. Panel (a) shows NeuroDI expression. Panel (b) shows Ngn3 expression. Panel (c) shows insulin expression. Panel (d) shows Hes- I expression, the expression level is normalized to pancreatic endoderm cells. [0036] Figure 11 shows the expression of pancreatic endoderm markers in the human embryonic stem cell line H9 following application of a differentiation protocol. Expression of the pancreatic endoderm markers was assayed by 11 PCR and normalized to expression levels in activin A treated human embryonic stem cells. Panel (a) shows Nkx2.2 expression. Panel (b) shows Pdx I expression. [0037] Figure 12 shows the expression of PDX- 1 in cells with each passage (PO, P1 and P2) in culture. Expression of the PDX-1 was assayed by PCR and normalized to expression levels in activin A treated human embryonic stem cells H9. [0038] Figure 13 shows the expression of hepatocyte markers in the human embryonic stem cell line H9 following application of a third differentiation protocol. Expression of the hepatocyte markers was assayed by PCR and normalized to expression levels in activin A treated human embryonic stem cells. Panel (a) shows AFP expression. Panel (b) shows albumin expression. [00391 Figure 14 shows the expression of markers of pluripotency in the human embryonic stem cell line H9. Expression of the markers of pluripotency was assayed by immunohistochemistry. Panel (a) shows Oct-4 expression. Panel (b) shows alkaline phosphatase expression. 100401 Figure 15 shows the karyotype of the human embryonic cell line H9. The Karyotype was determined on cells at passage number P36 that were cultured on mouse embryonic fibroblast feeder cells. [00411 Figure 16 depicts the outline of a differentiation protocol in this invention, where human embryonic stem cells are differentiated into definitive endoderm in a feeder free system. [00421 Figure 17 depicts the FACS profile of human embryonic stem cell line H9 at passage number 44, cultured on varying concentrations of MATRIGEL and exposed to (0.5-2%) low serum and high activin A (100 ng/ml) for 5 days. The expression of definite endoderm marker CXCR4 (CD 184) is shown on the Y-axis and the expression of ES marker CD9 is shown on the X-axis. 12 [0043] Figure 18 shows the real-time PCR results for markers of definitive endoderm, from cultures of the human embryonic stem cell line H9 at passage 44 cultured on a 1:10 dilution of MATRIGEL (M), a 1:20 dilution of MATRIGEL (0), or a 1:30 dilution of MATRIGEL (0) and exposed to the differentiation protocol disclosed in Example 14. The fold induction is relative to undifferentiated cells of the human embryonic stem cell line H9, at passage number 44, cultured in medium conditioned using mouse embryonic fibroblasts. [00441 Figure 19 shows the scatter plots for global gene expression in undifferentiated pluripotent stem cells and definitive endoderm cells obtained from differentiating pluripotent stem cells. Data shown is from cultures of the human embryonic stem cell line H.9 cell line at passage 44 cultured on mouse embryonic fibroblasts (right panel) and passage 83 cultured on MATRIGEL (left panel). 10045] Figure 20 depicts the expression of CXCR4 by FACS at day 5 for the human embryonic stem cell line H I (panel a), the human embryonic stem cell line H7 (panel b), and the human embryonic stem cell line H9 (panel c) cultured on mouse embryonic fibroblast feeder cells exposed to the definitive endoderm differentiation protocol disclosed in Example 4. [00461 Figure 21 shows the real-time PCR results of expression of the indicated definitive endoderm markers in cultures of the human embryonic stem cell line H7 (panel a) and the human embryonic stem cell line H9 (panel b) cultured on mouse embryonic fibroblast feeder cells. Results are expressed as fold increase over undifferentiated cells. [00471 Figure 22 depicts the expression of CXCR4 by FACS at day 5 for the human embryonic stem cell line H I (panel a), the human embryonic stem cell line H7 (panel b), and the human embryonic stem cell line H9 (panel c) cultured on MATRIGEL (1:30 dilution) and exposed to the definitive endoderm differentiation protocol disclosed in Example 4. 13 [00481 Figure 23 shows the real-time PCR results of the expression of the indicated definitive endoderm markers in cultures of the human embryonic stem cell line H7 (panel a) and the human embryonic stem cell line H9 (panel b) and the human embryonic stem cell line HI (panel c). Results are expressed as fold increase over undifferentiated cells. Cells were treated according to the methods disclosed in Example 4. [0049] Figure 24 depicts phase contrast images of cultures of the human embryonic stem cell line H9 at passage 46 in the presence of 100 ng/ml of activin A (panel a) or 100 ng/ml of activin A + 20 ng/ml Wnt-3a (panel b). Cells were treated for five days. [0050] Figure 25 depicts the expression of CXCR4 by FACS in cultures of the human embryonic stem cell line H7 at passage 44 (panels a & b) and H9 at passage 46 (panels c & d), following treatment according to the methods disclosed in Example 4. Panels b and d show the effect of 20 ng/ml of Wnt-3a on CXCR4 expression. Panels a and c show CXCR4expression in the absence of Wnt-3a. Results were obtained 5 days post treatment. [00511 Figure 26 displays the real-time PCR data for expression of the genes indicated in cultures of the human embryonic stem cell line H7 (panel a) and H9 (panel b). Cultures were treated with the differentiation protocol disclosed in Example 4. The effects of Wnt agonists Wnt-3a (20 ng/ml), Wnt-5a (20 ng/ml) and Wnt-7a (20 ng/ml) were also tested, as indicated in the panels. Cells were treated for 5 days. Results are expressed as fold increase over undifferentiated cells. [00521 Figure 27 depicts the expression of CXCR4 in cultures of the human embryonic stem cell line H9 at passage 46, by FACS at five days post treatment. Panel (a) depicts CXCR4 expression in the absence of Wnt-3a. Panel (b) depicts CXCR4 expression following treatment with 10 ng/ml Wnt 3a. Panel (c) depicts CXCR4 expression following treatment with 20 ng/ml Wnt-3a, and panel (d) depicts CXCR4 expression following treatment with 50 ng/ml Wnt-3a. 14 [00531 Figure 28 depicts the expression of definitive markers indicated in cultures of the human embryonic stem cell line H9 after 5 days of treatment. Results are shown as fold increase in expression over untreated cells, as determined by real-time PCR. Panel (a) shows the effect of 10, 20 and 50 ng/ml Wnt-3a on the expression of definitive endoderm marker genes indicated. Panel (b) shows the effect of 1, 5 or 10 ng/ml Wnt-3a (x-axis labels: 10, 5, 1)on the expression on goosecoid (0) and CXCR4 (D) expression, at 2 (2d) and 5 (5d)days post treatment. Panel (c) shows the effect of 1, 5 or 10 ng/ml Wnt-3a on cell number, at 2 days (D) or 5 days (M). [00541 Figure 29 depicts the expression of CXCR4 in cultures of the human embryonic stem cell line H9 by FACS, following a 5 day treatment with the differentiation protocol disclosed in Example 4. Cells were cultured in the absence of Wnt-3a or GSK-3B inhibitor (panel a), 20 ng/ml Wnt-3a for the entire 5 day period (panel b), 1000 nM GSK-3B inhibitor IX for the entire 5 day period (panel c), 500 nM GSK-3B inhibitor IX for the entire 5 day period (panel d), 100 nM GSK-3B inhibitor IX for the entire 5 day period (panel e), 10 nM GSK-3B inhibitor IX for the entire 5 day period (panel f), 100 nM GSK-3B inhibitor IX for days 1-2 (panel g), 10 nM GSK-3B inhibitor IX for days 1-2 (panel h). [0055] Figure 30 depicts the gene expression of definitive endoderm markers by real time PCR. Results are expressed as fold increase over untreated cells. Panel (a) shows data obtained from the human embryonic cell line H9 at passage number 48, treated to the definitive endoderm protocol disclosed in Example 4, containing the Wnt-3a or GSK-3B inhibitor at the concentrations and the times indicated. Panel (b) shows data obtained from the human embryonic cell line H:9 at passage number 46, treated to the definitive endoderm protocol disclosed in Example 4, containing the Wnt-3a or GSK-3B inhibitor at the concentrations and the times indicated. 100561 Figure 31 depicts the expression of CXCR4 by FACS for embryonic stem cell lines used in the present invention. Panels (a-d) show data obtained from the 15 human embryonic stem cell line H9 at passage number 49. Panels (e-f) show data obtained from the human embryonic stem cell line Hl at passage number 46. Data was obtained 5 days post treatment. Cells were treated with the following conditions: Panel (a): 10 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3a for the first two days; panel (b): 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3a for the first two days; panel (c): 100 ng/ml activin A for all five days plus 100 nM of GSK-3B inhibitor IX for the first two days; panel (d): 10 ng/ml activin A for all five days plus 100 nM GSK-3B IX inhibitor for the first two days, panel (e): 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3a for the first two days, and panel (f):10 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3a for the first two days. 100571 Figure 32 depicts the gene expression of definitive endoderm markers, as determined by real-time PCR for cultures of the human embryonic stem cell line H9 at passage 49, treated with 10, 50, or 100 ng/ml of activin A plus 20 ng/ml of Wnt-3a: panel (a): expression of AFP, Bry, CXCR4, GSC, HNF-3B, and POU5F (Oct-4) and panel (b): SOX- 17 and GATA4. Results are expressed as fold increase over untreated cells. [0058] Figure 33 depicts the expression of CXCR4 by FACS for the embryonic stem cell line H9 at passage 53. Data was obtained 5 days post treatment. Cells were treated with the following conditions: Panel (a): 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3a for the first two days and 25 ng/ml BMP-4 for days 3-5; panel (b): 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3a for the first two days; panel (c): 100 ng/ml activin A for all five days plus 100 nM of GSK-3B inhibitor IX for the first two days; panel (d): 20 ng/ml Wnt-3a + 25 ng/ml BMP-4 for all five days; panel (e): 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3a + 100 nm GSK-3B inhibitor IX for the first two days, and panel (f): 100 ng/ml activin A + 25 ng/ml BMP-4 for all five days. For all the panels, the X-axis represents expression of CD9 and the Y-axis represents expression of CXCR4 (CD 184). 16 [00591 Figure 34 depicts the gene expression of definitive endoderm markers, as determined by real-time PCR for cultures of the human embryonic stem cell line HI at passage 46, treated with 10 or 100 ng/ml of activin A plus 20 ng/ml of Wnt-3a or 100 NM GSK-3B inhibitor: panel (a): expression of AFP, Bry, CXCR4, GSC, and POU5F (Oct-4) and panel (b): SOX-17, HNF-3B, and GATA4. Results are expressed as fold increase over untreated cells. [00601 Figure 35 depicts the gene expression of definitive endoderm markers, as determined by real-time PCR for cultures of the human embryonic stem cell line H9 at passage 49, treated with 50 or 100 ng/ml of activin A plus 10 or 100 nM GSK-3B inhibitor: panel (a): expression of AFP, Bry, CXCR4, GSC, HNF-3:B, and POU5F (Oct-4) and panel (b): SOX-1 7 and GATA4. Results are expressed as fold increase over untreated cells. [0061] Figure 36 depicts the gene expression of definitive endoderm markers, as determined by real-time PCR for cultures of the human embryonic stem cell line H9 at passage 53, treated with combinations of activin A, Wnt-3a, GSK-3 inhibitor, and BMP-4, for five days: panel (a): expression of AFP, Bry, CXCR4, GSC, HNF-3B, and SOX7 and panel (b): SOX-17, HNF-3B and GATA4. [00621 Figure 37 depicts the percentage of CXCR4 expression, determined by FACS, in cultures of the human embryonic stem cell line H9, treated with the conditions listed in Example 22. [00631 Figure 38 depicts the expression of definitive endoderm markers as determined by FACS in cultures of the human embryonic stem cell line H9, cultured on fibronectin (panel a) or MATRIGELTm (panel b). [0064] Figure 39 depicts the expression of definitive endoderm markers as determined by real-time PCR in cultures of the human embryonic stem cell line H9, cultured on fibronectin (EI) or a 1:10 dilution of growth factor reduced MATRIGEL (0). 17 [00651 Figure 40 depicts the effect of various concentrations of MATRIGEL in the presence of low serum, 100 ng/ml of activin A and 20 ng/ml of Wnt-3a on differentiating human embryonic stem cells into definitive endoderm. Cells were treated according to the methods disclosed in Example 4. Results shown are the expression levels of the genes indicated, as determined by real-time PCR. [0066] Figure 41 depicts the role of Wnt-3a in definitive endoderm formation by human embryonic stem cells maintained on MATRIGEL, but differentiated on mouse embryonic fibroblasts. Panels (a-d) show real-time PCR data for the genes indicated. Panels (e-g) show FACS data for the conditions indicated. [00671 Figure 42 shows the differentiation of human embryonic stem cells cultured on tissue culture substrate coated with MATRIGEL'rM to definitive endoderm following treatment with the Wnt Inhibitor DKK-1. Results shown are the expression of the genes indicated, as determined by real-time PCR in H9 cells treated according to the methods disclosed in Example 4 in the presence of 20 ng/ml of Wnt-3A plus 100 ng/ml of DKK1 (DE + DKKl), or in the absence of DKK1 (DE). [00681 Figure 43 shows immunofluoresence staining of definitive endoderm markers in cultures of the human embryonic stem cell line H:9 cultured on tissue culture substrate coated with MATRIGEL and differentiated in low serum plus 100 ng/ml of activin-A without (panel a), or with (panel b) 20 ng/ml of Wnt 3a. Ecad = E-cadherin, NCAM=N-cadherin, [00691 Figure 44 shows the differentiation of the human embryonic stem cell line SA002 at passage 38 into definitive endoderm. Cells were treated for five days with the conditions indicated and gene expression was determined by real-time PCR, for the genes indicated in the panels. 100701 Figure 45 shows the expression of CXCR4 by FACS in the human embryonic stem cell line SA002 at passage 38, following treatment with 100 ng/ml activin A treatment (panel a), 100 ng/ml activin A + 20 ng/ml Wnt-3a (panel 18 b), or 100 ng/ml activin A + 100 nM GSK-3B inhibitor IX (panel c). Cells were treated for five days. [00711 Figure 46 shows the differentiation of the human embryonic stem cell line HI at passage 55 into definitive endoderm on tissue culture substrate coated with human serum. Cells were treated with the conditions indicated and gene expression was determined by real-time PCR, for the genes indicated in the panels. [0072] Figure 47 shows the differentiation of cultures of the human embryonic stem cell line HI at P54, on tissue culture substrate coated with MATRIGELTM to definitive endoderm. The effects of various GSK-B inhibitors were tested following a five-day DE protocol. The following GSK-3B inhibitors were evaluated at 100 nM for the first two days of treatment: GSK-3B VIII, IX, XI, and XII. [00731 Figure 48 shows the expression of AFP (panel a), Pdx-I (panel b), Cdx-2 and Glut-2 (panel c) and HNF-3beta, HNF-6 and somatostatin (panel d) in cultures of the human embryonic stem cell line H9 at passage 49, cultured and treated according to the methods disclosed in Example 4 in the presence of 20 ng/ml of Wnt-3a for the first two days of treatment. Following the treatment, the cells were treated for three additional days with 2% FBS plus 1 IM retinoic acid, 0.1 to 1p M TTNPB (4-[(E)-2-(5,6,7,8-Tetrahydro-5,5,8,8-tetramethyl-2 naphthalenyl)-1-propenyl]benzoic acid Arotinoid acid), or 0.1-l0pM AM-580 (4-[(5,6,7,8-Tetrahydro-5,5,8,8-tetramethyl-2 naphthalenyl)carboxamido]benzoic acid). The cells were next treated for three additional days in 2% FBS plus 20 ng/ml of bFGF. [0074] Figure 49 shows the real-time PCR results of the expression of the definitive endoderm markers indicated in panels a and b. in cultures of the human embryonic stem cell line HI treated with activin A and Wnt-1 for the times and concentrations indicated. 19 DETAILED DESCRIPTION 100751 For clarity of disclosure, and not by way of limitation, the detailed description of the invention is divided into subsections that describe or illustrate certain features, embodiments, or applications of the present invention. Definitions [00761 Stem cells are undifferentiated cells defined by their ability at the single cell level to both self-renew and differentiate to produce progeny cells, including self-renewing progenitors, non-renewing progenitors, and terminally differentiated cells. Stem cells are also characterized by their ability to differentiate in vitro into functional cells of various cell lineages from multiple germ layers (endoderm, mesoderm and ectoderm), as well as to give rise to tissues of multiple germ layers following transplantation and to contribute substantially to most, if not all, tissues following injection into blastocysts. [00771 Stem cells are classified by their developmental potential as: (1) totipotent, meaning able to give rise to all embryonic and extraembryonic cell types; (2) pluripotent, meaning able to give rise to all embryonic cell types; (3) multipotent, meaning able to give rise to a subset of cell lineages, but all within a particular tissue, organ, or physiological system (for example, hematopoietic stem cells (HSC) can produce progeny that include HSC (self renewal), blood cell restricted oligopotent progenitors and all cell types and elements (e.g., platelets) that are normal components of the blood); (4) oligopotent, meaning able to give rise to a more restricted subset of cell lineages than multipotent stem cells; and (5) unipotent, meaning able to give rise to a single cell lineage (e.g. , spermatogenic stem cells). 100781 Differentiation is the process by which an unspecialized ("uncommitted") or less specialized cell acquires the features of a specialized cell such as, for example, a nerve cell or a muscle cell. A differentiated or differentiation induced cell is one that has taken on a more specialized ("committed") position within the lineage of a cell. The term "committed", when applied to 20 the process of differentiation, refers to a cell that has proceeded in the differentiation pathway to a point where, under normal circumstances, it will continue to differentiate into a specific cell type or subset of cell types, and cannot, under normal circumstances, differentiate into a different cell type or revert to a less differentiated cell type. De-differentiation refers to the process by which a cell reverts to a less specialized (or committed) position within the lineage of a cell. As used herein, the lineage of a cell defines the heredity of the cell, i.e., which cells it came from and what cells it can give rise to. The lineage of a cell places the cell within a hereditary scheme of development and differentiation. A lineage-specific marker refers to a characteristic specifically associated with the phenotype of cells of a lineage of interest and can be used to assess the differentiation of an uncommitted cell to the lineage of interest. [0079] "AFP" or "alpha-fetoprotein protein" as used herein, refers to an antigen produced at the onset of liver development. AFP may also be expressed in extraembryonic cells. [0080] "Albumin" is a soluble monomeric protein that makes up about half of all serum proteins in adults. [00811 "o-cell lineage" refer to cells with positive gene expression for the transcription factor PDX-1 and at least one of the following transcription factors: NGN-3, Nkx2.2, Nkx6.1, NeuroD, Isl-1, HNF-3 beta, MAFA, Pax4, and Pax6. Cells expressing markers characteristic of the p cell lineage include p cells. [00821 "Brachyuiy", as used herein, is a T-box gene family member. It is the marker for primitive streak and mesoderm cells. [0083] "Cells expressing markers characteristic of the definitive endoderm lineage" as used herein refer to cells expressing at least one of the following markers: SOX-17, GATA-4, HNF-3 beta, GSC, Cerl, Nodal, FGF8, Brachyury, Mix like homeobox protein, FGF4 CD48, eomesodermin (EOMES), DKK4, FGF17, GATA-6, CXCR4, C-Kit, CD99, or OTX2. Cells expressing markers 21 characteristic of the definitive endoderm lineage include primitive streak precursor cells, primitive streak cells, mesendoderm cells and definitive endoderm cells. 100841 "c-Kit" and "CD1 17" both refer to a cell surface receptor tyrosine kinase having a sequence disclosed in Genbank Accession No. X06182, or a naturally occurring variant sequence thereof (e.g., allelic variant). 100851 "CD99" as used herein refers to the protein encoded by the gene with the accession number NM 002414. [0086] "Cells expressing markers characteristic of the pancreatic endoderm lineage" as used herein refer to cells expressing at least one of the following markers: PDX- 1, HNF- I beta, PTF- 1 alpha, HNF-6, or HB9. Cells expressing markers characteristic of the pancreatic endoderm lineage include pancreatic endoderm cells. [0087 "Cells expressing markers characteristic of the pancreatic endocrine lineage" as used herein refer to cells expressing at least one of the following markers: NGN-3, NeuroD, Islet- 1, PDX- 1, NKX6. 1, Pax-4, or PTF- 1 alpha. Cells expressing markers characteristic of the pancreatic endocrine lineage include pancreatic endocrine cells, pancreatic hormone expressing cells, and pancreatic hormone secreting cells, and cells of the 13-cell lineage. [00881 "Cerl" or "Cerebrus" as used herein is a member of the cysteine knot superfamily of proteins. [0089] "CXCR4" as used herein refers to the stromal cell-derived factor I (SDF- 1) receptor, also known as "LESTR" or "fusin". In the gastrulating mouse embryo, CXCR4 is expressed in the definitive endoderm and mesoderm but not in extraembryonic endoderm. [0090] "Definitive endoderm" as used herein refers to cells which bear the characteristics of cells arising from the epiblast during gastrulation and which form the gastrointestinal tract and its derivatives. Definitive endoderm cells 22 2566195v express the following markers: HNF-3 beta, GATA-4, SOX-17, Cerberus, OTX2, goosecoid, C-Kit, CD99, and Mixil. 100911 "Extraembiyonic endoderm" as used herein refers to a population of cells expressing at least one of the following markers: SOX-7, AFP, and SPARC. [00921 "FGF-2", "FGF-4" "FGF-8" "FGF-10", and "FGF-17" as used herein, are members of the fibroblast growth factor family. [0093] "GATA-4" and "GATA-6" are members of the GATA transcription factor family. This family of transcription factors is induced by TGF-3 signaling, and contribute to the maintenance of early endoderm markers. [00941 "GLUT-2", as used herein, refers to the glucose transporter molecule that is expressed in numerous fetal and adult tissues, including pancreas, liver, intestine, brain, and kidney. 100951 "Goosecoid" or "GSC" as used herein, refers to a homeodomain transcription factor expressed in the dorsal lip of the blastopore. [00961 "HB9" as used herein, refers to the homeobox gene 9. [00971 "HNF-1 alpha", "HNF-1 beta", "HNF-3 beta", and "HNF-6" belong to the hepatic nuclear factor family of transcription factors, which is characterized by a highly conserved DNA binding domain and two short carboxy-terminal domains. 100981 "Islet-I" or "Isl-I" as used herein is a member of the LIM/homeodomain family of transcription factors, and is expressed in the developing pancreas. 100991 "MafA" as used herein is a transcription factor expressed in the pancreas, and controls the expression of genes involved in insulin biosynthesis and secretion. [001001 "Markers" as used herein, are nucleic acid or polypeptide molecules that are differentially expressed in a cell of interest. In this context, differential expression means an increased level for a positive marker and a decreased 23 level for a negative marker. The detectable level of the marker nucleic acid or polypeptide is sufficiently higher or lower in the cells of interest compared to other cells, such that the cell of interest can be identified and distinguished from other cells using any of a variety of methods known in the art. 1001011 "Mesendoderm cell" as used herein refers to a cell expressing at least one of the following markers: CD48, eomesodermin (EOMES), SOX-17, DKK4, HNF-3 beta, GSC, FGF17, GATA-6. 1001021 "Mixll" as used herein refers to a homeobox gene, which is marker for the cells in the primitive streak, mesoderm, and endoderm. 100103] "NeuroD" as used herein is basic helix-loop-helix (bHLH) transcription factor implicated in neurogenesis. 1001041 "NGN-3" as used herein, is a member of the neurogenin family of basic loop helix-loop transcription factors. [001051 "Nkx-2.2" and "Nkx-6.1" as used herein are members of the Nkx transcription factor family. 1001061 "Nodal" as used herein, is a member of the TGF beta superfamily of proteins. [00107] "Oct-4" is a member of the POU-domain transcription factor and is widely regarded as a hallmark of pluripotent stem cells. The relationship of Oct-4 to pluripotent stem cells is indicated by its tightly restricted expression to undifferentiated pluripotent stem cells. Upon differentiation to somatic lineages, the expression of Oct-4 disappears rapidly. [001081 "Pancreatic endocrine cell", or "pancreatic hormone expressing cell" as used herein refers to a cell capable of expressing at least one of the following hormones: insulin, glucagon, somatostatin, and pancreatic polypeptide. [001091 "Pancreatic hormone secreting cell" as used herein refers to a cell capable of secreting at least one of the following hormones: insulin, glucagon, somatostatin, and pancreatic polypeptide. 24 [00110] "Pax-4" and "Pax-6" as used herein are pancreatic P cell specific transcription factors that are implicated in islet development. [001111 "PDX-1" as used herein refers to a homeodomain transcription factor implicated in pancreas development. [001121 "Pre-primitive streak cell" as used herein refers to a cell expressing at least one of the following markers: Nodal, or FGF8 [001131 "Primitive streak cell" as used herein refers to a cell expressing at least one of the following markers: Brachyury, Mix-like homeobox protein, or FGF4. [001141 "PTF-1 alpha" as used herein refers to a basic helix-loop-helix protein of 48 kD that is a sequence-specific DNA-binding subunit of the trimeric pancreas transcription factor-I (PTF1). 1001151 "SOX-1", "SOX-2", "SOX-7", and "SOX- 1 7"as used herein, are a members of the SOX transcription factor family, and are implicated in embryogenesis. [001161 "SPARC" as used herein is also known as "secreted protein acidic and rich in cysteine". [001171 "SSEA-1" (Stage Specific Embiyonic Antigen-1) is a glycolipid surface antigen present on the surface of murine teratocarcinoma stem cells (EC), murine and human embryonic germ cells (EG), and murine embryonic stem cells (ES). [00118] "SSEA-3" (Stage Specific Embryonic Antigen-3) is a glycolipid surface antigen present on the surface of human teratocarcinoma stem cells (EC), human embryonic germ cells (EG), and human embryonic stem cells (ES). [00119] "SSEA-4" (Stage Specific Embryonic Antigen-4) is a glycolipid surface antigen present on the surface of human teratocarcinoma stem cells (EC), human embryonic germ cells (EG), and human embryonic stem cells (ES). 25 [00120] "TRA l-60" is a keratin sulfate related antigen that is expressed on the surface of human teratocarcinoma stem cells (EC), human embryonic germ cells (EG), and human embryonic stem cells (ES). [00121] "TRAl-81" is a keratin sulfate related antigen that is expressed on the surface of human teratocarcinoma stem cells (EC), human embryonic germ cells (EG), and human embryonic stem cells (ES). [001221 "TRA2-49" is an alkaline phosphatase isozyme expressed on the surface of human teratocarcinoma stem cells (EC) and human embryonic stem cells (ES). [001231 "UTF- 1" as used herein, refers a transcriptional coactivator expressed in pluripotent embryonic stem cells and extra-embryonic cells. [001241 "Zic1" as used herein is a member of the Zic transcription factor family. Zic1 regulates the expression of neural and neural crest-specific genes and is expressed in the cells of the dorsal neural tube and the premigratory neural crest. Isolation, expansion and culture of pluripotent stem cells Characterization ofpluripotent stem cells [00125] Pluripotent stem cells may express one or more of the stage-specific embryonic antigens (SSEA) 3 and 4, and markers detectable using antibodies designated Tra-1-60 and Tra-1-81 (Thomson et al., Science 282:1145, 1998). Differentiation of pluripotent stem cells in vitro results in the loss of SSEA-4, Tra- 1-60, and Tra-1-81 expression (if present) and increased expression of SSEA- 1. Undifferentiated pluripotent stem cells typically have alkaline phosphatase activity, which can be detected by fixing the cells with 4% paraformaldehyde, and then developing with Vector Red as a substrate, as described by the manufacturer (Vector Laboratories, Burlingame Calif.) Undifferentiated pluripotent stem cells also typically express Oct-4 and TERT, as detected by RT-PCR. 26 [001261 Another desirable phenotype of propagated pluripotent stem cells is a potential to differentiate into cells of all three germinal layers: endoderm, mesoderm, and ectoderm tissues. Pluripotency of pluripotent stem cells can be confirmed, for example, by injecting cells into severe combined immunodeficient (SCID) mice, fixing the teratomas that form using 4% paraformaldehyde, and then examining them histologically for evidence of cell types from the three germ layers. Alternatively, pluripotency may be determined by the creation of embryoid bodies and assessing the embryoid bodies for the presence of markers associated with the three germinal layers. [001271 Propagated pluripotent stem cell lines may be karyotyped using a standard G banding technique and compared to published karyotypes of the corresponding primate species. It is desirable to obtain cells that have a "normal karyotype," which means that the cells are euploid, wherein all human chromosomes are present and not noticeably altered. Sources of pluripotent sten cells [001281 The types of pluripotent stem cells that may be used include established lines of pluripotent cells derived from tissue formed after gestation, including pre embryonic tissue (such as, for example, a blastocyst), embryonic tissue, or fetal tissue taken any time during gestation, typically but not necessarily before approximately 10-12 weeks gestation. Non-limiting examples are established lines of human embryonic stem cells or human embryonic germ cells, such as, for example the human embryonic stem cell lines HI, H7, and H9 (WiCell). Also contemplated is use of the compositions of this disclosure during the initial establishment or stabilization of such cells, in which case the source cells would be primary pluripotent cells taken directly from the source tissues. Also suitable are cells taken from a pluripotent stem cell population already cultured in the absence of feeder cells. Also suitable are mutant human embryonic stem cell lines, such as, for example, BGOIv (BresaGen, Athens, GA). 27 [00129] In one embodiment, human embryonic stem cells are prepared as described by Thomson et al. (U.S. Pat. No. 5,843,780; Science 282:1145, 1998; Curr. Top. Dev. Biol. 38:133 ff., 1998; Proc. Natl. Acad. Sci. U.S.A. 92:7844, 1995). Culture ofpluripotent stem cells 1001301 In one embodiment, pluripotent stem cells are typically cultured on a layer of feeder cells that support the pluripotent stem cells in various ways. Alternatively, pluripotent stem cells are cultured in a culture system that is essentially free of feeder cells, but nonetheless supports proliferation of pluripotent stem cells without undergoing substantial differentiation. The growth of pluripotent stem cells in feeder-free culture without differentiation is supported using a medium conditioned by culturing previously with another cell type. Alternatively, the growth of pluripotent stem cells in feeder-free culture without differentiation is supported using a chemically defined medium. [00131] For example, Reubinoff et al (Nature Biotechnology 18: 399 - 404 (2000)) and Thompson et al (Science 6 November 1998: Vol. 282. no. 5391, pp. 1145 1147) disclose the culture of pluripotent stem cell lines from human blastocysts using a mouse embryonic fibroblast feeder cell layer. [00132] Richards et al, (Stem Cells 21: 546-556, 2003) evaluated a panel of 11 different human adult, fetal and neonatal feeder cell layers for their ability to support human pluripotent stem cell culture. Richards et al, states: "human embryonic stem cell lines cultured on adult skin fibroblast feeders retain human embryonic stem cell morphology and remain pluripotent". [001331 US20020072117 discloses cell lines that produce media that support the growth of primate pluripotent stem cells in feeder-free culture. The cell lines employed are mesenchymal and fibroblast-like cell lines obtained from embryonic tissue or differentiated from embryonic stem cells. US20020072117 also discloses the use of the cell lines as a primary feeder cell layer. 28 [001341 In another example, Wang et al (Stem Cells 23: 1221-1227, 2005) discloses methods for the long-term growth of human pluripotent stem cells on feeder cell layers derived from human embryonic stem cells. [001351 In another example, Stojkovic et al (Stem Cells 2005 23: 306-314, 2005) disclose a feeder cell system derived from the spontaneous differentiation of human embryonic stem cells. [001361 In a further example, Miyamoto et al (Stem Cells 22: 433-440, 2004) disclose a source of feeder cells obtained from human placenta. [001371 Amit et al (Biol. Reprod 68: 2150-2156, 2003) discloses a feeder cell layer derived from human foreskin. [00138] In another example, Inzunza et al (Stem Cells 23: 544-549, 2005) disclose a feeder cell layer from human postnatal foreskin fibroblasts. 1001391 US6642048 discloses media that support the growth of primate pluripotent stem (pPS) cells in feeder-free culture, and cell lines useful for production of such media. US6642048 states: "This invention includes mesenchymal and fibroblast-like cell lines obtained from embryonic tissue or differentiated from embryonic stem cells. Methods for deriving such cell lines, processing media, and growing stem cells using the conditioned media are described and illustrated in this disclosure." 1001401 In another example, W02005014799 discloses conditioned medium for the maintenance, proliferation and differentiation of mammalian cells. W02005014799 states: "The culture medium produced in accordance with the present invention is conditioned by the cell secretion activity of murine cells, in particular, those differentiated and immortalized transgenic hepatocytes, named MMH (Met Murine Hepatocyte)." [001411 In another example, Xu et al (Stem Cells 22: 972-980, 2004) discloses conditioned medium obtained from human embryonic stem cell derivatives 29 that have been genetically modified to over express human telomerase reverse transcriptase. [001421 In another example, US20070010011 discloses a chemically defined culture medium for the maintenance of pluripotent stem cells. 1001431 An alternative culture system employs serum-free medium supplemented with growth factors capable of promoting the proliferation of embryonic stem cells. For example, Cheon et al (BioReprod DOI: 10.1 095/biolreprod. 105.046870, October 19, 2005) disclose a feeder-free, serum-free culture system in which embryonic stem cells are maintained in unconditioned serum replacement (SR) medium supplemented with different growth factors capable of triggering embryonic stem cell self-renewal. [001441 In another example, Levenstein et al (Stem Cells 24: 568-574, 2006) disclose methods for the long-term culture of human embryonic stem cells in the absence of fibroblasts or conditioned medium, using media supplemented with bFGF. [001451 In another example, US20050148070 discloses a method of culturing human embryonic stem cells in defined media without serum and without fibroblast feeder cells, the method comprising: culturing the stem cells in a culture medium containing albumin, amino acids, vitamins, minerals, at least one transferrin or transferrin substitute, at least one insulin or insulin substitute, the culture medium essentially free of mammalian fetal serum and containing at least about 100 ng/ml of a fibroblast growth factor capable of activating a fibroblast growth factor signaling receptor, wherein the growth factor is supplied from a source other than just a fibroblast feeder layer, the medium supported the proliferation of stem cells in an undifferentiated state without feeder cells or conditioned medium. 100146] In another example, US20050233446 discloses a defined media useful in culturing stem cells, including undifferentiated primate primordial stem cells. In solution, the media is substantially isotonic as compared to the stem cells 30 being cultured. In a given culture, the particular medium comprises a base medium and an amount of each of bFGF, insulin, and ascorbic acid necessary to support substantially undifferentiated growth of the primordial stem cells. [00147] In another example, US6800480 states "In one embodiment, a cell culture medium for growing primate-derived primordial stem cells in a substantially undifferentiated state is provided which includes a low osmotic pressure, low endotoxin basic medium that is effective to support the growth of primate derived primordial stem cells. The basic medium is combined with a nutrient serum effective to support the growth of primate-derived primordial stem cells and a substrate selected from the group consisting of feeder cells and an extracellular matrix component derived from feeder cells. The medium further includes non-essential amino acids, an anti-oxidant, and a first growth factor selected from the group consisting of nucleosides and a pyruvate salt." 1001481 In another example, US20050244962 states: "In one aspect the invention provides a method of culturing primate embryonic stem cells. One cultures the stem cells in a culture essentially free of mammalian fetal serum (preferably also essentially free of any animal serum) and in the presence of fibroblast growth factor that is supplied from a source other than just a fibroblast feeder layer. In a preferred form, the fibroblast feeder layer, previously required to sustain a stem cell culture, is rendered unnecessary by the addition of sufficient fibroblast growth factor." [01001 In a further example, W02005065354 discloses a defined, isotonic culture medium that is essentially feeder-free and serum-free, comprising: a. a basal medium; b. an amount of bFGF sufficient to support growth of substantially undifferentiated mammalian stem cells; c. an amount of insulin sufficient to support growth of substantially undifferentiated mammalian stem cells; and d. an amount of ascorbic acid sufficient to support growth of substantially undifferentiated mammalian stem cells. [01011 In another example, W02005086845 discloses a method for maintenance of an undifferentiated stem cell, said method comprising exposing a stem cell to 31 a member of the transforming growth factor-beta (TGFp) family of proteins, a member of the fibroblast growth factor (FGF) family of proteins, or nicotinamide (NIC) in an amount sufficient to maintain the cell in an undifferentiated state for a sufficient amount of time to achieve a desired result. [0102] The pluripotent stem cells may be plated onto a suitable culture substrate. In one embodiment, the suitable culture substrate is an extracellular matrix component, such as, for example, those derived from basement membrane or that may form part of adhesion molecule receptor-ligand couplings. In one embodiment, a the suitable culture substrate is Matrigel@ (Becton Dickenson). Matrigel@ is a soluble preparation from Engelbreth-Holm-Swarm tumor cells that gels at room temperature to form a reconstituted basement membrane. [01031 Other extracellular matrix components and component mixtures are suitable as an alternative. Depending on the cell type being proliferated, this may include laminin, fibronectin, proteoglycan, entactin, heparan sulfate, and the like, alone or in various combinations. [01041 The pluripotent stem cells may be plated onto the substrate in a suitable distribution and in the presence of a medium that promotes cell survival, propagation, and retention of the desirable characteristics. All these characteristics benefit from careful attention to the seeding distribution and can readily be determined by one of skill in the art. [0105] Suitable culture media may be made from the following components, such as, for example, Dulbecco's modified Eagle's medium (DMEM), Gibco # 11965 092; Knockout Dulbecco's modified Eagle's medium (KO DMEM), Gibco # 10829-018; Ham's F 12/50% DMEM basal medium; 200 mM L-glutamine, Gibco # 15039-027; non-essential amino acid solution, Gibco 11140-050; D mercaptoethanol, Sigma # M7522; human recombinant basic fibroblast growth factor (bFGF), Gibco # 13256-029. 32 Differentiation of pluripotent stem cells into cells expressing markers characteristic of the pancreatic endocrine lineage [01061 Pluripotent stem cells suitable for use in the present invention include, for example, the human embryonic stem cell line H9 (NIH code: WA09), the human embryonic stem cell line HI (NIH code: WAO 1), the human embryonic stem cell line H7 (NIH code: WA07), and the human embryonic stem cell line SA002 (Cellartis, Sweden). Also suitable for use in the present invention are cells that express at least one of the following markers characteristic of pluripotent cells: ABCG2, cripto, CD9, FoxD3, Connexin43, Connexin45, Oct4, Sox2, Nanog, hTERT, UTF-l, ZFP42, SSEA-3, SSEA-4, Tral-60, Tral-8 1. [0107] Markers characteristic of the definitive endoderm lineage are selected from the group consisting of SOX 17, GATA4, Hnf-3beta, GSC, Cerl, Nodal, FGF8, Brachyury, Mix-like homeobox protein, FGF4 CD48, eomesodermin (EOMES), DKK4, FGF17, GATA6, CXCR4, C-Kit, CD99, and OTX2. Suitable for use in the present invention is a cell that expresses at least one of the markers characteristic of the definitive endoderm lineage. In one aspect of the present invention, a cell expressing markers characteristic of the definitive endoderm lineage is a primitive streak precursor cell. In an alternate aspect, a cell expressing markers characteristic of the definitive endoderm lineage is a mesendoderm cell. In an alternate aspect, a cell expressing markers characteristic of the definitive endoderm lineage is a definitive endoderm cell. [0108] Markers characteristic of the pancreatic endoderm lineage are selected from the group consisting of Pdx1, HNF-lbeta, PTFla, HNF-6, HB9 and PROX 1. Suitable for use in the present invention is a cell that expresses at least one of the markers characteristic of the pancreatic endoderm lineage. In one aspect of the present invention, a cell expressing markers characteristic of the pancreatic endoderm lineage is a pancreatic endoderm cell. [0109] Markers characteristic of the pancreatic endocrine lineage are selected from the group consisting of NGN-3, NeuroD, Islet- 1, Pdx- 1,NKX6. 1, Pax-4 33 2566195v1 , and PTF-1 alpha. In one embodiment, a pancreatic endocrine cell is capable of expressing at least one of the following hormones: insulin, glucagon, somatostatin, and pancreatic polypeptide. Suitable for use in the present invention is a cell that expresses at least one of the markers characteristic of the pancreatic endocrine lineage. In one aspect of the present invention, a cell expressing markers characteristic of the pancreatic endocrine lineage is a pancreatic endocrine cell. The pancreatic endocrine cell may be a pancreatic hormone expressing cell. Alternatively, the pancreatic endocrine cell may be a pancreatic hormone secreting cell. [0110] In one aspect of the present invention, the pancreatic endocrine cell is a cell expressing markers characteristic of the p cell lineage. A cell expressing markers characteristic of the P cell lineage expresses Pdxl and at least one of the following transcription factors: NGN-3, Nkx2.2, Nkx6.1. I, NeuroD, HNF 3 beta, MAFA, Pax4, and Pax6. In one aspect of the present invention, a cell expressing markers characteristic of the j cell lineage is a p cell. Formation of cells expressing markers characteristic of the definitive endoderm lineage [01111 Pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage by any method in the art or by any method proposed in this invention. [0112] For example, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage according to the methods disclosed in DAmour et al, Nature Biotechnology 23, 1534 - 1541 (2005). [0113] For example, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage according to the methods disclosed in Shinozaki et al, Development 131, 1651 - 1662 (2004). 34 2566195vl [01141 For example, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage according to the methods disclosed in McLean et al, Stem Cells 25, 29 - 38 (2007). [0115] For example, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage according to the methods disclosed in D'Amour et al, Nature Biotechnology 24, 1392 - 1401 (2006). [01161 For example, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage by culturing the pluripotent stem cells in medium containing activin A in the absence of serum, then culturing the cells with activin A and serum, and then culturing the cells with activin A and serum of a different concentration. An example of this method is disclosed in Nature Biotechnology 23, 1534 - 1541 (2005). [01171 For example, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage by culturing the pluripotent stem cells in medium containing activin A in the absence of serum, then culturing the cells with activin A with serum of another concentration. An example of this method is disclosed in D' Amour et al, Nature Biotechnology, 2005. [01181 For example, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage by culturing the pluripotent stem cells in medium containing activin A and a Wnt ligand in the absence of serum, then removing the Wnt ligand and culturing the cells with activin A with serum. An example of this method is disclosed in Nature Biotechnology 24, 1392 - 1401 (2006). 101191 In one aspect of the present invention, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage by plating the pluripotent stem cells on a tissue culture substrate coated with an extracellular matrix, then culturing the pluripotent 35 stem cells with activin A and a Wnt ligand in a first culture medium containing serum for a period of time, and then culturing the pluripotent stem cells with activin A in a second culture medium containing a greater concentration of serum for about another period of time. 10120] The concentration of serum in the first culture medium disclosed above may be from about zero to about 0.5 percent, and the culture time may be from about one to about three days. The concentration of serum in the second culture medium disclosed above may be from about 0.5 percent to about two percent, and the culture time may be from about one to about four days. [0121.1 In an alternate embodiment of the present invention, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage by plating the pluripotent stem cells on a tissue culture substrate coated with an extracellular matrix, then culturing the pluripotent stem cells with activin A and a Wnt ligand in a first culture medium containing serum for about a period of time, and then culturing the pluripotent stem cells with activin A and a Wnt ligand in a second culture medium containing a greater concentration of serum for another period of time. 101221 The concentration of serum in the first culture medium disclosed above may be from about zero to about 0.5 percent, and the culture time may be from about one to about three days. The concentration of serum in the second culture medium disclosed above may be from about 0.5 percent to about two percent, and the culture time may be from about one to about four days. 101231 In one embodiment, the present invention provides a method for differentiating pluripotent stem cells expressing markers characteristic of the definitive endoderm lineage, comprising the steps of: a. Plating the pluripotent stem cells on a tissue culture substrate coated with an extracellular matrix, and 36 b. Culturing the pluripotent stem cells with activin A and a Wint ligand. [01241 Culturing the pluripotent stem cells with activin A and a Wnt ligand may be performed in a single culture medium. Alternatively, culturing the pluripotent stem cells with activin A and a Wnt ligand may be performed separately or together in more than one culture media. In one embodiment, culturing the pluripotent stem cells with activin A and a Wnt ligand is performed in two culture media. Extracellular Matrix 101251 In one aspect of the present invention, the pluripotent stem cells are cultured and differentiated on a tissue culture substrate coated with an extracellular matrix. The extracellular matrix may be a solubilized basement membrane preparation extracted from mouse sarcoma cells (which is sold by BD Biosciences under the trade name MATRIGEL). Alternatively, the extracellular matrix may be growth factor-reduced MATRIGEL. Alternatively, the extracellular matrix may fibronectin. In an alternate embodiment, the pluripotent stem cells are cultured and differentiated on tissue culture substrate coated with human serum. [0126] The extracellular matrix may be diluted prior to coating the tissue culture substrate. Examples of suitable methods for diluting the extracellular matrix and for coating the tissue culture substrate may be found in Kleinman, H.K., et al., Biochemistry 25:312 (1986), and Hadley, M.A., et al., J.Cell.Biol. 101:1511 (1985). [0127] In one embodiment, the extracellular matrix is MATRIGEL. In one embodiment, the tissue culture substrate is coated with MATRIGEL at a 1:10 dilution. In an alternate embodiment, the tissue culture substrate is coated with MATRIGEL at a 1:15 dilution. In an alternate embodiment, the tissue culture substrate is coated with MATRIGEL at a 1:30 dilution. In an alternate embodiment, the tissue culture substrate is coated with MATRIGEL at a 1:60 dilution. 37 [0128] In one embodiment, the extracellular matrix is growth factor-reduced MATRIGEL. In one embodiment, the tissue culture substrate is coated with growth factor-reduced MATRIGEL at a 1:10 dilution. In an alternate embodiment, the tissue culture substrate is coated with growth factor-reduced MATRIGEL at a 1:15 dilution. In an alternate embodiment, the tissue culture substrate is coated with growth factor-reduced MATRIGEL at a 1:30 dilution. In an alternate embodiment, the tissue culture substrate is coated with growth factor-reduced MATRIGEL at a 1:60 dilution. Differentiation of pluripotent sten cells into cells expressing markers characteristic of the definitive endoderm lineage on an extracellular matrix, using a single culture medium [0129] When a single culture medium is used, it should contain sufficiently low concentrations of certain factors to allow the differentiation of pluripotent stem cells to definitive endoderm, such as, for example insulin and IGF (as disclosed in W02006020919). This may be achieved by lowing the serum concentration, or alternatively, by using chemically defined media that lacks insulin and IGF. Examples of chemically defined media are disclosed in Wiles et al (Exp Cell Res. 1999 Feb 25; 247(1): 241-8.). [0130] The culture medium may have a serum concentration in the range of about 0% to about 10%. In an alternate embodiment, the concentration may be in the range of about 0% to about 5%. In an alternate embodiment, the concentration may be in the range of about 0% to about 2%. In an alternate embodiment, the concentration may be about 2%. [0131] The time of culturing with activin A and a Wnt ligand may range from about 1 day to about 7 days. In an alternate embodiment, the time of culturing may range from about I day to about 3 days. In an alternate embodiment, the time of culturing may be about 3 days. [0132] Activin A may be used at any concentration suitable to cause differentiation of the pluripotent stem cells. The concentration maybe from about 1 pg/ml to 38 about 100pg/ml. In an alternate embodiment, the concentration may be about Ipg/ml to about 1 pg/ml. In another alternate embodiment, the concentration may be about lpg/ml to about lOOng/ml. In another alternate embodiment, the concentration may be about 50ng/ml to about 1OOng/ml. In another alternate embodiment, the concentration may be about IOOng/ml. [01331 The choice of the Wnt ligand may be optimized to improve the efficiency of the differentiation process. The Wnt ligand may be selected from the group consisting of Wnt-1, Wnt-3a, Wnt-5a and Wnt-7a. In one embodiment, the Wnt ligand is Wnt-l. In an alternate embodiment, the Wnt ligand is Wnt-3a. 101341 The Wnt ligand may be at a concentration of about Ing/ml to about 1000ng/ml. In an alternate embodiment, the concentration may be about 10ng/mi to about 100ng/mil. 101351 The single culture medium may also contain a GSK-3B inhibitor. The GSK 3B inhibitor may be selected from the group consisting of GSK-3B inhibitor IX and GSK-3B inhibitor XI. In one embodiment, the GSK-3B inhibitor is GSK-3B inhibitor IX. I did not see the definitions of IX and XI inhibitors. I did have these in the original WNT patent application. [01361 When culturing pluripotent stem cells with a GSK-3B inhibitor, the concentration of the GSK-3B inhibitor may be from about InM to about I OOOnM. In an alternate embodiment, the pluripotent stem cells are cultured with the GSK-3B inhibitor at a concentration of about 1OnM to about 1OOnM. [01371 The single culture medium may also contain at least one other additional factor that may enhance the formation of cells expressing markers characteristic of the definitive endoderm lineage from pluripotent stem cells. Alternatively, the at least one other additional factor may enhance the proliferation of the ells expressing markers characteristic of the definitive endoderm lineage formed by the methods of the present invention. Further, the at least one other additional factor may enhance the ability of the ells expressing markers characteristic of the definitive endoderm lineage formed 39 by the methods of the present invention to form other cell types, or improve the efficiency of any other additional differentiation steps. [0138] The at least one additional factor may be, for example, nicotinamide, members of the TGF-P family, including TGF-P1, 2, and 3, serum albumin, members of the fibroblast growth factor family, platelet-derived growth factor-AA, and BB, platelet rich plasma, insulin growth factor (IGF-I, II), growth differentiation factor (GDF-5, -6, -8, -10, 11), glucagon like peptide-I and II (GLP-I and II), GLP- 1 and GLP-2 mimetobody, Exendin-4, retinoic acid, parathyroid hormone, insulin, progesterone, aprotinin, hydrocortisone, ethanolamine, beta mercaptoethanol, epidermal growth factor (EGF), gastrin I and II, copper chelators such as, for example, triethylene pentamine, forskolin, Na-Butyrate, activin, betacellulin, ITS, noggin, neurite growth factor, nodal, valporic acid, trichostatin A, sodium butyrate, hepatocyte growth factor (HGF), sphingosine 1, VEGF, MG132 (EMD, CA), N2 and B27 supplements (Gibco, CA), steroid alkaloid such as, for example, cyclopamine (EMD, CA), keratinocyte growth factor (KGF), Dickkopf protein family, bovine pituitary extract, islet neogenesis-associated protein (INGAP), Indian hedgehog, sonic hedgehog, proteasome inhibitors, notch pathway inhibitors, sonic hedgehog inhibitors, or combinations thereof. [0139] The at least one other additional factor may be supplied by conditioned media obtained from pancreatic cells lines such as, for example, PANC-1 (ATCC No: CRL-1469), CAPAN-1 (ATCC No: HTB-79), BxPC-3 (ATCC No: CRL 1687), HPAF-II (ATCC No: CRL-1997), hepatic cell lines such as, for example, HepG2 (ATCC No: HTB-8065), intestinal cell lines such as, for example, FHs 74 (ATCC No: CCL-241), and primary or transformed endothelial cells. 40 Differentiation ofpluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage on an extracellular matrix, using two culture media [01401 Differentiation of pluripotent stem cells into cells of a definitive endoderm lineage may be accomplished by culturing the pluripotent stem cells with activin A and a Wnt ligand using two culture media. Thus, the differentiation of the pluripotent stem cells may be accomplished as follows: a. Plating the pluripotent stem cells on a tissue culture substrate coated with an extracellular matrix, b. Culturing the pluripotent stem cells with activin A and a Wnt ligand in a first culture medium, and c. Culturing the pluripotent stem cells with activin A in a second culture medium. [0141] The first culture medium may contain serum at a low concentration, and the second culture medium may contain serum at a higher concentration than the first culture medium. [01421 The second culture medium may contain a Wnt ligand. [01431 First Culture Medium: The first culture medium should contain sufficiently low concentrations of certain factors to allow the differentiation of pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage, such as, for example insulin and IGF (as disclosed in W02006020919). This may be achieved by lowing the serum concentration, or alternatively, by using chemically defined media that lacks insulin and IGF. Examples of chemically defined media are disclosed in Wiles et al (Exp Cell Res. 1999 Feb 25; 247(1):241-8.). [01441 In the first culture medium there may be a lower concentration of serum, relative to the second culture medium. Increasing the serum concentration in 41 the second culture medium increases the survival of the cells, or, alternatively, may enhance the proliferation of the cells. The serum concentration of the first medium may be in the range of about 0% to about 10%. Alternatively, the serum concentration of the first medium may be in the range of about 0% to about 2%. Alternatively, the serum concentration of the first medium may be in the range of about 0% to about 1%. Alternatively, the serum concentration of the first medium may be about 0.5%. [01451 When culturing the pluripotent stem cells with activin A and a Wnt ligand using at least two culture media, the time of culturing in the first culture medium may range from about 1 day to about 3 days. [01461 Activin A may be used at any concentration suitable to cause differentiation of the pluripotent stem cells. The concentration maybe from about 1 pg/ml to about 100tg/ml. In an alternate embodiment, the concentration may be about 1pg/ml to about 1p g/ml. In another alternate embodiment, the concentration may be about 1pg/ml to about 100ng/ml. In another alternate embodiment, the concentration may be about 50ng/ml to about 100ng/ml. In another alternate embodiment, the concentration may be about 1OOng/ml. [01471 The choice of the Wnt ligand may be optimized to improve the efficiency of the differentiation process. The Wnt ligand may be selected from the group consisting of Wnt-1, Wnt-3a, Wnt-5a and Wnt-7a. In one embodiment, the Wnt ligand is Wnt-I. In an alternate embodiment, the Wnt ligand is Wnt-3a. 101481 The Wnt ligand may be at a concentration of about lng/ml to about 1000ng/ml. In an alternate embodiment, the concentration may be about 1Ong/ml to about 1OOng/mI. [01491 The first culture medium may also contain a GSK-3B inhibitor. The GSK-3B inhibitor may be added to the first culture medium, to the second culture medium, or to both the first and second culture media. 42 [01501 The GSK-3B inhibitor may be selected from the group consisting of GSK-3B inhibitor IX and GSK-3B inhibitor XI. In one embodiment, the GSK-3B inhibitor is GSK-3B inhibitor IX. [0151] When culturing pluripotent stem cells with a GSK-3B inhibitor, the concentration of the GSK-3B inhibitor may be from about I nM to about 10OOnM. In an alternate embodiment, the pluripotent stem cells are cultured with the GSK-3B inhibitor at a concentration of about 1OnM to about 1 OOnM. 101521 The first culture medium may also contain at least one other additional factor that may enhance the formation of cells expressing markers characteristic of the definitive endoderm lineage from pluripotent stem cells. Alternatively, the at least one other additional factor may enhance the proliferation of the cells expressing markers characteristic of the definitive endoderm lineage formed by the methods of the present invention. Further, the at least one other additional factor may enhance the ability of the cells expressing markers characteristic of the definitive endodern lineage formed by the methods of the present invention to form other cell types, or improve the efficiency of any other additional differentiation steps. [01531 The at least one additional factor may be, for example, nicotinamide, members of TGF-$ family, including TGF- 1, 2, and 3, serum albumin, members of the fibroblast growth factor family, platelet-derived growth factor-AA, and -BB, platelet rich plasma, insulin growth factor (IGF-I, II), growth differentiation factor (GDF-5, -6, -8, -10, 11), glucagon like peptide-I and II (GLP-I and II), GLP-1 and GLP-2 mimetobody, Exendin-4, retinoic acid, parathyroid hormone, insulin, progesterone, aprotinin, hydrocortisone, ethanolamine, beta mercaptoethanol, epidermal growth factor (EGF), gastrin I and II, copper chelators such as, for example, triethylene pentamine, forskolin, Na-Butyrate, activin, betacellulin, ITS, noggin, neurite growth factor, nodal, valporic acid, trichostatin A, sodium butyrate, hepatocyte growth factor (HGF), sphingosine 1, VEGF, MG132 (EMD, CA), N2 and B27 supplements (Gibco, CA), steroid alkaloid such as, for example, cyclopamine (EMD, CA), keratinocyte growth 43 factor (KGF), Dickkopf protein family, bovine pituitary extract, islet neogenesis-associated protein (INGAP), Indian hedgehog, sonic hedgehog, proteasome inhibitors, notch pathway inhibitors, sonic hedgehog inhibitors, or combinations thereof. [01541 The at least one other additional factor may be supplied by conditioned media obtained from pancreatic cells lines such as, for example, PANC- 1 (ATCC No: CRL-1469), CAPAN-1 (ATCC No: HTB-79), BxPC-3 (ATCC No: CRL 1687), HPAF-II (ATCC No: CRL-1997), hepatic cell lines such as, for example, HepG2 (ATCC No: HTB-8065), and intestinal cell lines such as, for example, FHs 74 (ATCC No: CCL-241). [01551 Second Culture Medium: The second culture medium should contain certain factors, such as, for example, insulin and IGF (as disclosed in W02006020919), at a sufficient concentration to promote the survival of the cultured cells. This may be achieved by increasing the serum concentration, or, alternatively, by using chemically defined media where the concentrations of insulin and IGF are increased relative to the first culture medium. Examples of chemically defined media are disclosed in Wiles et al (Exp Cell Res. 1999 Feb 25; 247(l):241-8.). [01561 In a second culture medium having higher concentrations of serum, the serum concentration of the second culture medium may be in the range about 0.5% to about 10%. Alternatively, the serum concentration of the second culture medium may be in the range of about 0.5% to about 5%. Alternatively, the serum concentration of the second culture medium may be in the range of about 0.5% to about 2%. Alternatively, the serum concentration of the second culture medium may be about 2%. When culturing pluripotent stem cells with the second culture medium, the time of culturing may range from about I day to about 4 days. [0157] Similar to the first culture medium, Activin A may be used at any concentration suitable to cause differentiation of the pluripotent stem cells. The concentration maybe from about lpg/ml to about 1 00pg/ml. In an 44 alternate embodiment, the concentration may be about 1 pg/mI to about I pg/ml. In another alternate embodiment, the concentration may be about 1 pg/ml to about 100ng/ml. In another alternate embodiment, the concentration may be about 50ng/ml to about 100ng/ml. In another alternate embodiment, the concentration may be about 1 OOng/ml. [01581 The Wnt ligand may be at a concentration of about ing/ml to about 10OOng/ml. In an alternate embodiment, the concentration may be about lOng/mI to about 100ng/ml. [01591 The Wnt ligand may be selected from the group consisting of Wnt-1, Wnt-3a, Wnt-5a and Wnt-7a. In one embodiment, the Wnt ligand is Wnt-l. In an alternate embodiment, the Wnt ligand is Wnt-3a. [01601 The second culture medium may also contain a GSK-3B inhibitor. The GSK 3B inhibitor may be added to the first culture medium, to the second culture medium, or to both the first and second culture media. [01611 The GSK-3B inhibitor may be selected from the group consisting of GSK-3B inhibitor IX and GSK-3B inhibitor XI. In one embodiment, the GSK-3B inhibitor is GSK-3B inhibitor IX. 101621 When culturing pluripotent stem cells with a GSK-3B inhibitor, the concentration of the GSK-3B inhibitor may be from about InM to about 1000nM. In an alternate embodiment, the pluripotent stem cells are cultured with the GSK-3B inhibitor at a concentration of about 1OnM to about 1 OOnM. [01631 Similar to the first culture medium, the second culture medium may also contain at least one other additional factor that may enhance the formation of cells expressing markers characteristic of the definitive endoderm lineage from pluripotent stem cells. Alternatively, the at least one other additional factor may enhance the proliferation of the cells expressing markers characteristic of the definitive endoderm lineage formed by the methods of the present invention. Further, the at least one other additional factor may 45 enhance the ability of the cells expressing markers characteristic of the definitive endoderm lineage formed by the methods of the present invention to form other cell types, or improve the efficiency of any other additional differentiation steps. [0164] The at least one additional factor may be, for example, nicotinamide, members of TGF-P family, including TGF- 1, 2, and 3, serum albumin, members of the fibroblast growth factor family, platelet-derived growth factor-AA, and -BB, platelet rich plasma, insulin growth factor (IGF-I, II), growth differentiation factor (GDF-5, -6, -8, -10, 11), glucagon like peptide-I and II (GLP-I and II), GLP- 1 and GLP-2 mimetobody, Exendin-4, retinoic acid, parathyroid hormone, insulin, progesterone, aprotinin, hydrocortisone, ethanolamine, beta mercaptoethanol, epidermal growth factor (EGF), gastrin I and II, copper chelators such as, for example, triethylene pentamine, forskolin, Na-Butyrate, activin, betacellulin, ITS, noggin, neurite growth factor, nodal, valporic acid, trichostatin A, sodium butyrate, hepatocyte growth factor (HGF), sphingosine 1, VEGF, MG132 (EMD, CA), N2 and B27 supplements (Gibco, CA), steroid alkaloid such as, for example, cyclopamine (EMD, CA), keratinocyte growth factor (KGF), Dickkopf protein family, bovine pituitary extract, islet neogenesis-associated protein (INGAP), Indian hedgehog, sonic hedgehog, proteasome inhibitors, notch pathway inhibitors, sonic hedgehog inhibitors, or combinations thereof. [0165] The at least one other additional factor may be supplied by conditioned media obtained from pancreatic cells lines such as, for example, PANC-I (ATCC No: CRL-1469), CAPAN-1 (ATCC No: HTB-79), BxPC-3 (ATCC No: CRL 1687), HPAF-II (ATCC No: CRL-1997), hepatic cell lines such as, for example, HepG2 (ATCC No: HTB-8065), and intestinal cell lines such as, for example, FHs 74 (ATCC No: CCL-241). 46 Detection of cells expressing markers characteristic of the definitive endoderni linage [01661 Formation of cells expressing markers characteristic of the definitive endoderm lineage may be determined by testing for the presence of the markers before and after following a particular protocol. Pluripotent stem cells typically do not express such markers. Thus, differentiation of pluripotent cells is detected when cells begin to express them. [01671 The efficiency of differentiation may be determined by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker expressed by cells expressing markers characteristic of the definitive endoderm lineage. [01681 Methods for assessing expression of protein and nucleic acid markers in cultured or isolated cells are standard in the art. These include quantitative reverse transcriptase polymerase chain reaction (RT-PCR), Northern blots, in situ hybridization (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 2001 supplement)), and immunoassays such as immunohistochemical analysis of sectioned material, Western blotting, and for markers that are accessible in intact cells, flow cytometry analysis (FACS) (see, e.g., Harlow and Lane, Using Antibodies: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press (1998)). [0169] Examples of antibodies useful for detecting certain protein markers are listed in Table IA. It should be noted that alternate antibodies directed to the same markers that are recognized by the antibodies listed in Table IA are available, or can be readily developed. Such alternate antibodies can also be employed for assessing expression of markers in the cells isolated in accordance with the present invention. 101701 For example, characteristics of pluripotent stem cells are well known to those skilled in the art, and additional characteristics of pluripotent stem cells continue to be identified. Pluripotent stem cell markers include, for example, 47 the expression of one or more of the following: ABCG2, cripto, FoxD3, Connexin43, Connexin45, Oct4, Sox2, Nanog, hTERT, UTF-1, ZFP42, SSEA-3, SSEA-4, Tral-60, Tral-81. [0171] After treating pluripotent stem cells with the methods of the present invention, the differentiated cells may be purified by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker, such as CXCR4, expressed by cells expressing markers characteristic of the definitive endoderm lineage. Formation of cells expressing markers characteristic of the pancreatic endoderm lineage [01721 Cells expressing markers characteristic of the definitive endoderm lineage may be differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage by any method in the art or by any method proposed in this invention. [01731 For example, cells expressing markers characteristic of the definitive endoderm lineage may be differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage according to the methods disclosed in D'Amour et al, Nature Biotechnology 24, 1392 - 1401 (2006). [0174] For example, cells expressing markers characteristic of the definitive endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage, by treating the cells expressing markers characteristic of the definitive endoderm lineage with a fibroblast growth factor and the hedgehog signaling pathway inhibitor KAAD cyclopamine, then removing the medium containing the fibroblast growth factor and KAAD-cyclopamine and subsequently culturing the cells in medium containing retinoic acid, a fibroblast growth factor and KAAD cyclopamine. An example of this method is disclosed in Nature Biotechnology 24, 1392 - 1401 (2006). 48 [01751 In one aspect of the present invention, cells expressing markers characteristic of the definitive endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage, by treating the cells expressing markers characteristic of the definitive endoderm lineage with retinoic acid and at least one fibroblast growth factor for a period of time. That period of time may be from about one to about six days. [0176] In an alternate aspect of the present invention, cells expressing markers characteristic of the definitive endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage, by treating the cells with retinoic acid for a period of time. That period of time maybe from about one to about three days. The retinoic acid is subsequently removed and the cells are treated with at least one fibroblast growth factor for another period of time. That period of time may be from about one to about three days. 101771 In one embodiment, the present invention provides a method for differentiating cells expressing markers characteristic of the definitive endoderm lineage into cells expressing markers characteristic of the pancreatic endoderm lineage, comprising the steps of: a. Culturing cells expressing markers characteristic of the definitive endoderm lineage, and b. Treating the cells expressing markers characteristic of the definitive endoderm lineage with retinoic acid and at least one fibroblast growth factor. [01781 Any cell expressing markers characteristic of the definitive endoderm lineage is suitable for differentiating into a cell expressing markers characteristic of the pancreatic endoderm lineage using this method. [0179] In one embodiment, the cells expressing markers characteristic of the definitive endoderm are treated with retinoic acid and at least one fibroblast 49 growth factor for about one to about six days. In one embodiment, the cells expressing markers characteristic of the definitive endoderm are treated with retinoic acid and at least one fibroblast growth factor for about six days. [0180] The at least one fibroblast growth factor is selected from the group consisting of FGF-2, FGF-4 and FGF-10. [0181] Any cell expressing markers characteristic of the definitive endoderm lineage is suitable for differentiating into a cell expressing markers characteristic of the pancreatic endoderm lineage using this method. [0182] In an alternate embodiment, the present invention provides a method for differentiating cells expressing markers characteristic of the definitive endoderm lineage into cells expressing markers characteristic of the pancreatic endoderm lineage, comprising the steps of: a. Culturing cells expressing markers characteristic of the definitive endoderm lineage, b. Treating the cells expressing markers characteristic of the definitive endoderm lineage treating the cells with retinoic acid, and c. Removing the retinoic acid and subsequently treating the cells with at least one fibroblast growth factor. [01831 Any cell expressing markers characteristic of the definitive endoderm lineage is suitable for differentiating into a cell expressing markers characteristic of the pancreatic endoderm lineage using this method. [01841 In one embodiment, the cells expressing markers characteristic of the definitive endoderm are treated with retinoic acid for about one to about three days. In one embodiment, the cells expressing markers characteristic of the definitive endoderm are treated with retinoic acid for about three days. In one embodiment, the cells expressing markers characteristic of the definitive endoderm are treated with at least one fibroblast growth factor for about one to 50 about three days. In one embodiment, the cells expressing markers characteristic of the definitive endoderm are treated with at least one fibroblast growth factor for about three days. 10185] The at least one fibroblast growth factor is selected from the group consisting of FGF-2, FGF-4 and FGF-10. [01861 Any cell expressing markers characteristic of the definitive endoderm lineage is suitable for differentiating into a cell expressing markers characteristic of the pancreatic endoderm lineage using this method. [01871 In one embodiment, the cells expressing markers characteristic of the definitive endoderm lineage are treated with retinoic acid. Alternatively, the cells expressing markers characteristic of the definitive endoderm lineage are treated with FGF-2, or alternatively FGF-4, or alternatively FGF-i 0. In an alternate embodiment, the cells expressing markers characteristic of the definitive endoderm lineage are treated with at least one of the following factors: retinoic acid, FGF-2, FGF-4 or FGF-10. In an alternate embodiment, the cells expressing markers characteristic of the definitive endoderm lineage are treated with retinoic acid and at least one of the following fibroblast growth factors: FGF-2, FGF-4 or FGF- 10. In one embodiment, the cells expressing markers characteristic of the definitive endoderm lineage are treated with retinoic acid and FGF-2. In another embodiment, the cells expressing markers characteristic of the definitive endoderm lineage are treated with retinoic acid and FGF-4. In a further embodiment, the cells expressing markers characteristic of the definitive endoderm lineage are treated with retinoic acid and FGF-10. [0188] Retinoic acid may be used at a concentration from about InM to about 1mM. In one embodiment, retinoic acid is used at a concentration of lptM. [01891 FGF-2 may be used at a concentration from about 50pg/ml to about 50ptg/ml. In one embodiment, FGF-2 is used at a concentration of 50ng/ml. 51 [01901 FGF-4 may be used at a concentration from about 50pg/ml to about 50pg/ml. In one embodiment, FGF-4 is used at a concentration of 50ng/ml. [0191] FGF-10 may be used at a concentration from about 50pg/mI to about 50pig/ml. In one embodiment, FGF-10 is used at a concentration of 50ng/ml. 101.921 Cells expressing markers characteristic of the definitive endoderm lineage may be treated with at least one other additional factor that may enhance the formation of cells expressing markers characteristic of the pancreatic endoderm lineage. Alternatively, the at least one other additional factor may enhance the proliferation of the cells expressing markers characteristic of the pancreatic endoderm lineage formed by the methods of the present invention. Further, the at least one other additional factor may enhance the ability of the cells expressing markers characteristic of the pancreatic endoderm lineage formed by the methods of the present invention to form other cell types, or improve the efficiency of any other additional differentiation steps. [01931 The at least one additional factor may be, for example, nicotinamide, members of TGF-3 family, including TGF-1, 2, and 3, serum albumin, members of the fibroblast growth factor family, platelet-derived growth factor-AA, and -BB, platelet rich plasma, insulin growth factor (IGF-I, II), growth differentiation factor (GDF-5, -6, -8, -10, 11), glucagon like peptide-i and II (GLP-I and II), GLP- 1 and GLP-2 mimetobody, Exendin-4, retinoic acid, parathyroid hormone, insulin, progesterone, aprotinin, hydrocortisone, ethanolamine, beta mercaptoethanol, epidermal growth factor (EGF), gastrin I and II, copper chelators such as, for example, triethylene pentamine, forskolin, Na-Butyrate, activin, betacellulin, ITS, noggin, neurite growth factor, nodal, valporic acid, trichostatin A, sodium butyrate, hepatocyte growth factor (HGF), sphingosine 1, VEGF, MG132 (EMD, CA), N2 and B27 supplements (Gibco, CA), steroid alkaloid such as, for example, cyclopamine (EMD, CA), keratinocyte growth factor (KGF), Dickkopf protein family, bovine pituitary extract, islet neogenesis-associated protein (INGAP), Indian hedgehog, sonic hedgehog, 52 proteasome inhibitors, notch pathway inhibitors, sonic hedgehog inhibitors, or combinations thereof. [0194] The at least one other additional factor may be supplied by conditioned media obtained from pancreatic cells lines such as, for example, PANC-I (ATCC No: CRL-1469), CAPAN-1 (ATCC No: HTB-79), BxPC-3 (ATCC No: CRL 1687), HPAF-II (ATCC No: CRL-1997), hepatic cell lines such as, for example, HepG2 (ATCC No: HTB-8065), and intestinal cell lines such as, for example, FHs 74 (ATCC No: CCL-241). Detection of cells expressing markers characteristic of the pancreatic endoderm linage [01951 Markers characteristic of the pancreatic endoderm lineage are well known to those skilled in the art, and additional markers characteristic of the pancreatic endoderm lineage continue to be identified. These markers can be used to confirm that the cells treated in accordance with the present invention have differentiated to acquire the properties characteristic of the pancreatic endoderm lineage. Pancreatic endoderm lineage specific markers include the expression of one or more transcription factors such as, for example, Hlxb9, PTF-la, PDX-1, HNF-6, HNF-ibeta. [01961 The efficiency of differentiation may be determined by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker expressed by cells expressing markers characteristic of the pancreatic endoderm lineage. [0197] Methods for assessing expression of protein and nucleic acid markers in cultured or isolated cells are standard in the art. These include quantitative reverse transcriptase polymerase chain reaction (R.T-PCR), Northern blots, in situ hybridization (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 2001 supplement)), and immunoassays such as immunohistochemical analysis of sectioned material, Western blotting, and for markers that are accessible in intact cells, flow cytometry analysis (FACS) 53 (see, e.g., Harlow and Lane, Using Antibodies: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press (1998)). [0198] Examples of antibodies useful for detecting certain protein markers are listed in Table IA. It should be noted that alternate antibodies directed to the same markers that are recognized by the antibodies listed in Table IA are available, or can be readily developed. Such alternate antibodies can also be employed for assessing expression of markers in the cells isolated in accordance with the present invention. Formation of cells expressing markers of the pancreatic endocrine lineage: 101991 Cells expressing markers characteristic of the pancreatic endoderm lineage may be differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage by any method in the art or by any method disclosed in this invention. [0200] For example, cells expressing markers characteristic of the pancreatic endoderm lineage may be differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage according to the methods disclosed in D'Amour et al, Nature Biotechnology 24, 1392 - 1401 (2006). [02011 For example, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing DAPT and exendin 4, then removing the medium containing DAPT and exendin 4 and subsequently culturing the cells in medium containing exendin 1, IGF-1 and HGF. An example of this method is disclosed in Nature Biotechnology 24, 1392 - 1401 (2006). [0202] For example, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by culturing the cells 54 expressing markers characteristic of the pancreatic endoderm lineage in medium containing exendin 4, then removing the medium containing exendin 4 and subsequently culturing the cells in medium containing exendin 1, IGF-1 and HGF. An example of this method is disclosed in D' Amour et al, Nature Biotechnology, 2006. [02031 For example, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing DAPT and exendin 4. An example of this method is disclosed in D' Amour et al, Nature Biotechnology, 2006. [02041 For example, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing exendin 4. An example of this method is disclosed in D' Amour et al, Nature Biotechnology, 2006. [02051 In one aspect of the present invention, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by treating the cells expressing markers characteristic of the pancreatic endoderm lineage with a factor that inhibits the Notch signaling pathway. The factor that inhibits the Notch signaling pathway may be an antagonist for the Notch extracellular receptor. Alternatively, the factor may inhibit the biological activity of the Notch receptor. Alternatively, the factor may inhibit or be an antagonist of an element in the Notch signal transduction pathway within a cell. [0206] In one embodiment the factor that inhibits the Notch signaling pathway is a y secretase inhibitor. In one embodiment, the I-secretase inhibitor is I SBenzyl 4R-[ 1-(1 S-carbamoyl-2-phenethylcarbamoyl)- I S-3-methylbutylcarbamoyl]-5 55 2Rhydrozy- 5 phenylpentyl] carbamic Acid tert-butyl Ester, also known as L 685,458. [02071 L-685,458 may be used at a concentration from about 0. 1IM to about 100pM. In one embodiment, L-685,458 is used at a concentration of about 90pM. In one embodiment, L-685,458 is used at a concentration of about 80pM. In one embodiment, L-685,458 is used at a concentration of about 70PM. In one embodiment, L-685,458 is used at a concentration of about 60pM. In one embodiment, L-685,458 is used at a concentration of about 50PM. In one embodiment, L-685,458 is used at a concentration of about 40PM. In one embodiment, L-685,458 is used at a concentration of about 30pM. In one embodiment, L-685,458 is used at a concentration of about 20ptM. In one embodiment, L-685,458 is used at a concentration of about 10pM. [0208] In one embodiment, the present invention provides a method for differentiating cells expressing markers characteristic of the pancreatic endoderm lineage into cells expressing markers characteristic of the pancreatic endocrine lineage, comprising the steps of: a. Culturing cells expressing markers characteristic of the pancreatic endoderm lineage, and b. Treating the cells with a factor that inhibits the Notch signaling pathway. [0209] Any cell expressing markers characteristic of the pancreatic endoderm lineage is suitable for differentiating into a cell expressing markers characteristic of the pancreatic endocrine lineage using this method. 102101 In one embodiment, factor that inhibits the Notch signaling pathway is ay secretase inhibitor. In one embodiment, the y-secretase inhibitor is 1 S-Benzyl 4R-[1-(1S-carbamoyl-2-phenethylcarbamoyl)-1S-3-methylbutylcarbamoyl] 2R-hydrozy-5-phenylpentyl] carbamic Acid tert-butyl Ester, also known as L 685,458. 56 [021.11 The cells expressing markers characteristic of the pancreatic endoderm lineage are treated with the factor that inhibits the Notch signaling pathway for about one to about five days. Alternatively, the cells expressing markers characteristic of the pancreatic endoderm lineage are treated with the factor that inhibits the Notch signaling pathway for about three to about five days. Alternatively, the cells expressing markers characteristic of the pancreatic endoderm lineage are treated with the factor that inhibits the Notch signaling pathway for about five days. [02121 In one embodiment, factor that inhibits the Notch signaling pathway is a y secretase inhibitor. In one embodiment, the y-secretase inhibitor is 1 S-Benzyl 4R-[1-(IS-carbamoyl-2-phenethylcarbamoyl)-1 S-3-methylbutylcarbamoyl] 2R-hydrozy-5-phenylpentyl] carbamic Acid tert-butyl Ester, also known as L 685,458. [0213] L-685,458 may be used at a concentration from about 0.1 PM to about 100pM. In one embodiment, L-685,458 is used at a concentration of about 90pM. In one embodiment, L-685,458 is used at a concentration of about 80pM. In one embodiment, L-685,458 is used at a concentration of about 70PM. In one embodiment, L-685,458 is used at a concentration of about 60pM. In one embodiment, L-685,458 is used at a concentration of about 50pM. In one embodiment, L-685,458 is used at a concentration of about 40PM. In one embodiment, L-685,458 is used at a concentration of about 30PM. In one embodiment, L-685,458 is used at a concentration of about 20pM. In one embodiment, L-685,458 is used at a concentration of about I 0pM. [0214] Cells expressing markers characteristic of the pancreatic endoderm lineage may be treated with at least one other additional factor that may enhance the formation of cells expressing markers characteristic of the pancreatic endocrine lineage. Alternatively, the at least one other additional factor may enhance the proliferation of the cells expressing markers characteristic of the pancreatic endocrine lineage formed by the methods of the present invention. Further, the at least one other additional factor may enhance the ability of the 57 cells expressing markers characteristic of the pancreatic endocrine lineage formed by the methods of the present invention to form other cell types, or improve the efficiency of any other additional differentiation steps. 10215] The at least one additional factor may be, for example, nicotinamide, members of TGF-P family, including TGF-01, 2, and 3, serum albumin, members of the fibroblast growth factor family, platelet-derived growth factor-AA, and -BB, platelet rich plasma, insulin growth factor (IGF-I, II), growth differentiation factor (GDF-5, -6, -8, -10, 11), glucagon like peptide-I and II (GLP-I and II), GLP- 1 and GLP-2 mimetobody, Exendin-4, retinoic acid, parathyroid hormone, insulin, progesterone, aprotinin, hydrocortisone, ethanolamine, beta mercaptoethanol, epidermal growth factor (EGF), gastrin I and II, copper chelators such as, for example, triethylene pentamine, forskolin, Na-Butyrate, activin, betacellulin, ITS, noggin, neurite growth factor, nodal, valporic acid, trichostatin A, sodium butyrate, hepatocyte growth factor (HGF), sphingosine 1, VEGF, MG132 (EMD, CA), N2 and B27 supplements (Gibco, CA), steroid alkaloid such as, for example, cyclopamine (EMD, CA), keratinocyte growth factor (KGF), Dickkopf protein family, bovine pituitary extract, islet neogenesis-associated protein (INGAP), Indian hedgehog, sonic hedgehog, proteasome inhibitors, notch pathway inhibitors, sonic hedgehog inhibitors, or combinations thereof. [02161 The at least one other additional factor may be supplied by conditioned media obtained from pancreatic cells lines such as, for example, PANC-1 (ATCC No: CRL-1469), CAPAN-1 (ATCC No: HTB-79), BxPC-3 (ATCC No: CRL 1687), HPAF-11 (ATCC No: CRL-1997), hepatic cell lines such as, for example, H~epG2 (ATCC No: HTB-8065), and intestinal cell lines such as, for example, FHs 74 (ATCC No: CCL-241). Detection of cells expressing markers characteristic of the pancreatic endocrine linage [02171 Markers characteristic of cells of the pancreatic endocrine lineage are well known to those skilled in the art, and additional markers characteristic of the 58 pancreatic endocrine lineage continue to be identified. These markers can be used to confirm that the cells treated in accordance with the present invention have differentiated to acquire the properties characteristic of the pancreatic endocrine lineage. Pancreatic endocrine lineage specific markers include the expression of one or more transcription factors such as, for example, NGN-3, NeuroD, Islet-1. [02181 Markers characteristic of cells of the [ cell lineage are well known to those skilled in the art, and additional markers characteristic of the P cell lineage continue to be identified. These markers can be used to confirm that the cells treated in accordance with the present invention have differentiated to acquire the properties characteristic of the p-cell lineage. P cell lineage specific characteristics include the expression of one or more transcription factors such as, for example, Pdxl (pancreatic and duodenal homeobox gene-1), Nkx2.2, Nkx6. 1, Isll, Pax6, Pax4, NeuroD, Hnflb, Hnf-6, Hnf-3beta, and MafA, among others. These transcription factors are well established in the art for identification of endocrine cells. See, e.g., Edlund (Nature Reviews Genetics 3: 524-632 (2002)). [0219] The efficiency of differentiation may be determined by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker expressed by cells expressing markers characteristic of the pancreatic endocrine lineage. Alternatively, the efficiency of differentiation may be determined by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker expressed by cells expressing markers characteristic of the p cell lineage. [02201 Methods for assessing expression of protein and nucleic acid markers in cultured or isolated cells are standard in the art. These include quantitative reverse transcriptase polymerase chain reaction (RT-PCR), Northern blots, in situ hybridization (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 2001 supplement)), and immunoassays such as immunohistochemical analysis of sectioned material, Western blotting, and for 59 markers that are accessible in intact cells, flow cytometry analysis (FACS) (see, e.g., Harlow and Lane, Using Antibodies: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press (1998)). [0221] Examples of antibodies useful for detecting certain protein markers are listed in Table IA. It should be noted that alternate antibodies directed to the same markers that are recognized by the antibodies listed in Table IA are available, or can be readily developed. Such alternate antibodies can also be employed for assessing expression of markers in the cells isolated in accordance with the present invention. Therapies 102221 In one aspect, the present invention provides a method for treating a patient suffering from, or at risk of developing, Type1 diabetes. This method involves culturing pluripotent stem cells, differentiating the pluripotent stem cells in vitro into a p-cell lineage, and implanting the cells of a p-cell lineage into a patient. [0223] In yet another aspect, this invention provides a method for treating a patient suffering from, or at risk of developing, Type 2 diabetes. This method involves culturing pluripotent stem cells, differentiating the cultured cells in vitro into a $-cell lineage, and implanting the cells of ap-cell lineage into the patient. [02241 If appropriate, the patient can be further treated with pharmaceutical agents or bioactives that facilitate the survival and function of the transplanted cells. These agents may include, for example, insulin, members of the TGF-Q family, including TGF- 1, 2, and 3, bone morphogenic proteins (BMP-2, -3, 4, -5, -6, -7, -l1, -12, and -13), fibroblast growth factors-I and -2, platelet derived growth factor-AA, and -BB, platelet rich plasma, insulin growth factor (IGF-I, II) growth differentiation factor (GDF-5, -6, -7, -8, -10, -15), vascular endothelial cell-derived growth factor (VEGF), pleiotrophin, endothelin, among others. Other pharmaceutical compounds can include, for 60 example, nicotinamide, glucagon like peptide-I (GLP-1) and II, GLP-1 and 2 mimetibody, Exendin-4, retinoic acid, parathyroid hormone, MAPK inhibitors, such as, for example, compounds disclosed in U.S. Published Application 2004/0209901 and U.S. Published Application 2004/0132729. [02251 The pluripotent stem cells may be differentiated into an insulin-producing cell prior to transplantation into a recipient. In a specific embodiment, the pluripotent stem cells are fully differentiated into $-cells, prior to transplantation into a recipient. Alternatively, the pluripotent stem cells may be transplanted into a recipient in an undifferentiated or partially differentiated state. Further differentiation may take place in the recipient. [0226] Definitive endoderm cells or, alternatively, pancreatic endoderm cells, or, alternatively, Q cells, may be implanted as dispersed cells or formed into clusters that may be infused into the hepatic portal vein. Alternatively, cells may be provided in biocompatible degradable polymeric supports, porous non degradable devices or encapsulated to protect from host immune response. Cells may be implanted into an appropriate site in a recipient. The implantation sites include, for example, the liver, natural pancreas, renal subcapsular space, omentum, peritoneum, subserosal space, intestine, stomach, or a subcutaneous pocket. [0227] To enhance further differentiation, survival or activity of the implanted cells, additional factors, such as growth factors, antioxidants or anti-inflammatory agents, can be administered before, simultaneously with, or after the administration of the cells. In certain embodiments, growth factors are utilized to differentiate the administered cells in vivo. These factors can be secreted by endogenous cells and exposed to the administered cells in situ. Implanted cells can be induced to differentiate by any combination of endogenous and exogenously administered growth factors known in the art. [02281 The amount of cells used in implantation depends on a number of various factors including the patient's condition and response to the therapy, and can be determined by one skilled in the art. 61 [0229] In one aspect, this invention provides a method for treating a patient suffering from, or at risk of developing diabetes. This method involves culturing pluripotent stem cells, differentiating the cultured cells in vitro into a p-cell lineage, and incorporating the cells into a three-dimensional support. The cells can be maintained in vitro on this support prior to implantation into the patient. Alternatively, the support containing the cells can be directly implanted in the patient without additional in vitro culturing. The support can optionally be incorporated with at least one pharmaceutical agent that facilitates the survival and function of the transplanted cells. [02301 Support materials suitable for use for purposes of the present invention include tissue templates, conduits, barriers, and reservoirs useful for tissue repair. In particular, synthetic and natural materials in the form of foams, sponges, gels, hydrogels, textiles, and nonwoven structures, which have been used in vitro and in vivo to reconstruct or regenerate biological tissue, as well as to deliver chemotactic agents for inducing tissue growth, are suitable for use in practicing the methods of the present invention. See, for example, the materials disclosed in U.S. Patent 5,770,417, U.S. Patent 6,022,743, U.S. Patent 5,567,612, U.S. Patent 5,759,830, U.S. Patent 6,626,950, U.S. Patent 6,534,084, U.S. Patent 6,306,424, U.S. Patent 6,365,149, U.S. Patent 6,599,323, U.S. Patent 6,656,488, U.S. Published Application 2004/0062753 A l, U.S. Patent 4,557,264and U.S. Patent 6,333,029. [02311 To form a support incorporated with a pharmaceutical agent, the pharmaceutical agent can be mixed with the polymer solution prior to forming the support. Alternatively, a pharmaceutical agent could be coated onto a fabricated support, preferably in the presence of a pharmaceutical carrier. The pharmaceutical agent may be present as a liquid, a finely divided solid, or any other appropriate physical form. Alternatively, excipients may be added to the support to alter the release rate of the pharmaceutical agent. In an alternate embodiment, the support is incorporated with at least one pharmaceutical compound that is an anti-inflammatory compound, such as, for example compounds disclosed in U.S. Patent 6,509,369. 62 [02321 The support may be incorporated with at least one pharmaceutical compound that is an anti-apoptotic compound, such as, for example, compounds disclosed in U.S. Patent 6,793,945. [02331 The support may also be incorporated with at least one pharmaceutical compound that is an inhibitor of fibrosis, such as, for example, compounds disclosed in U.S. Patent 6,331,298. [02341 The support may also be incorporated with at least one pharmaceutical compound that is capable of enhancing angiogenesis, such as, for example, compounds disclosed in U.S. Published Application 2004/0220393 and U.S. Published Application 2004/0209901. 102351 The support may also be incorporated with at least one pharmaceutical compound that is an immunosuppressive compound, such as, for example, compounds disclosed in U.S. Published Application 2004/0171623. [02361 The support may also be incorporated with at least one pharmaceutical compound that is a growth factor, such as, for example, members of the TGF f family, including TGF-P 1, 2, and 3, bone morphogenic proteins (BMP-2, -3, -4, -5, -6, -7, -11, -12, and -13), fibroblast growth factors-I and -2, platelet derived growth factor-AA, and -BB, platelet rich plasma, insulin growth factor (IGF-I, II) growth differentiation factor (GDF-5, -6, -8, -10, -15), vascular endothelial cell-derived growth factor (VEGF), pleiotrophin, endothelin, among others. Other pharmaceutical compounds can include, for example, nicotinamide, hypoxia inducible factor 1-alpha, glucagon like peptide-I (GLP-1), GLP-1 and GLP-2 mimetibody, and II, Exendin-4, nodal, noggin, NGF, retinoic acid, parathyroid hormone, tenascin-C, tropoelastin, thrombin-derived peptides, cathelicidins, defensins, laminin, biological peptides containing cell- and heparin-binding domains of adhesive extracellular matrix proteins such as fibronectin and vitronectin, MAPK inhibitors, such as, for example, compounds disclosed in U.S. Published Application 2004/0209901 and U.S. Published Application 2004/0132729. 63 [02371 The incorporation of the cells of the present invention into a scaffold can be achieved by the simple depositing of cells onto the scaffold. Cells can enter into the scaffold by simple diffusion (J. Pediatr. Surg. 23 (1 Pt 2): 3-9 (1988)). Several other approaches have been developed to enhance the efficiency of cell seeding. For example, spinner flasks have been used in seeding of chondrocytes onto polyglycolic acid scaffolds (Biotechnol. Prog. 14(2): 193 202 (1998)). Another approach for seeding cells is the use of centrifugation, which yields minimum stress to the seeded cells and enhances seeding efficiency. For example, Yang et al. developed a cell seeding method (J. Biomed. Mater. Res. 55(3): 379-86 (2001)), referred to as Centrifugational Cell Immobilization (CCI). [02381 The present invention is further illustrated, but not limited by, the following examples. 64 EXAMPLES Example 1 Human Embryonic Stem Cell Culture 102391 The human embryonic stem cell lines Hl, H7 and H9 were obtained from WiCell Research Institute, Inc., (Madison, WI) and cultured according to instructions provided by the source institute. Briefly, cells were cultured on mouse embryonic fibroblast (MEF) feeder cells in ES cell medium consisting of DMEM/F12 (Invitrogen/GIBCO) supplemented with 20% knockout serum replacement, 100 nM MEM nonessential amino acids, 0.5 mM beta mercaptoethanol, 2mM L-glutamine with 4ng/ml human basic fibroblast growth factor (bFGF) (all from Invitrogen/GIBCO). MEF cells, derived from E13 to 13.5 mouse embryos, were purchased from Charles River. MEF cells were expanded in DMEM medium supplemented with 10% FBS (Hyclone), 2mM glutamine, and 100 mM MEM nonessential amino acids. Sub-confluent MEF cell cultures were treated with 1Opg/ml mitomycin C (Sigma, St. Louis, MO) for 3h to arrest cell division, then trypsinized and plated at 2x 10 4 /cm 2 on 0. 1% bovine gelatin-coated dishes. MEF cells from passage two through four were used as feeder layers. Human embryonic stem cells plated on MEF cell feeder layers were cultured at 37'C in an atmosphere of 5% C0 2 / within a humidified tissue culture incubator. When confluent (approximately 5-7 days after plating), human embryonic stem cells were treated with 1mg/ml collagenase type IV (Invitrogen/GIBCO) for 5-10 min and then gently scraped off the surface using a 5-ml pipette. Cells were spun at 900 rpm for 5 min, and the pellet was resuspended and re-plated at a 1:3 to 1:4 ratio of cells in fresh culture medium. Example 2 Formation of Definitive Endoderm 65 [0240] The effects of activin A on the expression of markers of definitive endoderm were examined. Activin A (100ng/ml) was added to populations of human embryonic stem cells cultured on mouse embryonic fibroblasts. Cells were cultured continuously in the presence of activin A and harvested at the times indicated. The level of expression of definitive endoderm markers was examined by PCR (Figure 1), FACS (results summarized in Table II), and immunohistochemistry (Figure 2). [0241] Activin A evoked a time-dependent increase in the expression of CXCR4, GATA4, HNF-3beta, MixIl and Sox-17 mRNA in the H9 line (Figure 1, panel a). A significant up regulation of anterior endoderm markers, Cerberus, Otx-l and Hex genes was also observed (Figure 1, panel b). An increase in CXCR4 protein was observed by FACS analysis following activin A treatment. The expression of E-cadherin and N-cadherin did not change following activin A treatment (Table 11A). CXCR4 positive cells were also highly positive for C-kit, EPCAM, CD99, and negative for CD9. The expression pattern for these markers was consistent among all three hES cell lines examined (Table IIB for H7 and Table IIC for H1). Immunocytochemistry conducted on cells treated with activin A for five days revealed that 30-40% cells in the treated culture were positive for Sox17 and HNF-3beta. In parallel, almost 100% of the differentiated cells were still Oct4 positive (Figure 2). With the decrease in expression of surface markers of pluripotency, combined with an increase in the expression of definitive endoderm markers, these data suggest that activin A promotes the differentiation of human embryonic stem cells to definitive endoderm. Example 3 Formation of Pancreatic Endoderm 102421 Growth factors known to induce the differentiation of human embryonic stem cells to pancreatic endoderm were added to cell cultures. In particular, activin 66 A, bFGF, and retinoic acid, known to induce the formation of pancreatic endoderm, were added to cell cultures. [02431 In a first series of experiments, activin A, was added to populations of human embryonic stem cells cultured on mouse embryonic fibroblasts for up to seven days in DMEM/F12 supplemented with 0% to 2% serum and Activin A (100 ng/ml). Cells were harvested at the time points indicated in Figure 3 and assayed by PCR for the expression of genes shown (Figures 3, 4 and 5). In Figure 3, PCR analysis indicated that activin treated cells expressed a broad spectrum of genes associated with endoderm development, including GATA4 (Figure 3, panel a), Sox-17 (Figure 3, panel b), HNF-3beta (Figure 3, panel c), and Mixl-1 (Figure 3, panel d). However, no Pdxl gene expression was observed. The same expression pattern of endoderm lineage markers was observed in Activin A treated H7 cells (Figure 6, panels a to f). At this stage, there was no significant decrease of Oct4 expression. [02441 Activin A evoked a time-dependent decrease in the expression of the extraembryonic endoderm markers Sox7 (Figure 4, panel a) and AFP (Figure 4, panel b). Activin A decreased the expression of Brachyury (Figure 5, panel a) but had no effect on expression of the neuronal marker ZicI (Figure 5, panel b). [02451 Taken together, these data suggest that the increased expression of Sox-17, Mixll, Gata4, and HNF-3beta together with the upregulation of anterior endoderm markers Otxl, Cerl and Hex genes, corresponds to the formation of definitive endoderm in response to activin A treatment. Analysis of definitive endoderm markers by immunocytochemistry revealed that protein expression for these genes also reflected the trends observed in mRNA expression. Levels of expression for HNF-3beta, Sox- 17, and GATA4 were low in untreated cells, approximately 10 to 20% of all cells. Activin A (100ng/ml) treatment for five days increased the expression of HNF-3beta, Sox-17, and GATA4 to approximately 50% to 90%of all cells (Figure 7). 67 [0246] In a second series of experiments, cultures of human embryonic stem cells were maintained in undifferentiated culture conditions for 2-3 days according to the methods described in Example 1. After the cells were 70-80% confluent, the medium was changed to DMEM/F 12 with 0 to 2% FBS with addition of activin A at 100 ng/ml and cultured in the presence of activin A for either three, five, or seven days. After this time interval, the cells were then further treated for five to six days with combinations of retinoic acid and bFGF as shown in Figure 8. Cultures were harvested and samples of mRNA were collected for analysis. Control cultures consisting of cells treated with activin A alone for five days were also included. 102471 Gene expression analysis revealed that activin A or retinoic acid alone did not induce the expression of Pdxl. Similar results were observed in cultures of cells treated with retinoic acid in combination with FGF and in the presence of activin A (Figure 8, panel a). However, treatment of cells with retinoic acid and FGF in the absence of activin A increased the expression of Pdx1 still further (Figure 8, panel a). Cells treated for three days with activin A, then treated for 5 days with IpM retinoic acid and 50ng/ml bFGF (also known as FGF-2) in the absence of activin A showed a level of Pdx 1 expression that was approximately 3500-fold higher than that observed in samples with activin A treatment alone for 5 days (Figure 8, panel a). Immunocytochemistry showed that 5 to 20% of all cells expressed Pdxl (Figure 9). [02481 Treatment with 1 pM retinoic acid and bFGF in the absence of activin A also caused an increase in the expression of GLUT-2 and PTF 1 a (Figure 8, panel c) that was not observed in cells treated in the presence of activin A alone. The largest increase in expression of GLUT-2 and PTF la was observed in cells treated with IpM retinoic acid and 50ng/ml bFGF. Taken together, these data suggest that the formation of pancreatic endoderm is further enhanced by removal of activin A from cell cultures after definitive endoderm has been formed. Example 4 68 Formation of Pancreatic Endocrine Cells [02491 Cultures of human embryonic stem cells were maintained in undifferentiated culture conditions for 3-4 days according to the methods described in Example 1. After the cells were 50-60% confluent, the medium was changed to DMEM/F12 without FBS, containing activin A at 100 ng/ml, and the cells were cultured in this medium for one day. Following the one day culture, the medium was removed and replaced with medium containing 0.5% FBS with 100 ng/ml activin A, and the cells were cultured for one day. Following the second one-day culture, the medium was removed and replaced with medium containing 2% FBS with 100 ng/ml activin A, and the cells were cultured for one day. After this time interval, the cells were then treated for six days with combinations of retinoic acid and FGF as outlined in Example 2, then the culture medium was removed and replaced with medium comprising DMEMIF12 with 2% FBS, containing the y-secretase inhibitors L-685,458 at 10pM for three days. Cultures were harvested and samples of mRNA were collected for analysis. Control cultures consisting of cells treated with activin A alone for five days were also included. [02501 Gene expression analysis revealed that activin A alone or in combination with retinoic acid and FGFs did not induce the expression of Ngn3 or Insulin (Figure 10, panel a, c). A decrease in the expression of Hes-1 was also observed following treatment with L- 685,458. The maximal inhibition was observed on day three post treatment (Figure 10, panel d). However, treatment of cells with L-685,458 induced the expression of Ngn3 to a level approximately 50-fold higher than that observed in samples treated with activin A alone or retinoic acid with FGFs in combination. A 70-fold increase of insulin expression was observed in samples treated with the y-secretase inhibitor. NeuroDI expression was also increased further by the L-685,458 treatment (FigurelO, panel a). Taken together, these data suggest that the formation of endocrine cells is further enhanced by removal of retinoic acid 69 and FGFs from cell culture and the addition of i-secretase inhibitors after pancreatic endoderm has been formed. Example 5 Formation of Pancreatic Endocrine Cells Expressing Nkx2.2 [02511 Definitive endoderm cells obtained according to the methods outlined in Example 2 were treated as follows: Cells were cultured in basal medium, comprising DMEM/F 12 with 2% FBS plus 50 ng/ml activin A, 50 ng/ml basic FGF and 1 pM of Retinoic Acid for 3 to 5 days. Cells were continuously cultured for another 3 to 5 days in basal medium with retinoic acid at I PM, alone or with bFGF. RNA samples were harvested from cells at various time points along this process to help evaluate the directed differentiation of the cells. Furthermore, culture medium and factors were regularly removed and replenished throughout the differentiation protocol. Addition of activin A showed an increase of Nkx2.2 expression about 35-fold compared to samples without activin A. Samples treated with activin A for the first three days of culture maintained Pdx1 expression at a level similar to samples containing no activin A (Figure 11). Taken together, these data suggest that the expression of the pancreatic endocrine marker Nkx2.2 is further enhanced by adding Activin A to the first three days of retinoic acid and bFGF treatment. Example 6 Passage and Expansion of Pancreatic Endoderm Cells in Culture 10252] This example demonstrates that pancreatic endoderm cells derived from human embryonic stem cells herein can be maintained in cell culture and passaged without further differentiation. Pancreatic endoderm cells were differentiated in the presence of 100 ng/ml activin A in low serum DMEM/F 12. The low serum DMEM/F12 contained 0% (v/v) fetal bovine serum (FBS) on day 1, 0.5 % (v/v) FBS on day two and 2% (v/v) FBS on each day thereafter. After four days of differentiation, the cells were cultured in 70 low serum DMEM/F12 contained 2% (v/v) FBS, I pAM retinoic acid and 50 ng/ml bFGF for a total of six more days. After the six days of differentiation, the cells were maintained in culture in low serum DMEM/F12 contained 2% (v/v) FBS in the presence of 50 ng/ml FGF 10 for a total of 6 days. During the six-day culture period, the pancreatic endoderm cells were passaged twice and cell population-doubling time is about 36 to 48 hours during this 6-day culture. On days 0, 3, and 6 of culture, Q-PCR was used to measure the expression of marker genes indicative of pancreatic endoderm. Figure 12 shows that cells grown in the presence of 5Ong/ml FGF10 maintained expression of the pancreatic endoderm marker Pdx 1 during the 6 day culture period subsequent to their derivation. Example 7 Derivation of Hepatocytes from Human Embryonic Stem Cells [02531 Cultures of human embryonic stem cells were maintained in undifferentiated culture conditions for 2-3 days according to the methods described in Example 1. After cells were 70-80% confluent, the medium was changed to DMEM/F12 with 2% FBS containing activin A at 100 ng/ml, and cells were cultured in the presence of activin A for seven days. After 7 days treatment with activin A, the cells were then treated for five days with the conditions shown in Figure 13. After this time, the cells were harvested, and samples of mRNA were collected for analysis. 102541 An increase in the expression of a-fetoprotein (AFP) and albumin was observed (Figure 13, panel a) for cells cultured in the absence of activin A. This was further increased by retinoic acid and FGF-4 (Figure 13, panel b). Taken together, these data suggest that cultures of human embryonic stem cells are capable of expressing hepatocyte markers following the treatment described above. Furthermore, human embryonic stem cells are capable of being differentiated into cells expressing markers that are characteristic of hepatocytes. 71 Example 8 Characterization of the H9 Human Embryonic Stem Cell Line [02551 The quality of H9 cells was monitored over time by evaluating expression of several markers expressed by undifferentiated ES cells (Carpenter et al., 2001; Reubinoff et al., 2000; Thomson et al., 1998a). H9 cells exhibited reciprocal expression of stage-specific embryonic antigens (Table 111). H9 cells play strong immunoreactivity for SSEA-3, SSEA-4, Tra-1-60, Tra-l-81, AP and CD9 antigens, all of which are characteristic of undifferentiated human embryonic stem cells. [02561 RT-PCR was performed to assess the expression of genes characteristic of embryonic stem cells, such as, for example, OCT3/4, SOX-2, UTF-l, REX-1, Cx43, Cx45, ABCG-2 and TERT, confirming that the cells grown in this example appeared similar to previously described undifferentiated embryonic stem cells (Table 11). OCT3/4 protein expression and Alkaline Phosphatase activity (Chemicon) were confirmed by immunostaining. A majority of H9 cells were positive for OCT3/4 and AP (Figure 14). Overall, these results demonstrate that the H9 cells used in this example were not significantly different in morphology, antigen immunostaining, or pluripotency marker expression when compared to reports from other laboratories. Example 9 Fluorescence-Activated Cell Sorting (FACS) Analysis [02571 Adhered cells were removed from culture plates by five-minute incubation with TrypLETM Express solution (Invitrogen, CA). Released cells were resuspended in human embryonic stem cell culture medium and recovered by centrifugation, followed by washing and resuspending the cells in a staining buffer consisting of 2% BSA, 0.05% sodium azide in PBS (Sigma, MO). As appropriate, the cells were Fc-receptor blocked for 15 minutes using a 0.1% y-globulin (Sigma) solution. Aliquots (approximately 105 cells) were 72 incubated with either phycoerythirin (PE) or allophycocyanin (APC) conjugated monoclonal antibodies (5 pl antibody per 106 cells), as indicated in Table 1, or with an unconjugated primary antibody. Controls included appropriate isotype matched antibodies, unstained cells, and cells stained only with secondary conjugated antibody. All incubations with antibodies were performed for 30 mins at 4'C after which the cells were washed with the staining buffer. Samples that were stained with unconjugated primary antibodies were incubated for an additional 30 mins at 4'C with secondary conjugated PE or -APC labeled antibodies. See Table I for a list of secondary antibodies used. Washed cells were pelleted and resuspended in the staining buffer, and the cell surface molecules were identified using a FACS Array (BD Biosciences) instrument, collecting at least 10,000 events. Example 10 Immunocytochemistry [02581 Cells seeded on 0.1% Matrigel (BD) coated dishes were fixed with 4% paraformaldheyde for 20 min at room temperature. Fixed cells were blocked for 1 h at room temperature with PBS/0.1%BSA10% normal chick serum /0.5% Triton X-100 and then incubated overnight with primary antibodies in PBS/0.1%BSA/10% normal chick serum at 4'C. The list of primary antibodies and their working dilutions are shown in Table IB. After three washes in PBS/0.1% BSA, fluorescent secondary antibodies at a 1:100 dilution in PBS were incubated with cells for 1 h at room temperature to allow binding. Control samples included reactions where the primary antibody was omitted or where the primary antibody was replaced with corresponding matched negative control immunoglobulins at the same concentration as the primary antibodies. Stained samples were rinsed; a drop of PROLONG@ (Invitrogen, CA) containing diamidino-2-phenylindole, dihydrochloride (DAPI) was added to each sample to counter-stain the nucleus and to function as an anti-fade reagent. Images were acquired using a Nikon Confocal Eclipse C-I inverted microscope (Nikon, Japan) and a 10-60X objective. 73 Example 11 PCR Analysis of Undifferentiated Cells 102591 RNA extraction, purification, and cDNA synthesis. RNA samples were purified by binding to a silica-gel membrane (Rneasy Mini Kit, Qiagen, CA) in the presence of an ethanol-containing, high-salt buffer followed by washing to remove contaminants. The RNA was further purified using a TURBO DNA-free kit (Ambion, INC), and high-quality RNA was then cluted in water. Yield and purity were assessed by A260 and A280 readings on a spectrophotometer. cDNA copies were made from purified RNA using an ABI (ABI, CA) high capacity cDNA archive kit. [02601 Real-time PCR amplification and quantitative analysis. Unless otherwise stated, all reagents were purchased from Applied Biosystems. Real-time PCR reactions were performed using the ABI PRISM@ 7900 Sequence Detection System. TAQMAN@ UNIVERSAL PCR MASTER MIX@ (ABI, CA) was used with 20 ng of reverse transcribed RNA in a total reaction volume of 20 pl. Each cDNA sample was run in duplicate to correct for pipetting errors. Primers and FAM-labeled TAQMAN@probes were used at concentrations of 200 nM. The level of expression for each target gene was normalized using a human glyceraldehyde-3 -phosphate dehydrogenase (GAPDH) endogenous control previously developed by Applied Biosystem. Primer and probe sets are listed as follows: Oct3/4 (Hs00742896), SOX-2 (Hs00602736), UTF-1 (Hs00747497), Rex-1 (Hs00399279), Connexin 43 (Hs00748445), Connexin 45 (Hs00271416), ABCG2 (Hs00184979), Otx-1 (Hs00222238), Cerberus (HsO0 193 796)m, Albumin (Hs006094 11). [02611 After an initial incubation at 50'C for 2 min followed by 95 0 C for 10 min, samples were cycled 40 times in two stages - a denaturation step at 95'C for 15 sec followed by an annealing/extension step at 60'C for 1 min. Data analysis was carried out using GENEAMP@7000 Sequence Detection System software. For each primer/probe set, a Ct value was determined as the cycle 74 number at which the fluorescence intensity reached a specific value in the middle of the exponential region of amplification. Relative gene expression levels were calculated using the comparative Ct method. Briefly, for each cDNA sample, the endogenous control C, value was subtracted from the gene of interest Ct to give the delta Ct value (ACt). The normalized amount of target was calculated as 2 -ACt, assuming amplification to be 100% efficiency. Final data were expressed relative to a calibrator sample. Example 12 Karyotype analysis [02621 The karyotype of H9 cells was determined by standard G-banding karyotype analysis. A total of 100 metaphase spreads were evaluated (Applied Genetics Laboratories, Inc.). No chromosome aberrations were found in 100 cells analyzed. Cytogenetic analysis showed that the cells had a normal number of autosomes and a modal chromosome number of 46. Figure 15 depicts a typical karyotype obtained from the human embryonic stem cell line H9. Example 13 Human Embryonic Stem Cell Culture on Tissue Culture Substrate Coated with Extracellular Matrix 10263] The human embryonic stem cell lines HI, H7, and H9 were obtained from WiCell Research Institute, Inc., (Madison, WI) and cultured according to instructions provided by the source institute. Briefly, cells were cultured on mouse embryonic fibroblast (MEF) feeder cells in ES cell medium consisting of DMEM/F 12 (Invitrogen/GIBCO) supplemented with 20% knockout serum replacement, 100 nM MEM nonessential amino acids, 0.5 mM beta mercaptoethanol, 2mM L-glutamine with 4ng/ml human basic fibroblast growth factor (bFGF). MEF cells, derived from E13 to 13.5 mouse embryos, were purchased from Charles River. MEF cells were expanded in DMEM medium supplemented with 10% FBS (Hyclone), 2mM glutamine, and 100 75 mM MEM nonessential amino acids. Sub-confluent MEF cell cultures were treated with 10pg/ml mitomycin C (Sigma, St. Louis, MO) for 3h to arrest cell division, then trypsinized and plated at 2x104/cm2 on 0.1% bovine gelatin coated dishes. MEF cells from passage two through four were used as feeder layers. Human embryonic stem cells plated on MEF cell feeder layers were cultured at 37 0 C in an atmosphere of 5% CO 2 within a humidified tissue culture incubator. When confluent (approximately 5 to 7 days after plating), human embryonic stem cells were treated with lmg/ml collagenase type IV (Invitrogen/GIBCO) for 5 to 10 min and then gently scraped off the surface using a 5ml glass pipette. Cells were centrifuged at 900 rpm for 5 min, and the pellet was resuspended and re-plated at a 1:3 to 1:4 ratio of cells on plates coated with a 1:30 dilution of growth factor reduced MATRIGEL TM (BD Biosciences). Cells were subsequently cultured in MEF-conditioned media supplemented with 8 ng/ml bFGF and collagenase passaged on MATRIGEL coated plates for at least five passages. The cells cultured on MATRIGELTM were routinely passaged with collagenase IV (Invitrogen/GIBCO), Dispase (BD Biosciences) or Liberase enzyme (Roche, IN). Example 14 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with Extracellular Matrix to Definitive Endoderm 102641 Differentiation of embryonic stem cells to definitive endoderm was carried out as previously described in Nature Biotechnology 23, 1534-1541 (Dec 2005). Briefly, H9 cultures at approximately 60 to 70% confluency were exposed to DMEM:/F 12 medium supplemented with 0.5% FBS and 100 ng/ml activin A for two days, followed by treatment with DMEM/F 12 medium supplemented with 2% FBS and 100 ng/ml activin A (AA) for an additional three days. H9 cells were cultured on plates coated with growth factor reduced MATRIGEL at a 1:30 to 1:10 dilution or on regular MATRIGEL at al:30 to 1:10 dilution The plates were coated with MATRIGEL for 1 hr at room temperature. 76 [0265] At day 5, the cultures were analyzed by FACS for CXCR4, E-cadherin, CD9, and N-cadherin expression and by real time PCR for SOX-17, SOX-7, Alpha fetal protein (AFP), CXCR4, Brychyury (Bry), gooscecoid (GSC), HNF-3 beta, and GATA4. AFP and SOX-7 are regarded as visceral endoderm markers, while GATA4, HNF-3 beta and SOX-17 represent definite endoderm markers, and GSC, Biy, and CXCR4 represent markers of primitive streak. Figure 17 depicts the expression of CXCR4 by FACS. There was a significant increase in expression of CXCR4 by cells cultured on plates coated with MATRIGEL at a 1:10 dilution as compared to lower concentrations of MATRIGEL. Furthermore, growth factor reduced MATRIGEL was not as effective in formation of definitive endoderm cells as compared to regular MATRIGEL. 102661 Figure 18 shows the real-time PCR results verifying that cells cultured on plates coated with a 1:10 dilution of MATRIGEL showed a significant upregulation of definitive endoderm markers as compared to cells cultured on a 1:30 dilution of MATRIGEL. Example 15 Microarray Analysis of Changes in Gene Expression in Embryonic Stem Cells Following Formation of Definitive Endoderm [02671 Total RNA was isolated from the following human embryonic stem cell cultures using an RNeasy mini kit (Qiagen): H9P83 cells cultured on MATRIGEL -coated plates and exposed to DMEM/F12 medium supplemented with 0.5% FBS and 100 ng/ml activin A for two days followed by treatment with DMEM/F 12 medium supplemented with 2% FBS and 100 ng/ml Activin A (AA) for an additional three days; H9P44 cells cultured on MEFs and exposed to DMEM/F12 medium supplemented with 0.5% FBS and 100 ng/ml activin A for two days followed by treatment with DMEM/F12 medium supplemented with 2% FBS and 100 ng/ml activin A for an additional three days. Controls for each group included cells plated on MATRIGEL 77 coated dishes and cultured in MEF-conditioned medium or cells plated on MEFs and cultured in ES medium. 102681 Sample preparation, hybridization, and image analysis were performed according to the Affymetrix Human Genome U133 Plus 2.0 Array. Following normalization and a log transformation, data analysis was performed using OmniViz@) software (MA) and GENESIFTER (VizXLabs, WA). The variability within each treatment and among the different treatments was compared using the Pearson correlation coefficient. Variance in gene expression profiles between the different treatments along with the correlation coefficient between the lines are depicted in Figure 19. Significant differences in gene expression between the samples were evaluated using analysis of variance and an F-test with adjusted P-value (Benjamini and Hochberg correction) of -: 0.05. Only genes with a present call were included in the analysis. Table IV lists the genes that are differentially expressed with a difference at least 5-fold between the various samples. The normalized intensity value of the genes that are significantly expressed along with the standard error of the mean (SEM) for each gene are listed. Example 16 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with MATRIGELTNI to Definitive Endoderm [02691 Differentiation of embryonic stem cells to definitive endoderm was carried out as previously described in Nature Biotechnology 23, 1534-1541 (Dec 2005). Briefly, H9, H7, or HI cells seeded on growth factor reduced MATRIGELTM (1:30 dilution) cultures at approximately 60 to 70% confluency were exposed to DMEM/F12 medium supplemented with 0.5% FBS and 100 ng/ml activin A (R&D Systems, MN)) for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS and 100 ng/ml activin A (AA) for an additional three days. In all subsequent examples unless otherwise noted, this treatment regimen will be referred to as the definite endoderm (DE) protocol. 78 In parallel, H9, H7, or Hi cells cultured on MEF feeders were also exposed to the same DE protocol outlined above. 10270] At day 5, the cultures were analyzed by FACS for CXCR4, E-cadherin, CD9, CD99, and N-cadherin (CD56) expression and by real time PCR for SOX-17, SOX-7, Alpha-fetal protein (AFP), CXCR4, Brychyury (Bry), gooscecoid (GSC), HNF-3 beta, and GATA4. AFP and SOX-7 are regarded as visceral endoderm markers while GATA4, HNF-3beta and SOX-17 represent definite endoderm markers and GSC, Bry, and CXCR4 represent markers of primitive streak. [0271] H-lines cultured on mouse feeders and exposed to the DE protocol resulted in a robust expression of DE markers and expression of CXCR4 by FACS (Figure 20). There was also a significant decrease in expression of E cadherin following treatment with the DE protocol. Lastly, the CXCR4 + population also stained positive for CDI 17. Figure 21 shows a significant upregulation of definitive endoderm markers as compared to untreated H7 (Figure 21, panel a) and H9 cells (Figure 21, panel b). [02721 Unlike H-lines cultured on MEF feeders, H-lines cultured on MATRIGELTM (1:30 dilution) and treated with the definitive endoderm protocol failed to show robust expression of definitive endoderm markers. In particular, the expression of CXCR4 by FACS and by real-time PCR was significantly lower for cells cultured on MATRIGELTM as compared to cells cultured on mouse embryonic fibroblasts. Expression of definitive endoderm markers follows a general response pattern with H being greater than H9, which is greater than H7 (Figures 22 and 23). From Figure 22, HI cells showed a significant increase in CXCR4 expression as compared to H7 and H9 lines. Note that in all cases, the expression of CXCR4 was lower for cells cultured on MATRIGELTM (1:30 dilution) as compared to cells cultured on mouse embryonic fibroblasts. Figure 23 (panels a-c) shows the real-time PCR results showing that there was modest increase in upregulation of definitive endoderm markers in H7 (Figure 23, panel a) and H9 (Figure 23, panel b) 79 lines. However, HI (Figure 23, panel c) line showed a more robust upregulation of definitive endoderm markers as compared to H7 and H9 lines. Example 17 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with MATRIGELTM to Definitive Endoderm (DE)- Role of Wnt Ligands [0273] H7P44 and H9P46 embryonic stem cells were cultured on MATRIGELTM (1:10 dilution) coated dishes and exposed to DMEM/F12 medium supplemented with 0.5% FBS, and 100 ng/ml activin A (R&D Systems, MN) for two days followed by treatment with DMEM/F 12 media supplemented with 2% FBS and 100 ng/ml activin A (AA) for an additional three days. In some of the cultures 20 ng/ml Wnt-3a (Catalog# 1324-WN-002, R&D Systems, MN), 20 ng/ml Wnt-5a (Catalog# 654-WN-010, R&D Systems, MN), 25 ng/ml Wnt-7a (Catalog# 3008-WN-025, R&D Systems, MN), or 25 ng/ml Wnt-5b (Catalog# 3006-WN-025, R&D Systems, MN) was added throughout the five day treatment. Figure 24 depicts phase contrast images of H9P46 definitive endoderm culture in the presence of high concentration of (a) AA or (b) AA+ 20 ng/ml Wnt-3a. Figure 25 depicts the expression of CXCR4 by FACS at day 5 for H7P44, and H9P46 lines cultured on MATRIGELTM (1:30 dilution) and exposed to the DE protocol + Wnt-3a (Figure 25, panels b and d) and -Wnt-3a (Figure 25, panels a and c). Presence of Wnt-3a in DE cultures resulted in robust expression of CXCR4 (CD184) as compared to DE cultures treated with low serum plus high concentration of AA. Figure 26 displays the real-time PCR data for a) H7 and b) H9 cultures treated with low serum + AA +/- Wnt ligands. For both H lines, addition of WNT-3a resulted in significant upregulation of definitive endoderm markers. In contrast, Wnt 5a, Wnt-5b and Wnt-7a had minimal impact on expression of definitive endoderm markers. 80 Example 18 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with MATRIGELm to Definitive Endoderm: Effective dose of Wnt-3a [02741 H9P46 embryonic stem cells were cultured on MATRIGELTM coated dishes (1:10 dilution) and exposed to DMEM/F12 medium supplemented with 0.5% FBS, 100 ng/ml Activin A (AA), and 10-50 ng/ml WNt-3a (R&D Systems, MN) for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS, 100 ng/ml activin A (AA), and 10-50 ng/ml Wnt 3a for an additional three days. Control cultures were not treated with Wnt-3a. Figure 27, panel a depicts the expression of CXCR4 by FACS at day 5 in the absence of Wnt-3a, b) 10 ng/ml Wnt-3a, c) 20 ng/ml Wnt-3a and d) 50 ng/ml Wnt-3a. In the absence of Wnt-3a the expression of CXCR4 was very low. In contrast, addition of 10-50 ng/ml of Wnt-3a significantly increased the number of CXCR4 positive cells. Furthermore, addition of 10 ng/ml of Wnt-3a was as effective as addition of 50 ng/ml of Wnt-3a. Real-time PCR results (Figure 28, panel a) also confirm this finding. [02751 In a separate study, H9p52 cells were plated on 1:30 low growth factor MATRIGELTM. For the first 2 days of the DE protocol a range of Wnt3A doses was used: 1Ong/ml, 5ng/ml and I ng/ml. Figure 28, panel b shows PCR analysis of the DE markers after 5 days of treatment. The number of cells at the end of the experiment is noted in Figure 28, panel c. This indicates that cells are proliferating when higher doses of Wnt-3a are used. Extension to 5 days of Wnt3a treatment (5D) had little effect on DE markers by PCR and did not significantly increase cell numbers (Figure 28, panel c). These data indicate that I Ong/ml Wnt3a for 2 days is sufficient to reach optimal cell expansion and definitive endoderm differentiation. 81 Example 19 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with MATRIGELHI to Definitive Endoderm (DE)- Effect of GSK-3B inhibitor [0276] In order to confirm that the effect of Wnt-3a was through the Wnt pathway, a GSK-3 inhibitor was used to activate the downstream targets of Wnt, such as beta catenin. H9P46-P48 embryonic stem cells were cultured on

MATRIGEL

TM coated dishes (1:10 dilution) and exposed to DMEM/F12 medium supplemented with 0.5% FBS, 100 ng/ml activin-A (AA), and 10 1000 nM GSK-3B inhibitor IX (Catalog# 361550, Calbiochem, CA) for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS, 100 ng/ml activin A (AA), and 0-1000 nM GSK-3B inhibitor IX (Catalog# 361550, Calbiochem, CA) for an additional three days. Control cultures were treated with low serum plus high dose of activin A +/- Wnt-3a. Figure 29, panel a depicts the expression of CXCR4 by FACS at day 5 in the absence of Wnt-3a or GSK-3B inhibitor, b) +20 ng/ml Wnt-3a, c) +1000 nM GSK-3B inhibitor IX, d) +500 nM GSK-3B inhibitor IX, e) +100 nM GSK-3B inhibitor IX, f) +10 nM GSK-3B inhibitor IX, g) +100 nM GSK-3B inhibitor IX for days 1-2, and h) +10 nM GSK-3B inhibitor IX for days 1-2. 102771 In the absence of Wnt-3a or at 10 nmGSK-3B inhibitor the expression of CXCR4 was very low. In contrast, addition of 20 ng/ml of Wnt-3a or 100 1000 nM GSK-3B inhibitor significantly increased the number of CXCR4 positive cells. Furthermore, addition of 100 nM GSK-3B inhibitor for days I 2 was as effective as addition of 100 nM GSK-3B inhibitor for the entire five day period. Figure 30 depicts the gene expression of definitive endoderm markers for (panel a) H9P48 cells and (panel b) H9P46 cells. [02781 Figure 16 depicts the outline of a differentiation protocol in this invention, where embryonic stem cells are differentiated into definitive endoderm in a feeder free system. 82 Example 20 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with MATRIGELTm to Definitive Endoderm (DE)- Effective dose of Activin-A in the presence of GSK-3B inhibitor or Wnt-3A [0279] H9P49 and H1P46 embryonic stem cells were cultured on MATRIGELTM coated dishes (1:10 dilution) and exposed to DMEM/F12 medium supplemented with 0.5% FBS, 10-100 ng/ml activin A (AA), and 100 nM GSK-3B inhibitor IX (Catalog# 361550, Calbiochem, CA) or 20 ng/ml Wnt 3a for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS, 10-100 ng/ml activin A (AA) for an additional three days. Control cultures were treated with low serum plus 100 ng/ml of activin A. Figure 31 depicts the expression of CXCR4 by FACS for H9P49 and H1P46 at day 5 with a) 10 ng/ml activin A for all five days plus 20 ng/mI of Wnt-3A for the first two days, b) 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3A for the first two days c) 100 ng/ml activin A for all five days plus 100 nM of GSK-3B inhibitor IX for the first two days d) 10 ng/ml activin A for all five days plus 100 nM of GSK-3B inhibitor IX for the first two dayse) 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3A for the first two days, and f) 10 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3A for the first two days. Figure 31 panels a-d is for H9P49 cells and panels e-f is for H1P46 cells. Figure 32 depicts the gene expression of definitive endoderm markers for H9P49 cultures treated with 10, 50, or 100 ng/ml of activin A plus 20 ng/mI of Wnt-3a: panel a: expression of AFP, Bry, CXCR4, GSC, HNF-3B, and POU5F (Oct-4) and panel b: SOX-17 and GATA4. This does not add up- It appears to be a problem with figure numbers or it is a cut and paste problem. It appears that robust expression of definitive endoderm markers can be obtained by using 50 ng/ml of AA + 20 ng/ml of Wnt-3A or 100 nM GSK-3B inhibitor IX. Lower doses of activin A lead to formation of extraembryonic endoderm. 83 Example 21 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with MATRIGELTHI to Definitive Endoderm (DE)- Combination of Wnt-3a and GSK-3B inhibitor [0010] H9P53 embryonic stem cells were cultured on MATRIGELTM coated dishes (1:30 dilution) and exposed to DMEM/F12 medium supplemented with 0.5% FBS, 100 ng/ml activin A (AA), and 100 nM GSK-3B inhibitor IX (Catalog# 361550, Calbiochem, CA) +/- 20 ng/ml Wnt-3a for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS, 10-100 ng/ml activin-A (AA) for an additional three days. In parallel, H9P53 cultures were treated with 25 ng/ml BMP-4 (Catalog# 314-BP-010, R&D Systems, MN) +/ 20 ng/ml Wnt-3A +/- 100 ng/ml activin A. Control cultures were treated with low serum plus 100 ng/ml of activin A. Figure 33 depicts the expression of CXCR4 by FACS at day 5 with a) 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3A for the first two days and 25 ng/ml BMP-4 for days 3-5, b) 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3A for the first two days c) 100 ng/ml activin A for all five days plus 100 nM of GSK-3B inhibitor IX for the first two days d) 20 ng/ml Wnt-3a + 25 ng/ml BMP-4 for all five days, e) 100 ng/ml activin A for all five days plus 20 ng/ml of Wnt-3A + 100 nm GSK-3B inhibitor IX for the first two days, and f) 100 ng/ml activin A + 25 ng/ml BMP-4 for all five days. Figure 34 depicts the gene expression of definitive endoderm markers, as determined by real-time PCR for cultures of the human embryonic stem cell line HI at passage 46, treated with 10 or 100 ng/ml of activin A plus 20 ng/ml of Wnt-3a or 100 NM GSK-3B inhibitor: panel (a): expression of AFP, Bry, CXCR4, GSC, and POU5F (Oct-4) and panel (b): SOX-17, HNF-3B, and GATA4. Results are expressed as fold increase over untreated cells. Figure 35 depicts the gene expression of definitive endoderm markers, as determined by real-time PCR for cultures of the human embryonic stem cell line H9 at passage 49, treated with 50 or 100 ng/ml of activin A plus 10 or 100 nM GSK-3B inhibitor: panel (a): expression of AFP, Bry, CXCR4, GSC, HNF-3B, and POU5F (Oct-4) and panel (b): 84 SOX-17 and GATA4. Results are expressed as fold increase over untreated cells. Figure 36 depicts the gene expression of definitive endoderm markers for H9P53 culture treated with combinations of activin A, Wnt-3a, GSK-3 inhibitor, and BMP-4: a) expression of AFP, Bry, CXCR4, GSC, HNF-3B, and SOX7 and b) SOX-17, HNF-3B and GATA4. Addition of BMP-4 to the DE protocol appears to induce formation of mesoderm marker BRY and combination of Wnt-3A and GSK-4B inhibitor do not lead to significant upregulation of definitive endoderm markers as compared to addition of each agent by itself in the presence of activin A. Example 22 Differentiation of Human Embryonic Stem Cells Cultured on MEFs to Definitive Endoderm (DE)- Combination of Wnt-3a, Activin A, Wnt-5a, BMP-2, BMP-4, BMP-6, BMP-7, IL-4, and SDF-1 in low serum [02801 H9P44 cells were plated onto 6 well plates previously coated with mitomycin treated mouse embryonic fibroblasts (MEF). Cells were grown until 70 to 80% confluency in ES cell medium consisting of DMEM/F 12 (Invitrogen/GIBCO) supplemented with 20% knockout serum replacement, 100 nM MEM nonessential amino acids, 0.5 mM beta-mercaptoethanol, 2 mM L-glutamine (all from Invitrogen/GIBCO) and 8 ng/ml human basic fibroblast growth factor (bFGF) (R&D Systems). [0281] For DE formation, cells were treated in the presence or absence of Activin A (100ng/ml) in addition to other growth factors detailed below. Growth factors were added to increasing concentration of FBS in a stepwise manner as indicated in the following regimen: Day 0: 0% FBS in DMEM/F 12 Day 1: 0.5% FBS in DMEM/F12 Day 2: 2% FBS in DMEM/F 12. 85 Day 3: Cells were harvested for FACS analysis and RT-PCR. 102821 All growth factors were purchased from R&D Systems, MN. A detailed description and concentration of growth factors for each treatment group is shown below. 1. Control- No growth factor added 2. Activin A (100 ng/ml) 3. Activin A (100ng/ml) + Wnt-3a (1Ong/ml) + Wnt5a (lOng/ml) 4. Activin A (1OOng/ml) + Wnt-3a (1Ong/ml) + Wnt5a (lOng/ml) + BMP2 (100ng/ml) 5. Activin A (100 ng/ml) + BMP-4 (100 ng/ml) 6. Activin A (100 ng/ml) + BMP-6 (100 ng/ml) 7. Activin A (100 ng/ml) + BMP-7 (100 ng/ml) 8. Activin A (100 ng/ml) + BMP-4 (100 ng/ml) +BMP-6 (100 ng/ml) + BMP-7 (100 ng/ml) 9. IL-4 (10 ng/ml) 10. SDF Ia (20ng/ml) 11. Activin A (100 ng/ml) + IL-4 (10 ng/ml) + SDF 1 a (20ng/ml) 12. BMP2 (00ng/ml) + BMP-4 (100ng.ml) + BMP-6 (100ng/ml) + BMP 7 (100ng/mi) 13. Activin A (100 ng/ml) BMP-2 (IOOng/ml) + BMP-4 (1OOng.ml) + BMP-6 (100ng/ml) + BMP-7 (100ng/ml) 14. Activin A (100 ng/ml) + IL-4 (10 ng/ml) 15. ActivinA (100 ng/ml) + (SDFia (20 ng/ml) 86 16. Activin A (100 ng/ml) + Wnt-3a (10 ng/ml) + Wnt-5a (10 ng/ml) + Wnt-7a (10 ng/ml) 17. Activin A (100 ng/ml) + IL-4 (10 ng/ml) + SDF1a (20ng/ml) + BMP 4 (100 ng/ml) Results: 102831 Cells were harvested on Day 3 of DE protocol treatment. For analysis, an aliquot of treated cells was used for RNA preparation for RT-PCR and the rest of cells used for FACS analysis. The frequency (%) of CXCR4 is shown in Figure 37. Addition of the above growth factor(s) did not enhance expression of CXCR4 above treatment with 100 ng/ml AA in low serum. [0284] For RT-PCR analysis, cells were analyzed for expression of selected panel of definitive endoderm markers. Results shown were calibrated against cells grown in the base medium but not treated with Activin A or any of the other growth factors. In agreement with the FACS data, Table V shows that there was no significant upregulation of definitive endoderm markers by addition of growth factors, such as Wnt-3a to cultures treated with a high dose of activin A in low serum. This is in contrast to the previous examples showing a significant increase in DE markers for ES cells cultured on feeder-free conditions in the presence of activin A, WNT3A, and low serum. Example 23 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with MATRIGELHI or human Fibronectin to Definitive Endoderm (DE) [0285] H9P55 cells were grown and differentiated on human fibronectin or regular growth factor MATRIGELTM (BD Biosciences). Iml of DMEM/F12 (Invitrogen/GIBCO) containing lug/ml of human fibronectin (R&D systems, MN) was added to each well of 6 well tissue culture treated dish. Alternatively, regular growth factor MATRIGELTM was diluted 1:10 in 87 DMEM/F12 and Iml of diluted MATRIGEL TM was added to each well of 6 well tissue culture treated dish. Cells were passed with collagenase. After cells reached 80% confluency, there were treated as follows: 2 days 0.5%FBS containing lOng/ml mouse recombinant Wnt3a (R&D) and 1Ong/mI Activin A (R&D). This was followed by 3 days 2%FBS plus lOOng/ml Activin A. Figure 38, panels a-b depict the expression of CXCR4 by embryonic stem cells cultured on fibronectin and MATRIGEL, respectively. Real-time PCR results (Figure 39) confirm that formation of definitive endoderm was equivalent on fibronectin and MATRIGELTM coated plates. Example 24 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with Varying Concentrations of MATRIGELTM to Definitive Endoderm [02861 H9 cultures at approximately 60 to 70% confluency were exposed to DMEM/F12 medium supplemented with 0.5% FBS, 20ng/ml Wnt-3a and 100 ng/ml activin A for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS, 20ng/ml Wnt-3a and 100 ng/ml activin A (AA) for an additional three days. H9 cells were cultured on plates coated with regular MATRIGEL at a 1:60 to 1:10 dilution. The plates were coated with MATRIGEL for 1 hr at room temperature. [02871 Real time PCR results are shown in Figure 40. Treatment of human embryonic stem cells with low serum, Activin A and Wnt3a led to the expression of CXCR4, GATA4, Goosecoid, HNF-3beta, and SOX-17 genes, suggesting that the cells were differentiating to the definitive endoderm stage. However, it does not appear that the in the presence of Wnt-3A concentration of the MATRIGELTM coating plays an important role in differentiation. 88 Example 25 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with Extracellular Matrix and subsequently cultured on MEFS and differentiated to Definitive Endoderm- role of Wnt-3a [02881 Cells from the human embryonic stem cell line H9 cultured on MATRIGELTM for at least five passages were seeded onto MEF feeders in ES media. When the cells reached 60 to 70% confluency they were exposed to DMEM/F12 medium supplemented with 0.5% FBS and 100 ng/ml activin A for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS and 100 ng/ml activin A (AA) for an additional three days. Additional treatment groups include Wnt-3a at 20ng/ml for all five days + 10-100 ng/ml of activin A. 10289] At day 3 and 5, the cultures were analyzed by real time PCR for SOX-17, SOX-7, Alpha-fetal protein (AFP), CXCR4, Brychyury (Bry), gooscecoid (GSC), HNF-3 beta, GATA4, hTERT and Oct4. AFP and SOX-7 are regarded as visceral endoderm markers while GATA4, HNF-3beta and SOX-] 7 represent definite endoderm markers and GSC, Bry, and CXCR4 represent markers of primitive streak. hTERT and Oct-4 are markers for self renewal and pluripotency respectively. Real time-PCR results are shown in Figure 41, panels a-d. FACS analysis was also performed at day 3 and 5. Expression levels of CXCR-4, and CD9 were analyzed and reported in Figure 41, panel e. [02901 In the absence of Wnt3a, AFP expression levels of cells cultured in 100ng/ml Activin A are similar to those seen in untreated controls. However, with the addition of Wnt3a to cells cultured in 1OOng/ml activin A, there is an increase in the expression of AFP that increases over time. When a lower concentration of Activin A is used, AFP expression is very high, regardless of the presence of Wnt3a (Figure 41, panel a). This suggests that a high 89 concentration of Activin A is necessary to keep the cells from differentiating to extra-embryonic tissues. 102911 By FACS analysis, CXCR4 positive cells ranged from 32-42% of the population in samples treated with a high concentration of Activin A but not treated with Wnt3a as compared to 23-33% of the population in samples treated with a high concentration of Activin A and Wnt3a at day 3 (Figure 41, panel e). By day 5 of treatment, 28-32% of cells treated with a high concentration of activin A but not treated with Wnt-3a expressed CXCR4 as compared to 43-51% of cells treated with a high concentration of Activin A and Wnt3a (Figure 41, panel f). In cells treated with a low concentration of Activin A, there were more CXCR4 positive cells in the treatment group without Wnt3a (11 to 20%) as compared to the Wnt-3a treated group (3 to 4%) (Figure 41, panel g). Overall, Wnt-3a does not appear to play a significant role in differentiation of human embryonic stem cells, cultured on MEFs, to definitive endoderm. This suggests that the feeder layer is probably secreting sufficient Wnt-3a or analogous ligand to enhance activin A induced definitive endoderm formation. Example 26 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with Extracellular Matrix to Definitive Endoderm Following Treatment with a Wnt Inhibitor- DKK-1 102921 To determine if the addition of Wnt-3a was causing the increase in differentiation, an inhibitor of Wnt-3 signaling was added to the cultures. H9 cultures at approximately 60 to 70% confluency were exposed to DMEM/F12 medium supplemented with 0.5% FBS, 20ng/ml Wnt3a, 100ng/ml Dikkopf-1 (DKK- 1) and 100 ng/ml activin A for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS and 100 ng/ml activin A (AA) for an additional three days. H9 cells were cultured on plates coated with Growth Factor Reduced MATRIGEL at a 1:30 dilution. The plates were coated with MATRIGEL for 1 hr at room temperature. 90 [02931 At day 5, the cultures were analyzed by real time PCR for SOX-17, SOX-7, Alpha-fetal protein (AFP), CXCR4, Brychyury (Bry), gooscecoid (GSC), HNF-3 beta, GATA4, hTERT and Oct4. AFP and SOX-7 are regarded as visceral endoderm markers while GATA4, HNF-3beta and SOX- 17 represent definite endoderm markers and GSC, Bry, and CXCR4 represent markers of primitive streak. hTERT and Oct-4 are markers for self renewal and pluripotency respectively. Results are shown in Figure 42. [0294] In the presence of Wnt3a, cells express CXCR4, GATA4, HNF-3beta and SOX 17, all markers of definitive endoderm. Markers of primitive streak formation such as goosecoid were also detected at levels higher than that detected in untreated controls. With the addition of DKK1, the expression level of the aforementioned differentiation markers dramatically decrease to levels similar to that of untreated cells. Example 27 Imuunofluorescence staining of DE markers for H9 Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated MATRIGEL and differentiated in low serum plus activin-a and +/- Wnt-3a [02951 Day 5 DE cultures of H9 cells were stained according to Example 10 for SOX-17, HNF-3B, GATA-4, N-cadherin, and E-cadherin. All nuclei were counter stained with DAPI. 20 ng/ml Wnt-3a resulted in significantly larger number of nuclei stained positive for SOX- 17, H.N.F-3beta. and GATA-4 as compared to cultures differentiated in the absence of Wnt-3a. Furthermore, addition of Wnt-3a resulted in significant loss of expression of e-cadherin and enhanced expression of N-cadherin (Figure 43, panel a and Figure 43, panel b). 91 Example 28 Microarray analysis of changes in gene expression in embryonic stem cells following formation of definitive endoderm on MEFs vs MATRIGELTM [02961 Total RNA was isolated from the following embryonic stem cell cultures using an RNeasy mini kit (Qiagen): A) H9P33 cells cultured on MATRIGELTM-coated plates (1:30 dilution) and exposed to DMEM/F12 medium supplemented with 0.5% FBS and 100 ng/ml activin A for two days followed by treatment with DMEM/F12 medium supplemented with 2% FBS and 100 ng/ml activin A (AA) for an additional three days; B) H9P44 cells cultured on MEFs and exposed to DMEM/F 12 medium supplemented with 0.5% FBS and 100 ng/ml Activin A for two days followed by treatment with DMEM/F12 medium supplemented with 2% FBS and 100 ng/ml Activin A for an additional three days, and C) H9P48 cells cultured on MATRIGEL

TM

_ coated plates (1:30 dilution) and exposed to DMEM/F12 medium supplemented with 0.5% FBS and 100 ng/ml activin A plus 20 ng/mI Wnt-3A for two days followed by treatment with DMEM/F 12 medium supplemented with 2% FBS and 100 ng/ml Activin A (AA) for an additional three days. Controls for each group included cells plated on MATRIGEL -coated dishes and cultured in MEF-conditioned medium or cells plated on MEFs and cultured in ES medium. All groups contained three biological replicates and each biological replicate was repeated on two separate gene chips. 102971 Sample preparation, hybridization, and image analysis were performed according to the Affymetrix Human Genome U133 Plus 2.0 Array. Following normalization and a log transformation, data analysis was performed using OmniViz@) software (MA) and GENESIFTER (VizXLabs, WA). Significant differences in gene expression between the samples were evaluated using analysis of variance and an F-test with adjusted P-value (Benjamini and Hochberg correction) of 4 0.05. Only genes with a present call in at least one group were included in the analysis. Table VI lists the mean normalized log transformed signal intensity of genes showing at least 5-fold difference 92 between group A, group B, and group C along with the adjusted P-value for each gene. Example 29 Differentiation of SA002 ES line Cultured on Tissue Culture Substrate Coated with MATRIGELTM to Definitive Endoderm (DE) [02981 SA002 P38 cells (Cellartis, Sweden) previously cultured for at least three passages on MATRIGEL -coated plates (1:30 dilution) in MEF-CM supplemented with 8 ng/ml of bFGF were exposed to DMEM/F12 medium supplemented with 0.5% FBS, and 100 ng/ml activin A (R&D Systems, MN) +/- 20 ng/ml of Wnt-3a or 100 nm GSK-3B IX inhibitor for two days followed by treatment with DMEM/F 12 media supplemented with 2% FBS and 100 ng/ml activin A (AA) for an additional three days. Real time PCR results are shown in Figure 44, panels a & b. Similar to HI, H7, and H9 lines, SA002 line also required addition of Wnt-3A for robust expression of DE markers. Expression of CXCR4 is depicted in Figure 45: a) AA treatment b) AA + Wnt-3a c) AA + GSK-3B inhibitor. Example 30 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with human Serum to Definitive Endoderm (DE) 102991 Cultures of the human embryonic stem cell line H11 at passage 55 were grown and differentiated on human serum (Sigma, #H1388, MO) coated plates. 0.5 ml of human serum was added to each well of 6 well tissue culture treated dish, incubated for 1 hr at room temperature, and aspirated before adding human embryonic stem cells. After cells reached 80% confluency, they were treated as follows: 2 days 0.5%FBS containing l0ng/ml mouse recombinant Wnt3a (R&D) or 100 nM GSK-3B inhibitor IX (Catalog# 361550, Calbiochem, CA) and IOOng/ml Activin A (R&D). This was followed by 3 93 days 2%FBS plus 100ng/ml Activin A. Cultures were then analyzed by real time PCR (Figure 46, panels a & b). Robust expression of definitive endoderm markers were noted for cells treated with activin A + GSK-3B inhibitor or Wnt-3A as compared to cells treated with activin A only. These findings parallel our findings for human embryonic stem cells cultured on MATRIGELTM or human fibronectin coated plates. Example 31 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with MATRIGELTHI to Definitive Endoderm (DE)- Evaluation of various GSK-3B inhibitor [03001 The effectiveness of a number of commercially available GSK-3B inhibitors was evaluated in formation of DE from human embryonic stem cells. The following GSK-3B inhibitors were evaluated at 100 nM: GSK-3B inhibitor VIII (Catalog# 361549, Calbiochem, CA), GSK-3B inhibitor IX (Catalog# 361550, Calbiochem, CA), GSK-3B inhibitor XI (Catalog# 361553, Calbiochem, CA), GSK-3B inhibitor XII (Catalog# 361554, Calbiochem, CA). H1P54 ES cells were cultured on MATRIGELTM coated dishes (1:30 dilution) and exposed to DMEM/F12 medium supplemented with 0.5% FBS, 100 ng/ml activin A (AA) +/- various GSK-3B inhibitors for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS, 100 ng/ml activin A (AA) for an additional three days. Control cultures were treated with low serum plus high dose of AA. Figure 47, panels a and b depicts the gene expression of definitive endoderm markers at day 5. GSK-3B inhibitor IX and XI were both effective in inducing DE formation as compared to GSK-3B inhibitor VIII and XII. 94 Example 32 Formation of Pancreatic Endoderm by Human Embryonic Stem Cells Cultured Under Feeder-free Conditions:- Evaluation of Retinoic Acid Analogues [0301] H9P49 embryonic stem cells were cultured on MATRIGEL TM (1:30 dilution) coated dishes and exposed to DMEM/F12 medium supplemented with 0.5% FBS, 20 ng/ml Wnt-3a (Catalog# 1324-WN-002, R&D Systems, MN), and 100 ng/ml activin A (R&D Systems, MN) for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS and 100 ng/ml activin A (AA) for an additional three days. At day 5, cells were collected for evaluation by FACS and real-time PCR. As indicated in previous examples, this protocol resulted in robust upregulation of definitive endoderm markers, such as CXCR4 and SOX-17. The resulting definitive endoderm cells at day 5 were exposed to the following media conditions to induce pancreatic endoderm formation: culturing in DMEM/F12 media supplemented with 2% FBS and 1 pM all-trans retinoic acid (RA) (Catalog#R2625, Sigma, MO), or 0.1-10 pM AM-580 (4-[(5,6,7,8-Tetrahydro-5,5,8,8-tetrametiyl-2 naphthalenyl)carboxamido]benzoic acid, Catalog#A8843, Sigma, MO), or 0.1 1 pM TTNPB (4-[(E)-2-(5,6,7,8-Tetrahydro-5,5,8,8-tetramethyl-2 naphthalenyl)- 1 -propenyl] benzoic acid Arotinoid acid, Catalog#T3 757, Sigma, MO) for 3 days. AM-580 and TTNPB are retinoic acid analogs with affinity for retinoic acid receptors. RA treatment was followed by additional three day treatment in DMEM/F 12 media supplemented with 2% FBS and 20 50 ng/ml bFGF (Catalog#F0291, Sigma, MO). Cultures were harvested and samples of mRNA were collected for analysis. {03021 Gene expression analysis revealed that (Figure 48, panels a-d) addition of I pM RA followed by exposure to bFGF significantly upregulates pancreatic endoderm markers, such as PDX-1. Furthermore, this protocol resulted in robust expression of foregut endoderm markers, such as CDX-2 and AFP. At 1pM concentration, addition of RA analogs resulted in equivalent pancreatic 95 endoderm and foregut markers. However, addition of 1.pM RA analogs resulted in more robust expression of AFP as compared to all-trans retinoic acid. However, addition of 10pM AM-580 suppressed AFP and CDX-2 expression while maintaining a high expression of PDX-l. Example 34 The effect of Wnt-3a Treatment on Cytokine Expression in Human Embryonic Stem Cells [03031 The effect that Wnt-3a treatment has on cytokine expression was analyzed using a protein array. Cells of the human embryonic stem cell line H9 were cultured according to the methods described in Example 15. At passage 54, cells were differentiated in the presence of lOOng/mlActivinA +/ 10ng/mlWnt3a for 2 days in 0.5% FBS DMEM/F12. Cells were subsequently cultured for an additional three days in 1 00ng/ml Activin A and 2%FBS DMEM/F12. At the end of the 5th day, CXCR4 expression was determined by FACS for each treatment group. Cells treated with Activin A only had 1% of cells expressing CXCR4. Cells treated with Activin A and Wnt3a had 73% of cells positive for CXCR4 expression. [03041 Cell lysates were prepared from cells of each treatment group, with a mammalian cell lysis kit (Sigma-Aldrich,MO). Conditioned media from each treatment group was collected and concentrated. Cytokine array analysis was completed using Cytokine Array panels provided by RayBiotech, GA (http://www.raybiotech.com/). Table VII lists cytokine, growth factor, and receptor expression following normalization of the data and background subtraction. For each panel, positive and negative controls are also included. Th data shown are two independent samples per cell treatment group (1,2). [03051 Noticeable upregulation of Angiogenin, IGFBP-1 and EGF are seen in the Wnt3 treated cell conditioned media. Numerous proteins are upregulated in the Wnt3a treated cell lysates including IGFBP-1, TGFbeta-1 and TGFbeta-3. 96 These upregulated proteins can be added back into the differentiation media to replace or enhance Wnt3a effects on definitive endoderm formation. Example 35 Differentiation of Human Embryonic Stem Cells Cultured on Tissue Culture Substrate Coated with MATRIGELTM to Definitive Endoderm: Role of Wnt1 [03061 H.1P55 ES cells were cultured on MATRIGELTM (1:30 dilution) coated dishes and exposed to DMEM/F12 medium supplemented with 0.5% FBS, and 100 ng/ml activin A +/- 10-20 ng/ml of WNT-1 (PeproTech, NJ, Catalogue#120 17) for two days followed by treatment with DMEM/F12 media supplemented with 2% FBS, 100 ng/ml activin A (AA) and +/- 10 or 20 ng/ml of WNT-1 for an additional three days. The following combinations of WNTI + AA were tested: [0307] a) 20 ng/ml of WNT1 + 100 ng/ml AA in 0.5% FBS + DM-F12 for days 1-2 followed by 200 FBS +DM-F 12 + 100 ng/ml AA for day three, b) 20 ng/ml of WNT1 + 100 ng/ml AA in 0.5% FBS + DM-F12 for days 1-2 followed by 2% FBS +DM-F12 + 100 ng/ml AA for days 3-5, c) 10 ng/ml of WNT I + 100 ng/ml AA in 0.5% FBS + DM-F12 for days 1-2 followed by 2% FBS +DM F12 + 100 ng/mI AA for day three, d) 10 ng/ml of WNTl + 100 ng/ml AA in 0.5% FBS + DM-F12 for days 1-2 followed by 2% FBS +DM-F12 + 100 ng/ml AA for days 3-5, e) 20 ng/ml of WNTI + 100 ng/ml AA in 0.5% FBS + DM-F12 for days 1-2 followed by 2% FBS +DM-F12 + 100 ng/ml AA + 20 ng/ml of WNTl for day three, f) 20 ng/ml of WNTI + 100 ng/ml AA in 0.5% FBS + DM-F12 for days 1-2 followed by 2% FBS +DM-F12 + 100 ng/ml AA + 20 ng/ml of WNT1 for days 3-5. Figure 49, panels a and b displays the real-time PCR data for definitive endoderm markers following treatment of the HI cells with low serum, AA and Wnt-1. Addition of 20 ng/nil of WntI in the present of 100 ng/ml of AA resulted in significant upregulation of definitive endoderm markers (Bry, CXCR4, GSC, SOX17, HNF-3B, and GATA-4). 97 [03081 Publications cited throughout this document are hereby incorporated by reference in their entirety. Although the various aspects of the invention have been illustrated above by reference to examples and preferred embodiments, it will be appreciated that the scope of the invention is defined not by the foregoing description but by the following claims properly construed under principles of patent law. 98 TABLE IA: LIST OF PRIMARY ANTIBODIES USED FOR FACS AND IMMUNOSTAINININGANALYSIS. Antibody Supplier Isotype Clone SSEA-1 Chemicon (CA) Mouse IgM MC-480 SSEA-3 Chemicon (CA) Mouse IgG3 MC-631 SSEA-4 Chemicon (CA) Rat IgM MC-813-70 TRA 1-60 Chemicon (CA) Mouse IgM TRA 1-60 TRA 1-81 Chemicon (CA) Mouse IgM TRA 1-81 TRA 1-85 Chemicon (CA) Mouse IgGI TRA 1-85 AP R&D Systems Mouse IgG1 B4-78 HNF3P R&D Systems Goat IgG PDX1 Santa Cruz Goat IgG A-17 Biotechnology, INC GATA4 R&D Systems Goat IgG Sox 17 R&D Systems Goat IgG CD 9 BD Mouse IgG1 M-L13 99 TABLE IB: LIST OF SECONDARY CONJUGATED ANTIBODIES USED FOR FACS AND IMMUNOSTAINININGANALYSIS. Secondary Conjugated Supplier Dilution Antibody Goat Anti-Mouse IgG Jackson 1:200 APC conjugated ImmunoResearch (PA) Goat Anti-Mouse IgG Jackson 1:200 PE conjugated ImmunoResearch (PA) Donkey anti-rabbit PE Jackson 1:200 or -APC conjugated ImmunoResearch (PA) Donkey anti-goat PE or Jackson 1:200 -APC conjugated ImmunoResearch (PA) Goat anti-mouse IgM SouthernBiotech (AL) 1:200 PE Goat anti-Rat IgM PE SouthemBiotech (AL) 1:200 Goat anti-mouse IgG3 SouthemBiotech (AL) 1:200 PE 100 TABLE HA: CHANGES IN PROTEIN EXPRESSION IN HUMAN EMBRYONIC STEM CELLS WITH TIME, FOLLOWING ACTIVIN A TREATMENT. 0-DAY 2-DAY 5-DAY 8-DAY SSEA-3 98.67% 92.14% 42.9% 22.05% CD9 92.64% 29.42% 7.27% 4.1% ECAM 61.23% 20.87% 14.17% 1.02% NCAM 7.33% 5.04% 21.1% 8.86% CXCR4 8.53% 20.2% 55.26% 56.92% 101 TABLE IIB: CHANGES IN PROTEIN EXPRESSION IN HUMAN EMBRYONIC STEM CELLS WITH TIME, FOLLOWING ACTIVIN A TREATMENT. 1-day 3-day 5-day Untreated AA Untreated AA Untreated AA 100ng/ml 100 ng/ml 100 ng/mI CXCR4+ 13% 6% 7.6% 38% 3% 65.5% CXCR4+ 5.32% 2.97% 2.9% 31.56% 3% 55.21% C-Kit+ CXCR4+ 11.5% 14.58% 5.26% 36.67% 3% 54.5% EPCAM+ CXCR4+ 12.27% 8.13% 2.72% 24.11% 3% 2.1% CD9+ 102 TABLE HC: CHANGES IN PROTEIN EXPRESSION IN HUMAN EMBRYONIC STEM CELLS WITH TIME, FOLLOWING ACTIVIN A TREATMENT. 5-day AA treatment CXCR4+ 92.78% CXCR4+/C-kit+ 92.90% CXCR4+/EPCAM 87.99% CXCR4+/CD99+ 88.78% CXCR4+/CD9+ 7.03% 103 TABLE III: EXPRESSION PROFILE OF PLURIPOTENCY MARKERS FOR THE EMBRYONIC STEM CELL USED IN THE PRESENT INVENTION. Marker H9 FACS RT-PCR Staining OCT3/4 + + SOX-2 + UTF-1 + REX-1 + hTERT + Cx43 + Cx45 + ABCG-2 + SSEA-1 (36.35%) SSEA-3 +(94.38%) + SSEA-4 +(98.77%) + TRA-1-81 +(85.85%) + TRA-1-60 +(78.14%) + TRA-1-85 + (95.96%) CD9 + (92.02%) AP +(99%) + 104 TABLE IV: DIFFERENTIAL EXPRESSION OF GENES BETWEEN UNDIFFERENTIATED EMBRYONIC STEM CELLS AND DEFINITIVE ENDODERM STAGE CELLS CULTURED ON EITHER MATRIGELTM OR MOUSE EMBRYONIC FIBROBLASTS AFTER 5 DAYS OF TREATMENT. Gene Gene Title Gene ID H9P83 on SEM H9P83 on SEM H9P44 on SEM H9P44 on SEM Identifier Matrigel Matrigel- DE MEFs MEFs-DE stage stage D87811 Homo GATA6 -2.12 0.19 2.82 2.20 -2.56 0.46 5.34 1.79 sapiens mRNA for GATA-6, complete cds. /PROD=GAT A-6 /FL=gb:U660 75.1 gb:NM_0052 57.1 gb:D8781 1.1 AW157548 insulin-like IGFBP5 -3.28 0.17 3.31 2.11 -3.78 0.36 5.35 2.00 growth factor binding protein 5 /FL=gb:M650 62.1 gb:M62782.1 gb:NM_0005 99.1 gb:AF05503 3.1 NM_001898 Homo CST4 -2.15 1.26 2.54 1.95 -2.71 0.98 4.64 1.63 sapiens cystatin SN (CST1), mRNA. /PROD=cyst atin SN /FL=gb:J038 70.1 gb:NM_0018 98.1 AK000680 Homo PAG1 -2.87 0.91 1.61 0.22 -4.08 0.50 1.68 0.10 105 sapiens cDNA FU20673 fis, clone KAIA4464. /FL=gb:AF24 0634.1 gb:NM_0184 40.1 NM_022642 Homo - -2.24 0.12 2.97 0.42 -3.78 0.07 2.51 0.44 sapiens chorionic somatomam motropin hormone 1 (placental lactogen) (CSH1), transcript variant 4, mRNA. /PROD=chori onic somatomam motropin hormone 1, isoform4 /FL=gb:NM_ 022642.1 NM_001317 Homo CSHI -2.95 0.57 2.69 0.36 -4.04 0.51 1.86 0.68 sapiens chorionic somatomam motropin hormone 1 (placental lactogen) (CSH1), transcript variant 1, mRNA. /PROD-chori onic somatomam motropin hormone 1, isoform precursor 106 /FL=gb:NM_ 001317.2 gb:JO0118.1 BC005921 Homo CSHI -2.26 0.09 3.26 0.23 -2.96 0.37 2.58 045 sapiens, chorionic somatomam motropin hormone 1 (placental lactogen), done MGC:14518, mRNA, complete cds. /PROD=chori onic somatomam motropin hormone 1 (placentallact ogen) /FL=gb:BCOO 5921.1 A1796169 GATA- GATA3 -4.45 0.10 0.24 1.30 -4.72 0.13 0.80 2.05 binding protein 3 /FL=gb:NM_ 002051.1 gb:M69106.1 gb:BC00307 0.1 NM_020991 Homo CSHI -1.27 0.48 3.19 0.23 -2.91 0.35 2.62 0.54 sapiens chorionic somatomam motropin hormone 2 (CSH2), transcript variant 1, mRNA. /PROD=chor onic somatomam motropin hormone 2, 107 isoform 1precursor /FL=gb:NM_ 020991.2 gb:BC00271 7.1 NM_021827 Homo CCDC81 -0.37 0.35 3.16 2.05 -202 1.27 5.25 1.98 sapiens hypothetical protein FLJ23514 (FLJ23514), mRNA. /PROD=hypo thetical protein FLJ23514 IFL=gb:NM_ 021827.1 AB028021 Cluster Ind. FOXA2 -2.97 0.25 0.59 3.25 -3.43 0.57 4.12 2.57 AB028021:H omo sapiens HNF-3beta mRNA for hepatocyte nuclear factor-3 beta, complete cds /cds=(1 96,15 69) /gb=AB0280 21 /gi=4958949 /ug=Hs.1556 51 /len=1944 NM_002521 Homo NPPB 1.54 0.11 5.47 1.17 -0.15 0.38 6.24 1.23 sapiens natriuretic peptide precursor B (NPPB), mRNA. /PROD=natri uretic peptide precursor B /FL=gb:NM_ 002521.1 108 gb:M25296.1 AA352113 ESTs ST8SIA4 -4.01 1.24 -0.99 2.04 -4.79 1.00 1.05 1.62 BM128432 Homo IGFBP5 -2.73 1.11 2.31 2.30 -3.48 0.56 4.45 2.02 sapiens full length insert cDNA clone YA81 B05 NM_002770 Homo PRSS1 -2.77 0.33 1.59 2.68 -3.13 0.48 3.88 2.95 sapiens protease, serine, 2 (trypsin 2) (PRSS2), mRNA. /PROD=prot ease, serine, 2 (trypsin 2) /FL=gb:M276 02.1 gb:NM_0027 70.1 NM_022579 Homo CSHI -1.58 0.91 2.48 0.38 -3.33 0.13 1.77 0.49 sapiens chorionic somatomam motropin hormone-like 1 (CSHLI), transcript variant 3, mRNA. /PROD=chori onic somatomam motropin hormone-like 1,isoform 3 precursor /FL=gb:NM_ 022579.1 NM_005454 Homo CER1 2.82 0.09 5.78 1.04 1.48 0.05 6.74 1.18 sapiens cerberus 1 (Xenopus laevis) homolog (cysteine knot 109 superfamily) (CERI), mRNA. /PROD=cerb erus 1 /FL=gb:NM_ 005454.1 NM_022645 Homo CSHI -2.30 0.33 2.95 0.31 -2.78 0.24 2.45 0.34 sapiens chorionic somatomam motropin hormone 2 (CSH2), transcript variant 3, mRNA. /PROD=chori onic somatomam motropin hormone 2, isoform 3precursor /FL=gb:NM_ 022645.1 Al821586 ESTs, LOC440981 -3.22 0.97 0.66 3.19 -2.97 0.13 4.22 2.76 Moderately similar to JE0284 Mm 1 cell derived transplantabi lity associated protein lb (H.sapiens) AL121722 Human DNA - -2.95 0.36 -0.01 2.69 -3.43 0.38 2.95 2.66 sequence from clone RP4-788L20 on chromosome 20 Contains the HNF3B (hepatocyte nuclear factor 3, beta) gene. a 110 novel gene based on ESTs, ESTs, STSs, GSSs and CpG Islands NM_001311 Homo CRIP1 1.66 0.17 1.90 0.07 -2.96 0.66 1.80 0.24 sapiens cysteine-rich protein 1 (intestinal) (CRIP1), mRNA. /PROD=cyst eine-rich protein 1 (intestinal) /FL=gb:U586 30.1 gb:BC00273 8.1 gb:NM_0013 11.1 gb:U09770.1 AY177407 Homo GSC -4.59 0.18 -1.08 2.89 -4.64 0.06 1.89 2.79 sapiens homeobox protein goosecoid mRNA, complete cds. /PROD=hom eobox protein goosecoid /FL=gb:AY17 7407.1 gb:NM_1738 49.1 NM_005442 Homo EOMES -0.16 0.29 2.89 1.70 0.13 0.16 4.90 1.34 sapiens eomesoderm in (Xenopus laevis) homolog (EOMES), mRNA. 111 /PROD=eom esodermin (Xenopus laevis) homolog /FL=gb:AB03 1038.1 gb:NM_0054 42.1 L01639 Human CXCR4 0.64 0.26 3.71 1.78 -0.16 0.50 5.48 1.77 (clone HSY3RR) neuropeptide Y receptor (NPYR) mRNA, complete cds. /PROD=neur opeptide Y receptor /FL=gb:L067 97.1 gb:NM_0034 67.1 gb:AF02537 5.1 gb:AF14720 4.1 gb:M99293.1 gb:L01639.1 NM_022646 Homo - -1.57 0.60 2.67 0.26 -1.88 0.98 2.22 0.35 sapiens chorionic somatomam motropin hormone 2 (CSH2), transcript variant 4, mRNA. /PROD=chori onic somatomam motropin hormone 2, isoform4 /FL=gb:NM_ 112 022646.1 AW007532 Human IGFBP5 0.31 0.25 4.59 1.53 0.72 0.09 6.19 1.58 insulin-like growth factor binding protein 5 (IGFBP5) mRNA NM_002160 Homo TNC -0.24 0.29 2.23 0.80 -0.81 0.81 2.85 0.82 sapiens hexabrachio n (tenascin C, cytotactin) (HXB), mRNA. /PROD=hexa brachion (tenascin C, cytotactin) /FL=gb:M556 18.1 gb:NM_0021 60.1 AA149250 ESTs, LOC645638 1.27 0.61 4.23 1.26 -0.64 0.40 2.47 1.23 Weakly similar to WDNM RAT WDNM1 PROTEIN PRECURSO R (R.norvegicu S) AW977527 ESTs - -0.91 0.99 1.18 0.68 -2.52 1.01 1.59 0.64 NM_022454 Homo SOX17 -1.01 0.33 2.29 2.08 -0.14 0.15 4.60 1.73 sapiens hypothetical protein FLJ22252 similar to SRY-box containing gene 17 (FLJ22252), mRNA. /PROD=hypo thetical protein 113 FLJ22252 similar to

SRY

boxcontainin g gene 17 /FL=gb:NM_ 022454.1 A1640307 protocadheri PCDH10 -1.89 1.37 1.53 1.32 -1.33 0.38 2.99 1.19 n 10 AJ224869 Homo - 0.98 0.18 4.22 1.88 1.34 0.17 6.36 1.49 sapiens CXCR4 gene encoding receptor CXCR4 A1824037 ESTs, FREMI -1.42 0.36 1.22 1.95 -1.37 0.61 3.48 1.49 Weakly similar to FCE2 MOUSE LOW AFFINITY IMMUNOGL OBULIN EPSILON FC RECEPTOR (M.musculus BE222344 splicing - 0.50 0.05 3.01 0.93 -0.94 1.18 4.27 0.94 factor, arginineserin e-rich 5 NM_001643 Homo APOA2 -2.25 1.05 1.72 2.60 -1.20 0.44 4.47 2.42 sapiens apolipoprotei n A-Il (APOA2), mRNA. /PROD=apoli poprotein A Il precursor iFL=gb:M298 82.1 gb:NM_0016 43.1 gb:BC00528 2.1 114 A1821669 ESTs - -0.94 0.79 1.71 2.19 -0.89 0.21 3.91 1.94 NM_002608 Homo PDGFB -0.23 0.82 1.87 0.15 -2.27 0.65 1.92 0.13 sapiens platelet derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog) (PDGFB), mRNA. /PROD=plate let-derived growth factor beta polypeptide( simian sarcoma viral (v-sis) oncogene homolog) /FL=gb:M127 83.1 gb:NM_002 AW444761 ESTs CDKN2B -3.35 0.90 0.39 0.52 -3.11 0.88 0.80 0.25 BF223214 ESTs - -0.48 0.08 1.69 2.04 -1.51 0.25 4.09 1.98 AF154054 Homo GREM1 1.68 0.26 4.61 0.74 0.62 0.04 3.58 0.87 sapiens DRM (DRM) mRNA, complete cds. /PROD=DR M /FL=gb:NM_ 013372.1 gb:AF11013 7.2 gb:AF04580 0.1 gb:AF15405 4.1 NM_021223 Homo MYL7 1.81 0.05 4.28 0.81 0.17 0.08 4.87 0.96 sapiens 115 myosin light chain 2a (LOC58498), mRNA. /PROD=myo sin light chain 2a /FL=gb:NM_ 021223.1 Al817041 G protein- CMKORI -0.19 0.27 2.67 1.97 0.06 0.18 5.05 1.64 coupled receptor NM_003670 Homo BHLHB2 1.09 0.08 3.85 0.10 -0.11 0.17 3.46 0.03 sapiens basic helix loop-helix domain containing, class B, 2 (BHLHB2), mRNA. /PROD=diffe rentiated embryo chondrocyte expressed gene /FL=gb:ABOO 4066.1 gb:NM_0036 70.1 NM_023915 Homo GPR87 -1.70 0.61 1.64 0.18 -2.99 0.06 1.40 0.23 sapiens G protein coupled receptor 87 (GPR87), mRNA. /PROD=G protein coupled receptor 87 /FL=gb:NM_ 023915.1 gb:AF23776 3.1 NM_003867 Homo FGF17 -3.05 0.39 0.03 2.07 -2.13 0.41 2.49 1.35 sapiens 116 fibroblast growth factor 17 (FGF1 7), mRNA. /PROD=fibro blast growth factor 17 /FL=gb:NM_ 003867.1 gb:AB00924 9.1 NM_024426 Homo WT1 -3.23 0.37 -1.11 0.62 -4.20 0.56 -2.44 1.26 sapiens Wilms tumor 1 (WT1), transcript variant D, mRNA. /PROD=Wil ms tumor 1 isoform D /FL=gb:NM_ 024424.1 gb:NM_0244 26.1 NM_033136 Homo FGF1 -3.10 1.42 0.09 0.83 -3.16 0.63 -0.78 1.21 sapiens fibroblast growth factor 1 (acidic) (FGF1), transcript variant 2, mRNA. /PROD=fibro blast growth factor 1 (acidic) isoform 2precursor /FL=gb:NM_ 033137.1 gb:NM_0331 36.1 X99268 H.sapiens TWISTi 0.10 0.33 3.94 0.24 0.34 0.22 3.45 0.34 mRNA for B HLH DNA binding 117 protein.

/PROD=B

HLH DNA binding protein /FL=gb:NM_ 000474.1 AL524520 G protein- LGR5 -2.27 1.43 0.76 1.40 -1.58 0.40 2.51 1.35 coupled receptor 49 NM_022557 Homo CSH1 -0.91 0.19 1.40 0.22 -2.12 0.08 1.47 0.14 sapiens growth hormone 2 (GH2), transcript variant2, mRNA. /PROD=grow th hormone 2, isoform 2 precursor /FL=gb:J037 56.1 gb:NM_0225 57.1 AL544576 ESTs TMEM88 -1.96 0.68 1.75 0.58 -1.45 0.86 2.08 0.70 NM_022580 Homo CSHI -1.20 0.86 2.30 0.39 -1.78 0.64 1.55 0.63 sapiens chorionic somatomam motropin hormone-like 1 (CSHL1), transcript variant 4, mRNA. /PROD=chori onic somatomam motropin hormone-like 1,isoform 4 /FL=gb:NM_ 022580.1 J03580 Human, PTHLH -2.72 0.33 -0.80 0.40 -4.05 0.41 -1.42 0.73 parathyroid like protein 118 (associated with humoral hypercalcemi a of malignancy) mRNA, complete cds. /FL=gb:J035 80.1 BC029835 Homo LOC646867 -2.66 1.12 1.01 1.85 -1.40 0.41 3.03 1.61 sapiens, clone IMAGE:5169 759, mRNA. A1452798 ESTs MYOCD 0.98 0.13 3.31 0.66 -0.07 0.28 2.80 0.98 NM_022559 Homo CSHI -1.56 0.38 2.00 0.32 -2.07 0.42 1.47 0.28 sapiens growth hormone 1 (GH1), transcript variant 2, mRNA. /PROD=grow th hormone 1, isoform 2 precursor /FL=gb:NM_ 022559.1 NM_001318 Homo CSHI 0.15 0.41 2.83 0.40 -1.30 0.34 2.37 0.50 sapiens chorionic somatomam motropin hormone-like 1 (CSHLI), transcript variant 1, mRNA. /PROD=chori onic somatomam motropin hormone-like lisoform 1 /FL=gb:NM_ 001318.2 119 M65062 Human IGFBP5 -2.80 1.17 2.19 2.00 -0.99 0.23 4.11 1.81 insulin-like growth factor binding protein 5 (IGFBP-5) mRNA, complete cds. /PROD=insul in-like growth factor binding protein 5 /FL=gb:M650 62.1 gb:M62782.1 gb:NM_0005 99.1 gb:AF05503 3.1 AF207990 Homo FER1L3 0.49 0.40 3.00 0.81 -0.16 0.09 4.02 0.92 sapiens fer-1 like protein 3 (FER1L3) mRNA, complete cds. /PROD=fer-1 like protein 3 IFL=gb:AF20 7990.1 A1079944 ESTs - -0.78 0.22 0.08 0.59 -3.56 0.24 -0.13 0.73 BC003070 Homo GATA3 1.07 0.04 3.23 0.96 0.31 0.26 4.45 0.80 sapiens,

GATA

binding protein 3, done MGC:2346, mRNA, complete cds. /PROD=GAT A-binding protein 3 /FL=gb:NM_ 002051.1 120 gb:M69106.1 gb:BC00307 0.1 BE877796 collagen, COL8A1 -3.76 1.17 -1.28 0.73 -4.89 0.54 -1.33 1.64 type Vill, alpha 1 /FL=gb:NM_ 001850.1 NM_022560 Homo CSH1 -2.23 0.74 1.95 0.08 -2.01 0.51 1.47 0.31 sapiens growth hormone 1 (GH1), transcript variant 3, mRNA. /PROD=grow th hormone 1, isoform 3 precursor /FL=gb:NM_ 022560.1 BE328496 hypothetical - -0.59 0.25 1.76 0.13 -2.01 0.97 1.73 0.26 protein PR02032 IFL=gb:AF1 1 6683.1 gb:NM_0186 15.1 NM_022469 Homo GREM2 -1.15 0.25 0.09 0.88 -3.43 0.90 0.76 0.47 sapiens hypothetical protein FLJ21195 similar to protein related to DAC and cerberus (FLJ21195), mRNA. /PROD=hypo thetical protein FLJ21195 similar to proteinrelate d to DAC 121 and cerberus /FL=gb:NM_ 022469.1 NM_001362 Homo D103 -1.73 0.70 1.99 1.92 -1.05 0.79 4.23 1.51 sapiens deiodinase, lodothyronin e, type IlIl (DI03), mRNA. /PROD=thyr oxine deiodinase type Ill /FL=gb:NM_ 001362.1 gb:S79854.1 NM_022581 Homo CSHI -1.56 0.67 2.08 0.42 -1.63 0.80 1.47 0.53 sapiens chorionic somatomam motropin hormone-like 1 (CSHL1), transcript variant 5, mRNA. /PROD=chor onic somatomam motropin hormone-like 1,isoform 5 precursor IFL=gb:NM_ 022581.1 NM_013372 Homo GREM1 1.61 0.07 4.15 0.64 0.91 0.15 3.20 0.81 sapiens cysteine knot superfamily 1, BMP antagonist 1 (CKTSF1B1) , mRNA /PROD=cyst eine knot superfamily 1, BMP 122 antagonist 1 /FL=gb:NM_ 013372.1 gb:AF11013 7.2 gb:AF04580 0.1 gb:AF1 5405 4.1 NM_022561 Homo CSHI -1.32 0.60 1.91 0.25 -1.66 0.46 1.57 0.22 sapiens growth hormone 1 (GH1), transcript variant 4, mRNA. /PROD=grow th hormone 1, isoform 4 precursor /FL=gb:NM_ 022561.1 NM_022659 Homo - -1.58 0.75 -1.24 1.79 -3.62 0.20 -1.81 1.25 sapiens hypothetical protein FLJ11500 similar to EBF2 (FLJ1 1500), mRNA. /PROD=hypo thetical protein FLJ11500 similar to EBF2 /FL=gb:NM_ 022659.1 AF006060 Homo CSHI -1.21 0.06 1.13 0.05 -3.08 0.63 0.50 0.17 sapiens placental growth hormone 20kDa isoform (hGH-V) 123 mRNA, complete cds. /PROD=plac ental growth hormone 20kDa isoform /FL=gb:AFOO 6060.1 gb:NM_0225 56.1 A1688418 plexin A2 PLXNA2 -0.18 0.14 0.84 1.58 -1.28 0.53 2.74 0.96 M86849 Homo - -5.08 0.26 0.54 0.47 -1.64 0.19 -0.09 0.44 sapiens connexin 26 (GJB2) mRNA, complete cds. /PROD=conn exin 26 /FL=gb:NM_ 004004.1 gb:M86849.2 N71923 fibronectin - 0.30 0.24 2.83 1.46 0.53 0.12 4.38 1.46 leucine rich transmembra ne protein 3 /FL=gb:AF16 9677.1 gb:NM_0132 81.1 NM_013281 Homo FLRT3 -0.20 0.33 2.14 1.61 0.00 0.15 3.96 1.39 sapiens fibronectin leucine rich transmembra ne protein 3 (FLRT3), mRNA. /PROD=fibro nectin leucine rich transmembra ne protein3 /FL=gb:AF16 9677.1 124 gb:NM_0132 81.1 A1601101 Homo FAM84A 0.46 0.38 3.07 0.46 -0.32 0.46 3.82 0.48 sapiens cDNA: FLJ21410 fis, clone COL03938 NM_000325 Homo PITX2 1.37 0.17 3.51 0.47 0.89 0.16 4.02 0.47 sapiens paired-like homeodomai n transcription factor 2 (PITX2), mRNA. /PROD=pair ed-like homeodomai n transcription factor 2 /FL=gb:NM_ 000325.1 gb:U69961.1 gb:AF04872 0.1 A1692659 heat shock PRDM1 0.21 0.25 1.67 0.77 -0.67 0.17 2.61 0.80 9OkD protein 1, alpha NM_000602 Homo SERPINE1 2.97 0.16 4.75 1.89 1.55 0.22 2.75 1.87 sapiens serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (SERPINEl), mRNA. /PROD=serin e (or 125 cysteine) proteinase inhibitor, cladeE (nexin, plasminogen activator inhibitor type 1), membe NM_001480 Homo GALRI -1.90 0.68 0.04 0.73 -2.42 0.72 -0.34 0.73 sapiens galanin receptor 1 (GALR1), mRNA. /PROD=gala nin receptor 1 /FL=gb:NM_ 001480.2 gb:U23854.1 gb:L34339.1 gb:U53511.1 NM_000393 Homo COL5A2 4.29 0.14 5.25 0.21 2.62 0.02 5.48 0.13 sapiens collagen, type V, alpha 2 (COLSA2), mRNA. /PROD=colla gen, type V, alpha2 /FL=gb:NM_ 000393.1 N63706 ESTs - 0.06 0.18 1.73 1.89 -0.74 0.13 3.75 1.75 AF132818 Homo KLF5 0.63 0.11 3.16 0.50 0.07 0.42 3.40 0.44 sapiens colon Kruppel-like factor (CKLF) mRNA, complete cds. /PROD=colo n Kruppel like factor /FL=gb:AF13 126 2818.1 gb:AF28727 2.1 gb:AB03082 4.1 gb:NM_0017 30.1 gb:D14520.1 X59065 H.sapiens - -1.17 1.11 -0.39 1.06 -2.61 0.26 -0.96 1.01 FGF gene, exon 3 /FL=gb:NM_ 000800.1 gb:M13361.1 R73554 Human IGFBP5 -0.12 0.15 2.63 1.41 -0.69 0.16 4.00 1.65 insulin-like growth factor binding protein 5 (IGFBPS) mRNA NM_002149 Homo HPCAL1 -0.18 0.28 1.81 0.44 -1.98 0.86 1.18 0.22 sapiens hippocalcin like 1 (HPCALI), mRNA. /PROD=hipp ocalcin-like 1 /FL=gb:NM_ 002149.1 gb:D16227.1 A1093327 ESTs - 0.69 0.11 3.09 0.58 0.45 0.07 2.29 0.85 NM_003240 Homo PYCR2 6.22 0.16 6.97 0.60 4.16 0.07 7.51 0.68 sapiens endometrial bleeding associated factor (left right determinatio n, factor A; transforming growth factor beta superfamily) (EBAF), mRNA. 127 /PROD=tran storming growth factor, beta 4 /FL=gb:U815 23.1 gb:NM_0032 40.1 gb:AF08151 3.1 A1263909 ras homolog RHOB 3.89 0.16 5.88 0.13 3.01 0.15 5.64 0.10 gene family, member B /FL=gb:NM_ 004040.1 NM_001792 Homo CDH2 3.83 0.17 6.01 0.11 2.85 0.13 5.74 0.17 sapiens cadherin 2, type 1, N cadherin (neuronal) (CDH2), mRNA. /PROD=cadh erin 2, type 1, N cadherin (neuronal) /FL=gb:NM_ 001792.1 gb:M34064.1 NM_003897 Homo IER3 5.45 0.15 6.97 0.17 4.33 0.11 6.75 0.27 sapiens immediate early response 3 (IER3), mRNA. /PROD=imm ediate early response 3 /FL=gb:BCOO 5080.1 gb:BC00084 4.1 gb:AF08342 1.1 gb:NM_0038 128 97.1 AF278532 Homo NTN4 -0.16 0.30 1.70 0.91 -0.67 0.48 2.66 0.74 sapiens beta-netrin mRNA, complete cds. /PROD=beta -netrin /FL=gb:AFI 1 9916.1 gb:AF29771 1.1 gb:NM_0212 29.1 gb:AF27853 2.1 AF348491 Homo CXCR4 1.39 0.21 4.05 1.58 1.45 0.07 5.67 1.65 sapiens chemokine receptor CXCR4 mRNA, complete cds. /PROD=che mokine receptor CXCR4 /FL=gb:AF34 8491.1 NM_030781 Homo COLEC12 1.93 0.13 3.64 1.66 1.96 0.18 5.68 1.51 sapiens scavenger receptor with C-type lectin (SRCL), mRNA. /PROD=scav enger receptor with C-type lectin /FL=gb:NM_ 030781.1 NM_000599 Homo IGFBP5 -0.31 0.34 3.03 1.85 0.12 0.24 4.51 1.75 sapiens insulin-like growth factor 129 binding protein 5 (IGFBP5), mRNA. /PROD=insul in-like growth factor binding protein 5 /FL=gb:M650 62.1 gb:M62782.1 gb:NM_0005 99.1 gb:AF05503 3.1 A1348094 KIAA0882 TBC1D9 0.13 0.26 3.21 1.13 0.96 0.13 4.67 1.08 protein BG287862 AHNAK AHNAK 1.47 0.20 3.72 0.51 1.37 0.17 4.34 0.58 nucleoprotei n (desmoyokin A1676059 ESTs FOXQ1 -0.32 0.55 3.08 1.63 0.50 0.17 4.81 1.47 A1127440 ESTs - -0.85 0.36 0.60 1.22 -0.65 0.27 2.13 1.13 AL574210 serine (or SERPINE1 2.81 0.24 5.07 0.88 2.13 0.15 3.96 0.86 cysteine) proteinase inhibitor, dade E (nexin, plasminogen activator inhibitor type 1), member 1 /FL=gb:NM_ 000602.1 gb:M16006.1 AB037810 Homo SIPAIL2 3.88 0.04 5.66 0.08 3.18 0.11 5.85 0.11 sapiens mRNA for KIAA1389 protein, partial eds. /PROD=KIA Al 389 protein 130 NM_001394 Homo DUSP4 0.22 0.37 2.88 1.09 0.50 0.14 4.12 0.99 sapiens dual specificity phosphatase 4 (DUSP4), mRNA. /PROD=dual specificity phosphatase 4 /FL=gb:NM_ 001394.2 gb:BC00267 1.1 gb:U48807.1 gb:U21108.1 BC029442 Homo - 2.04 0.20 3.80 0.74 1.18 0.05 4.50 0.65 sapiens, Similar to immunity associated protein 1, done MGC:32707 IMAGE:4618 467, mRNA, complete cds. /PROD=Simil ar to immunity associated protein 1 /FL=gb:BC02 9442.1 NM_000700 Homo ANXA1 5.00 0.18 6.27 1.28 3.67 0.05 4.96 1.25 sapiens annexin Al (ANXA1), mRNA. /PROD=ann exin I /FL=gb:BCOO 1275.1 gb:NM_0007 00.1 BC000740 Homo CCKBR 1.08 0.36 3.93 1.84 1.93 0.03 5.86 1.82 sapiens, 131 cholecystoki nin B receptor, clone MGC:2199, mRNA, complete cds. /PROD=chol ecystokinin B receptor /FL=gb:L077 46.1 gb:L08112.1 gb:S70057.1 gb:BC00074 0.1 gb:L04473.1 gb:NM_0007 31.1 N36408 hypothetical FOSL2 -0.09 0.40 2.07 0.04 -0.85 0.24 1.71 0.28 protein FLJ23306 IFL=gb:NM_ 024530.1 AF072242 Homo MBD2 -3.98 0.38 -0.59 0.27 -3.07 0.22 -1.70 0.68 sapiens methyl-CpG binding protein MBD2 (MBD2) mRNA, complete cds. /PROD=met hyl-CpG binding protein MBD2 /FL=gb:NM_ 003927.2 gb:AF07224 2.1 AF211891 Homo MIXL1 -0.63 0.38 0.77 0.95 -2.29 0.44 0.92 1.71 sapiens Mix like homeobox 132 protein 1 MILDD) mRNA, complete cds. /PROD=Mix like homeobox protein 1 /FL=gb:AF21 1891.1 BF063186 ESTs CALDI 1.16 0.19 2.03 0.42 -1.20 1.02 1.65 0.27 NM_000362 Homo TIMP3 0.08 0.32 1.98 0.09 -0.34 0.33 1.80 0.26 sapiens tissue inhibitor of metalloprotei nase 3 (Sorsby fundus dystrophy, pseudoinfla mmatory) (TIMP3), mRNA. /PROD=tissu e inhibitor of metalloprotei nase 3precursor /FL=gb:NM_ 000362.2 gb:U14394.1 gb:U67195.1 gb:U02571.1 AK022852 Homo SIPA1L2 2.87 0.12 4.50 0.09 1.87 0.01 4.55 0.09 sapiens cDNA FLJ12790 fis, clone NT2RP2001 985, weakly similar to Homo sapiens high-risk human papilloma 133 viruses E6 oncoproteins targeted protein E6TP1 alpha mRNA. BE500942 Homo C6orf155 3.23 0.10 4.68 0.86 1.95 0.03 3.77 0.96 sapiens mRNA; cDNA DKFZp761M 0111 (from clone DKFZp761M 0111) AW665892 paternally MFAP5 -1.82 0.54 0.37 0.60 -1.54 0.39 -0.01 0.28 expressed 3 AK025063 Homo FAM84A -1.34 0.84 0.75 0.45 -2.35 0.85 1.01 0.53 sapiens cDNA: FLJ21410 fis, clone COL03938. NM_001828 Homo CLC 2.17 0.21 3.53 1.07 0.45 0.08 2.11 1.27 sapiens Charot Leyden crystal protein (CLC), mRNA. /PROD=Char ot-Leyden crystal protein /FL=gb:NM_ 001828.3 gb:LO1664.1 M15329 Human IL1A 0.85 0.32 2.72 0.30 -0.88 0.60 2.20 0.22 interleukin 1 alpha (IL1A) mRNA, complete cds. IPROD=interd eukin 1 alpha /FL=gb:M153 134 29.1 BC002671 Homo DUSP4 1.79 0.03 4.30 1.39 2.10 0.10 5.60 1.22 sapiens, dual specificity phosphatase 4, clone MGC:3713, mRNA, complete cds. /PROD=dual specificity phosphatase 4 /FL=gb:NM_ 001394.2 gb:BC00267 1.1 gb:U48807.1 gb:U21108.1 AA524250 deleted in DLC1 1.02 0.05 2.35 0.98 0.10 0.38 3.26 0.96 liver cancer 1 BC001211 Homo KIFC3 -1.53 0.72 0.81 0.38 -2.08 0.42 0.75 0.16 sapiens, kinesin family member C3, done MGC:3226, mRNA, complete cds. /PROD=kine sin family member C3 /FL=gb:BCOO 1211.1 gb:NM_0055 50.1 gb:AF00442 6.1 NM_004560 Homo ROR2 0.76 0.08 2.20 0.81 0.08 0.14 3.06 0.95 sapiens receptor tyrosine kinase-like orphan 135 receptor 2 (ROR2), mRNA. /PROD=rece ptor tyrosine kinase-like orphan receptor 2 /FL=gb:M976 39.1 gb:NM_0045 60.1 BC000125 Homo TGFBI 1.16 0.18 3.43 0.08 0.72 0.14 3.30 0.16 sapiens, Similar to transforming growth factor, beta 1, clone MGC:31 19, mRNA, complete cds. IPROD=Simil ar to transforming growth factor, beta 1 /FL=gb:M384 49.1 gb:BC00118 0.1 gb:BC00012 5.1 gb:NM_0006 60.1 NM_016931 Homo NOX4 1.83 0.06 3.31 1.29 1.20 0.14 2.28 1.27 sapiens NADPH oxidase 4 (NOX4), moRNA. /PROD=NAD PH oxidase 4 /FL=gb:AF26 1943.1 gb:NM_0169 136 31.1 gb:AF25462 1.1 gb:AB04103 5.1 BC001830 Homo TGFB111 0.95 0.17 3.59 0.73 1.52 0.09 2.74 0.69 sapiens, Similar to transforming growth factor beta 1 induced transcript 1, clone MGC:4078, mRNA, complete cds. /PROD=Simil ar to transforming growth factor beta induced transcript 1 /FL=gb:NM_ 015927.1 gb:BC00183 0.1 gb:AF 11634 3.1 NM_024576 Homo OGFRL1 3.15 0.13 4.49 0.82 1.63 0.06 3.30 0.98 sapiens hypothetical protein FLJ21079 (FLJ21079), mRNA. /PROD=hypo thetical protein FLJ21079 /FL=gb:NM_ 024576.1 NM_001963 Homo EGF 0.12 0.22 1.82 1.15 -0.62 0.36 2.68 1.23 sapiens epidermal growth factor 137 (beta urogastrone) (EGF), mRNA. /PROD=epid ermal growth factor (beta urogastrone) /FL=gb:NM_ 001963.2 BE620374 ESTs C6orf155 1.97 0.05 3.35 1.01 0.59 0.17 2.10 1.05 AL359062 Homo COL8A1 -1.31 0.25 2.32 0.94 0.03 0.12 3.51 1.02 sapiens mRNA full length insert cDNA clone EUROIMAG E 1913076. AL117653 Homo MITF -0.12 0.61 2.32 0.10 0.21 0.13 2.56 0.06 sapiens mRNA; cDNA DKFZp586C 0224 (from clone DKFZp586C 0224). AL021977 Cluster Ind. - 1.92 0.14 4.53 0.43 2.15 0.12 4.66 0.22 AL021977:b K447C4.1 (novel MAFF (v-maf musculoapo neurotic fibrosarcoma (avian) oncogene family, protein F) LIKE protein) /cds=(0,494) /gb=AL02119 77 /gi=4914526 /ug=Hs.5130 5 /len=2128 NM_003564 Homo TAGLN2 5.43 0.12 6.76 0.06 3.48 0.27 6.69 0.04 sapiens 138 transgelin 2 (TAGLN2), mRNA. /PROD=tran sgelin 2 /FL=gb:D212 61.1 gb:NM_0035 64.1 BC005107 Homo - 7.08 0.07 6.42 0.26 2.60 0.07 6.93 0.22 sapiens, done IMAGE:3840 937, mRNA, partial cds. /PROD=Unk known (protein for IMAGE:3840 937) NM_001124 Homo ADM 4.70 0.22 7.61 0.19 5.21 0.06 7.58 0.21 sapiens adrenomedul lin (ADM), mRNA. /PROD=adre nomedullin /FL=gb:NM_ 001124.1 gb:D14874.1 AF280545 Homo NRP2 -0.29 0.33 1.40 0.30 -1.67 0.61 1.22 0.33 sapiens neuropilin 2b(5) (NRP2) mRNA, complete cds, alternatively spliced. /PROD=neur opilin-2b(5) /FL=gb:AF28 0544.1 gb:AF28054 5.1 NM_014624 Homo S10OA6 3.08 0.38 3.10 0.18 -0.57 0.37 3.24 0.19 sapiens 139 S100 calcium binding protein A6 (calcyclin) (S100A6), mRNA. /PROD=S10 0 calcium binding protein A6 /FL=gb:NM_ 014624.2 gb:BC00143 1.1 AB030824 Homo KLF5 0.57 0.24 2.16 0.49 -0.41 0.05 2.53 0.17 sapiens mRNA for transcription factor BTEB2, complete cds. /PROD-tran scription factor BTEB2 /FL=gb:AF13 2818.1 gb:AF28727 2.1 gb:AB03082 4.1 gb:NM_0017 30.1 gb:D14520.1 NM_015675 Homo GADD45B 2.47 0.22 4.44 0.46 2.02 0.09 4.64 0.33 sapiens growth arrest and DNA damage inducible, beta (GADD45B), mRNA. /PROD=DKF ZP566B133 protein 140 /FL=gb:NM_ 015675.1 gb:AF09095 0.1 BF347089 tissue TIMP3 0.57 0.13 2.01 0.29 -0.19 0.20 2.09 0.44 inhibitor of metalloprotei nase 3 (Sorsby fundus dystrophy, pseudoinfla mmatory) /FL=gb:NM_ 000362.2 gb:U14394.1 gb:U67195.1 gb:U02571.1 BF056473 ESTs - -0.64 0.87 1.79 0.10 -0.73 0.34 1.57 0.23 AA809487 Homo - 0.52 0.22 3.68 0.43 1.39 0.22 3.89 0.48 sapiens cDNA FLJ21715 fis, clone COL10287, highly similar to AF071569 Homo sapiens multifunction al calciumcalm odulin dependent protein kinase I delta2 isoform mRNA AL575735 collagen, - 5.54 0.11 6.65 0.14 4.57 0.08 6.68 0.07 type V, alpha 2 /FL=gb:NM_ 000393.1 AF003934 Homo GDF15 2.74 0.20 4.01 0.41 0.72 0.17 4.34 0.50 sapiens prostate differentiatio 141 n factor mRNA, complete cds. /PROD=pros tate differentiatio n factor IFL=gb:U883 23.1 gb:BC00052 9.1 gb:AF00393 4.1 gb:NM_0048 64.1 gb:AF01977 0.1 gb:AB00058 4.1 NM_000313 Homo PROSI -1.54 0.10 0.98 0.83 -0.62 0.09 179 0.86 sapiens protein S (alpha) (PROSI), mRNA. /PROD=prot ein S (alpha) /FL=gb:M150 36.1 gb:NM_0003 13.1 NM_016651 Homo DACTI 2.37 0.26 4.79 0.67 2.46 0.14 3.92 0.78 sapiens heptacellular carcinoma novel gene-3 protein (LOC51339), mRNA. /PROD=hept acellular carcinoma novel gene-3 protein /FL=gb:NM_ 016651.2 gb:AF25107 142 9.2 NM_020129 Homo LGALS14 1.38 0.30 3.15 0.70 0.79 0.04 2.47 0.66 sapiens placental protein 13 like protein (LOC56891), mRNA. /PROD=plac ental protein 13-like protein /FL=gb:NM_ 020129.1 gb:AF26785 2.1 NM_013451 Homo FER1L3 1.75 0.15 4.02 0.97 1.59 0.13 5.14 0.82 sapiens fer-1 (C.elegans) like 3 (myoferlin) (FER1L3), mRNA. /PROD=fer-1 (C.elegans) like 3 (myoferlin) /FL=gb:NM_ 013451.1 gb:AF18231 6.1 R72286 microfibrillar- MFAP4 -1.15 0.60 -1.76 0.61 -2.37 0.22 -0.60 0.72 associated protein 4 A1417362 ESTs, FUTI 2.42 0.14 2.32 0.72 -0.46 0.53 1.70 0.59 Moderately similar to ALU1_HUM AN ALU SUBFAMILY J SEQUENCE CONTAMIN ATION WARNING ENTRY (H.sapiens) NM_001553 Homo IGFBP7 3.41 0.19 4.63 1.07 1.65 0.10 3.34 1.16 143 sapiens insulin-like growth factor binding protein 7 (IGFBP7), mRNA. /PROD=insul in-like growth factor binding protein 7 /FL=gb:NM_ 001553.1 gb:L19182.1 BG285011 Homo ARID5B 0.05 0.22 1.79 0.21 -0.95 0.42 1.16 0.55 sapiens mRNA; cDNA DKFZp586N 012 (from done DKFZp586N 012) BE967311 Homo - 1.99 0.06 4.08 0.92 2.28 0.17 5.01 0.87 sapiens mRNA; cDNA DKFZp7620 1615 (from done DKFZp762O 1615) BC005047 Homo DUSP6 2.50 0.32 4.04 0.67 1.56 0.16 2.94 0.84 sapiens, done MGC:12852, mRNA, complete cds. /PROD=Unk nown (protein for MGC:12852) /FL=gb:NM_ 001946.1 gb:ABO1338 2.1 144 gb:BC00356 2.1 gb:BC00314 3.1 gb:BC00504 7.1 AW005572 putative47 ANKS1B -0.59 0.12 0.19 0.70 -1.59 0.07 0.86 0.92 kDa protein AW294092 ESTs RERG 0.54 0.16 -0.68 1.55 -2,78 0.92 -0.58 0.97 NM_001899 Homo CST4 0.14 0.52 2.46 1.59 0.53 0.14 3.87 1.40 sapiens cystatin S (CST4), mRNA. /PROD=cyst atin S /FL=gb:NM_ 001899.1 A1917371 ESTs - -1.47 0.95 0.18 1.43 -1.24 0.33 2.21 1.17 NM_000515 Homo CSH1 -2.36 0.29 1.92 0.10 -0.73 0.57 1.37 0.21 sapiens growth hormone 1 (GH1), transcript variant 1, mRNA. /PROD=grow th hormone 1, isoform I precursor /FL=gb:NM_ 000515.2 NM_004414 Homo DSCRI 2.14 0.03 3.85 0.26 1.74 0.16 3.34 0.36 sapiens Down syndrome critical region gene I (DSCRI), mRNA. /PROD=Dow n syndrome critical region protein 1 /FL=gb:U288 33.2 gb:NM_0044 145 14.2 Al355441 sprouty - 0.24 0.48 1.72 0.50 -1.12 0.40 2.03 0.61 (Drosophila) homolog 4 AB032953 Homo ODZ2 0.00 0.14 0.65 0.35 -1.74 0.74 0.88 0.03 sapiens mRNA for KIAAI127 protein, partial cds. /PROD=KIA A1127 protein BE048571 ESTs MGC16121 -1.66 0.78 1.44 1.00 -1.31 0.21 0.10 1.22 AW471145 ESTs PRSS23 0.87 0.10 3.46 0.35 1.13 0.11 3.37 0.53 BF196943 ESTs USP53 1.43 0.03 3.24 0.92 0.85 0.26 2.32 0.88 AF498927 Homo ARHGDIB -0.03 0.19 0.04 0.96 -3.00 0.54 -0.85 0.93 sapiens Rho GDP dissociation inhibitor beta (ARHGDIB) mRNA, complete cds. /PROD=Rho GDP dissociation inhibitor beta /FL=gb:AF49 8927.1 AF329092 Homo DOCI -2.38 0.45 1.00 0.19 -1.62 0.74 0.75 0.11 sapiens

GPBP

interacting protein 90 mRNA, complete cds. /PROD=GPB P-interacting protein 90 /FL=gb:AF32 9092.1 BG250721 Homo - 2.48 0.04 4.54 0.95 2.63 0.14 5.31 0.83 sapiens mRNA; cDNA 146 DKFZp564C 2063 (from done DKFZp564C 2063) N69091 ESTs PCDH17 0.59 0.10 1.49 0.88 -1.11 0.69 2.49 0.78 BF589359 ESTs PAGI -1.11 0.52 -0.09 0.43 -1.54 0.12 0.50 0.13 BF968270 ESTs SLC35F3 0.37 0.02 1.84 0.30 0.10 0.17 2.46 0.36 NM_006183 Homo NTS 4.77 0.15 4.73 1.45 3.01 0.19 3.21 1.47 sapiens neurotensin (NTS), mRNA. /PROD=neur otensin precursor /FL=gb:NM_ 006183.2 gb:U91618.1 D28124 Cluster Incl. NBLI 2.90 0.03 4.24 0.37 2.09 0.08 4.44 0.38 D28124:Hum an mRNA for unknown product, complete cds /cds=(61,603 /gb=D28124 /gi=641821 /ug=Hs.7630 7 /len=1929 AW129593 tudor repeat TDRD7 1.19 0.19 2.40 0.87 0.92 0.0A 3.27 0.89 associator with PCTAIRE 2 BE675435 core KLF6 0.29 0.30 2.91 1.02 0.54 0.24 3.68 094 promoter element binding protein /FL=gb:AFOO 1461.1 gb:BC00031 1.1 gb:NM_0013 00.2 gb:ABO1749 3.1 147 gb:BC00430 1.1 A1202327 ESTs CPEB2 1.88 0.09 3.42 0.07 0.99 0.10 3.36 0.03 NM_002228 Homo JUN 2.12 0.16 4.09 0.56 1.62 0.13 4.53 041 sapiens v-jun avian sarcoma virus 17 oncogene homolog (JUN), mRNA. /PROD=v-jun avian sarcoma virus 17 oncogene homolog /FL=gb:NM_ 002228.2 gb:BC00264 6.1 AF005775 Homo CFLAR 2.88 0.18 3.70 1.56 0.35 0.17 5.22 1.69 sapiens caspase-like apoptosis regulatory protein 2 (clarp) mRNA, alternatively spliced, complete cds. /PROD=casp ase-like apoptosis regulatory protein 2 /FL=gb:AFOO 5775.1 NM_007173 Homo PRSS23 3.02 0.10 5.11 0.21 2.90 0.05 5.22 0.23 sapiens protease, serine, 23 (SPUVE), mRNA. /PROD=prot 148 ease, serine, 23 IFL=gb:BC00 1278.1 gb:AF19361 1.1 gb:AF01528 7.1 gb:AL13691 4.1 gb:NM_0071 73.1 NM_012413 Homo QPCT 1.44 0.09 0.97 0.85 -2.46 0.65 0.19 1.10 sapiens glutaminyl peptide cyclotransfer ase (glutaminyl cyclase) (QPCT), mRNA. /PROD=gluta minyl peptide cyclotransfer ase precursor /FL=gb:NM_ 012413.2 BU683415 Homo KLF6 3.40 0.06 5.28 0.85 3.46 0.09 6.01 0.85 sapiens, done IMAGE:4096 273, mRNA AV729634 DnaJ DNAJC6 0.62 0.20 2.59 0.79 0.99 0.19 3.35 0.65 (Hsp4O) homolog, subfamily B, member 6 /FL=gb:AB00 7942.1 gb:NM_0147 87.1 BC038556 Homo - -0.79 0.40 0.12 0.99 -2.17 0.62 -0.08 0.38 sapiens, clone IMAGE:3446 149 976, mRNA. NM_014942 Homo ANKRD6 0.62 0.04 2.17 1.11 0.59 0.23 3.30 1.07 sapiens KIAA0957 protein (KIAA0957), mRNA. /PROD=KIA A0957 protein /FL=gb:AB02 3174.1 gb:NM_0149 42.1 AF260333 Homo C4orf18 -1.58 0.10 0.21 1.21 -3.19 1.07 1.60 1.12 sapiens AD036 mRNA, complete cds. /PROD=ADO 36 /FL=gb:AF26 0333.1 AA448956 Homo CAMK2D 1.47 0.18 2.75 0.42 0.21 0.21 2.97 0.39 sapiens cDNk FLJ21715 fis, clone COL10287, highly similar to AF071569 Homo sapiens multifunction al calciumcalm odulin dependent protein kinase II delta2 isoform mRNA /FL=gb:AF07 1569.1 BE349115 ESTs COL22A1 -0.02 0.52 2.04 0.25 0.24 0.06 2.38 0.22 BF209337 Homo LOC541471 4.83 0.17 5.80 0.73 3.13 0.02 4.84 0.81 150 sapiens cDNA FLJ10934 fis, clone OVARC1000 640 AB019695 Homo - 2.43 0.01 4.15 0.40 1.42 0.05 3.50 0.29 sapiens mRNA for thioredoxin reductase il beta, complete cds. /PROD=thior edoxin reductase il beta /FL=gb:ABO1 9695.1 AK090497 Homo LOC284576 -3.78 0.56 -2.87 1.42 -4.94 0.07 -4.74 0.53 sapiens cDNA FU33178 fis, cone ADRGL2002 753. NM_006763 Homo BTG2 2.30 0.10 3.28 0.62 0.85 0.25 3.84 0.74 sapiens BTG family, member 2 (BTG2), mRNA. /PROD=BTG family, member 2 /FL=gb:U726 49.1 gb:NM_0067 63.1 BC002616 Homo TAGLN2 5.61 0.20 5.56 0.17 2.91 0.18 5.40 0.12 sapiens, transgelin 2, done MGC:2989, mRNA, complete cds. 151 /PROD=tran sgelin 2 /FL=gb:BCOO 2616.1 AF078077 Homo GADD45B 1.30 0.17 3.41 0.31 0.61 0.12 3.05 0.29 sapiens growth arrest and DNA damage inducible protein GADD45bet a mRNA, complete cds. /PROD=grow th arrest and

DNA

damage inducible proteinGAD D45beta /FL=gb:AF08 7853.1 gb:AF07807 7.1 NM_001854 Homo COLI1A1 2.90 0.02 4.06 1.44 1.87 0.06 2.68 1.43 sapiens collagen, type Xl, alpha 1 (COL1 1A1), mRNA. /PROD=colla gen, type XI, alpha 1 /FL=gb:JO41 77.1 gb:NM_0018 54.1 A1830201 ESTs KIAA0773 -0.75 0.82 1.24 0.22 -1.87 0.51 0.40 0.22 N95437 ESTs LMCDI 0.74 0.12 2.72 0.57 0.39 0.14 3.05 0.42 BC002511 Homo CBR1 3.72 0.02 1.03 2.43 -4.10 0.16 -1.64 2.36 sapiens, carbonyl reductase 1, done MGC:1920, 152 mRNA, complete cds. /PROD=carb onyl reductase 1 /FL=gb:BCO0 2511.1 gb:NM_0017 57.1 gb:J04056.1 AV682252 HIV-1 rev - -0.33 0.15 1.78 1.36 -0.24 0.17 0.41 1.29 binding protein 2 AW263497 ESTs SYTL5 -1.05 0.25 1.44 0.38 -0.55 0.41 2.11 0.47 AF130095 Homo - 5.80 0.14 6.80 0.49 4.54 0.10 7.35 0.36 sapiens done FLC0562 PRO2841 mRNA, complete cds. /PROD=PRO 2841 /FL=gb:AF1 3 0095.1 H92988 tyrosine 3- C9orfI9 2.00 0.06 3.54 0.91 1.93 0.14 4.61 0.81 monooxygen asetryptopha n 5 monooxygen ase activation protein, eta polypeptide X02761 Human FN1 5.67 0.17 6.65 0.54 4.52 0.21 7.21 0.42 mRNA for fibronectin (FN precursor). /PROD=fibro nectin precursor A1016316 ESTs - 0.24 0.18 1.19 1.17 -0.33 0.18 0.25 1.18 NM_006622 Homo PLK2 4.64 0.14 5.88 0.45 3.50 0.06 5.19 0.47 sapiens serum 153 inducible kinase (SNK), mRNA. /PROD=seru m-inducible kinase /FL=gb:AF05 9617.1 gb:NM_0066 22.1 gb:AF22357 4.1 NM_013238 Homo DNAJC15 -2.27 0.60 3.79 2.03 4.07 0.09 5.58 2.31 sapiens DNAJ domain containing (MCJ), mRNA. /PROD=DNA J domain containing /FL=gb:NM_ 013238.1 gb:AF12674 3.1 AK026737 Homo FN1 5.86 0.14 6.85 0.49 4.66 0.08 7.39 0.37 sapiens cDNA: FLJ23084 fis, clone LNG06602, highly similar to HSFIB1 Human mRNA for fibronectin (FN precursor). NM_001458 Homo FLNC 3.28 0.17 4.17 0.70 2.11 0.17 3.39 0.64 sapiens filamin C, gamma (actin binding protein-280) (FLNC), 154 mRNA. /PROD=gam ma filamin /FL=gb:AF08 9841.1 gb:NM_0014 58.1 AK025843 Homo PALLD 1.58 0.31 3.38 0.15 1.03 0.20 3.29 0.19 sapiens cDNA: FLJ22190 fis, clone HRC01053. /FL=gb:AF15 1909.1 gb:AF07704 1.1 gb:NM_0160 81.1 BC005858 Homo FNI 5.86 0.10 6.86 0.49 4.70 0.19 7.37 0.36 sapiens, clone MGC:3255, mRNA, complete cds. /PROD=Unk known (protein for MGC:3255) /FL=gb:BCOO 5858.1 BG491844 v-jun avian JUN 3.53 0.08 5.45 0.47 3.42 0.11 5.91 0.34 sarcoma virus 17 oncogene homolog /FL=gb:NM_ 002228.2 gb:BC00264 6.1 AA284532 tyrosine 3- C9orf19 2.19 0.11 4.12 0.84 2.43 0.08 4.93 0.90 monooxygen asetryptopha n 5 monooxygen ase activation 155 protein, eta polypeptide AA192306 triadin TRDN -2.54 0.69 0.02 0.61 -1.99 0.31 0.57 0.63 IFL=gb:U189 85.1 gb:NM_0060 73.1 AF116676 Homo - 1.50 0.18 3.31 1.11 1.37 0.15 4.23 1.05 sapiens PRO1957 mRNA, complete cds. /PROD=PRO 1957 /FL=gb:AF11 6676.1 NM_003033 Homo ST3GAL1 -0.08 0.18 1.68 1.04 0.20 0.16 2.74 0.74 sapiens sialyltransfer ase 4A (beta galactosidas e alpha-2,3 sialytransfer ase) (SIAT4A), mRNA. /PROD=sialy Itransferase 4A (beta galactosidas ealpha-2,3 sialytransfer ase) /FL=gb:L139 72.1 gb:L29555.1 gb:NM_0030 33.1 A1222435 ESTs - -4.14 1.52 -0.73 0.32 -2.33 0.62 -0.33 0.12 NM_001924 Homo GADD45A 3.59 0.09 5.04 0.44 3.06 0.17 5.38 0.48 sapiens growth arrest and DNA damage inducible, alpha 156 (GADD45A), mRNA. /PROD=grow th arrest and

DNA

damage inducible, alpha /FL=gb:M609 74.1 gb:NM_0019 24.2 NM_001425 Homo EMP3 2.76 0.18 3.90 0.64 1.51 0.06 3.13 0.57 sapiens epithelial membrane protein 3 (EMP3), mRNA. /PROD=epith elial membrane protein 3 /FL=gb:U521 01.1 gb:NM_0014 25.1 gb:U87947.1 AB017493 Homo KLF6 1.69 0.20 4.02 1.01 1.80 0.08 4.87 0.87 sapiens mRNA for DNA-binding zinc finger(GBF), complete cds. /PROD=DNA -binding zinc finger(GBF) /FL=gb:AFOO 1461.1 gb:BC00031 1.1 gb:NM_0013 00.2 gb:AB01749 3.1 gb:BC00430 157 1.1 X58851 Human - 0.99 0.16 2.75 1.28 1.12 0.15 4.04 1.14 MLC1emb gene for embryonic myosin alkaline light chain, promoter and exon 1 BE327172 v-jun avian - 0.86 0.15 2.94 0.51 1.14 0.08 3.57 0.45 sarcoma virus 17 oncogene homolog U37283 Human MFAP5 0.48 0.19 1.87 0.26 0.15 0.35 1.36 0.47 microfibril associated glycoprotein 2 MAGP-2 mRNA, complete cds. IPROD=micr ofibril associated glycoprotein 2 MAGP-2 /FL=gb:NM_ 003480.1 gb:U37283.1 A1819043 ESTs CREBS 0.92 0.26 2.63 0.73 0.65 0.15 1.80 0.79 NM_001511 Homo CXCL1 1.01 0.13 2.95 0.35 0.31 0.08 2.39 0.27 sapiens GRO1 oncogene (melanoma growth stimulating activity, alpha) (GRO1), mRNA. /PROD=GR 01 oncogene (melanoma growth 158 stimulatingac tivity, alpha) /FL=gb:NM_ 001511.1 NM_006736 Homo DNAJB2 2.23 0.04 3.46 0.44 1.10 0.02 3.75 0.41 sapiens heat shock protein, neuronal DNAJ-ike 1 (HSJ1), mRNA. /PROD=heat shock protein, neuronal DNAJ-ike 1 /FL=gb:NM_ 006736.1 AA534817 ESTs, EDG3 2.32 0.06 3.28 1.04 2.08 0.04 4.58 1.04 Weakly similar to ALU8_HUM AN ALU SUBFAMILY Sx SEQUENCE CONTAMIN ATION WARNING ENTRY (H.sapiens) U82164 Human CD99 4.73 0.15 5.69 0.73 3.19 0.07 6.36 0.93 transmembra ne protein CD99 type il mRNA, complete cds. /PROD=CD9 9 typell /FL=gb:BC00 2584.1 gb:NM_0024 14.1 gb:M16279.1 gb:BC00314 7.1 159 gb:U82164.1 NM_000389 Homo CDKN1A 4.03 0.02 4.20 0.12 1.81 0.07 4.16 0.05 sapiens cyclin dependent kinase inhibitor 1A (p21, Cip1) (CDKNIA), mRNA. /PROD=cycli n-dependent kinase inhibitor 1A (p21,Cip1) /FL=gb:U031 06.1 gb:BC00027 5.1 gb:BC00193 5.1 gb:L25610.1 gb:U09579.1 gb:NM_0003 89.1 gb:L26165.1 NM_001299 Homo CNN1 3.75 0.15 5.75 0.50 3.47 0.11 5.14 0.43 sapiens calponin 1, basic, smooth muscle (CNN1), mRNA. /PROD=calp onin 1, basic, smooth muscle /FL=gb:U370 19.1 gb:NM_0012 99.1 gb:D17408.1 M36172 Human MYL4 1.55 0.21 3.30 1.05 1.21 0.13 4.11 1.06 embryonic myosin alkali light chain (MLCI) 160 mRNA, complete cds. /FL=gb:M361 72.1 gb:M24121.1 gb:NM_0024 76.1 AB033831 Homo PDGFC 0.48 0.21 0.63 0.15 -1.87 0.96 0.21 0.16 sapiens hSCDGF mRNA for spinal cord derived growth factor, complete cds. /PROD=spin al cord derived growth factor /FL=gb:NM_ 016205.1 gb:AB03383 1.1 gb:AF09143 4.1 gb:AF24481 3.1 NM_014333 Homo IGSF4 3.11 0.09 4.12 0.27 1.85 0.06 3.79 0.24 sapiens immunoglob ulin superfamily, member 4 (IGSF4), mRNA. /PROD=imm unoglobulin superfamily, member 4 /FL=gb:NM_ 014333.1 gb:AF13281 1.1 AF345910 Homo TTC29 0.35 0.26 1.53 0.93 -0.51 0.52 0.91 0.72 sapiens 161 NYD-SP14 mRNA, complete cds. /PROD=NYD -SP14 /FL=gb:AF34 5910.1 NM_004297 Homo GNA14 4.59 0.06 4.52 1.59 1.95 0.11 2.95 1.50 sapiens guanine nucleotide binding protein (G protein), alpha 14 (GNA14), mRNA. /PROD=gua nine nucleotide binding protein (G protein),alph a 14 /FL=gb:AF10 5201.1 gb:NM_0042 97.1 AK057525 Homo - 3.60 0.08 4.45 0.44 2.00 0.16 4.80 0.46 sapiens cDNA FLJ32963 fis, clone TEST120084 05. BC000893 Homo HIST1H2BK 2.80 0.06 3.99 0.90 2.48 0.09 4.81 0.82 sapiens, H2B histone family, member A, clone MGC:5132, mRNA, complete cds. /PROD=H2B histone 162 family, member A /FL=gb:BCOO 0893.1 NM_007038 Homo ADAMTS5 0.23 0.17 1.80 0.48 0.45 0.28 1.11 0.73 sapiens a disintegrin like and metalloprote ase (reprolysin type) with thrombospon din type 1 motif, 5 (aggrecanas e-2) (ADAMTS5), mRNA. /PROD=a disintegrin and metalloprote ase withthrombo spondin motifs-5 preproprotei n /FL=gb:NM_ 007038.1 gb:AF14209 AW241910 ESTs, COL22A1 -0.21 0.12 1.15 0.47 -0.57 0.18 1.90 0.51 Weakly similar to JX0369 collagen alpha 1(XIX) chain precursor (H.sapiens) A1860150 ESTs, FOSL2 -0.43 0.55 1.59 0.37 -0.34 0.10 1.08 0.20 Weakly similar to A49134 Ig kappa chain V-1 region (H.sapiens) 163 NM_005902 Homo SMAD3 1.09 0.41 1.49 0.25 -1.10 0.89 1.73 0.10 sapiens MAD (mothers against decapentapl egic, Drosophila) homolog 3 (MADH3), mRNA. /PROD=MA D (mothers against decapentap egic,Drosoph Ia) homolog 3 /FL=gb:U680 19.1 gb:U76622.1 gb:NM_0059 02.1 AA777512 Homo CAMK2D 2.27 0.15 3.67 0.47 1.67 0.08 3.99 0.51 sapiens cDNA FLJ21715 fis, clone COL10287, highly similar to AF071569 Homo sapiens multifunction al calciumcalm odulin dependent protein kinase 11 delta2 isoform mRNA A1130705 ESTs, FAM89A 0.80 0.00 1.96 0.99 0.43 0.18 2.70 0.97 Weakly similar to A46302

PTB

164 associated splicing factor, long form (H.sapiens) NM_007061 Homo CDC42EP1 1.86 0.11 2.51 0.29 0.16 0.27 2.00 0.17 sapiens serum constituent protein (MSE55), mRNA. /PROD=seru m constituent protein /FL=gb:M883 38.1 gb:NM_0070 61.1 NM_003407 Homo ZFP36 2.55 0.14 3.53 0.55 1.49 0.28 3.98 0.47 sapiens zinc finger protein homologous to Zfp-36 in mouse (ZFP36), mRNA. /PROD=zinc finger protein homologous to Zfp-36 inmouse /FL=gb:NM_ 003407.1 gb:M92843.1 gb:M63625.1 BC033088 Homo LMNA 2.03 0.22 2.89 0.45 0.69 0.24 1.79 0.50 sapiens, Similar to lamin AC, clone MGC:45654 IMAGE:3623 265, mRNA, complete cds. /PROD=Simil 165 ar to lamin AC /FL=gb:BC03 3088.1 U97075 Homo CFLAR 2.50 0.09 3.39 1.45 0.73 0.08 4.93 1.54 sapiens FLICE-like inhibitory protein short form mRNA, complete cds. /PROD=FLIC E-like inhibitory protein short form /FL=gb:U970 75.1 AF133207 Homo HSPB8 2.54 0.07 4.47 0.62 2.22 0.04 4.88 0.58 sapiens protein kinase (H1 1) mRNA, complete cds. /PROD=prot ein kinase /FL=gb:AF13 3207.1 NM_005979 Homo S100A13 4.10 0.11 5.67 1.17 3.92 0.02 6.81 1.20 sapiens S100 calcium binding protein A13 (S1OOA13), mRNA. IPROD=S1O 0 calcium binding protein Al 3 /FL=gb:BCOO 0632.1 gb:NM_0059 79.1 AL040178 ESTs PEAR1 -0.87 0.08 0.51 0.36 -1.16 0.30 0.48 0.26 AL117523 Homo SAMD4A 0.47 0.06 1.59 0.61 -0.24 0.30 1.28 0.53 166 sapiens mRNA; cDNA DKFZp434H 0350 (from clone DKFZp434H 0350); partial cds. /PROD=hypo thetical protein AB051826 Homo RHOU 0.55 0.23 2.18 0.61 0.17 0.29 2.73 0.65 sapiens hG28K mRNA for GTP-binding protein like 1, complete cds. /PROD=GTP -binding protein like I /FL=gb:AF28 2258.1 gb:NM_0212 05.1 gb:AB05182 6.1 BC005961 Homo PTHLH -3.33 0.69 -0.88 0.81 -2.86 0.77 -1.97 1.36 sapiens, parathyroid hormone-like hormone, done MGC:14611, mRNA, complete cds. /PROD=para thyroid hormone-like hormone /FL=gb:BCOO 5961.1 A1670948 ESTs NODAL 2.13 0.04 2.37 0.22 0.42 0.13 2.78 0.38 A1685060 caldesmon 1 CALDI 4.34 0.33 6.42 0.73 4.45 0.09 5.63 0.82 /FL=gb:M641 167 10.1 gb:NM_0043 42.2 BF797381 Homo CAMK2D 3.16 0.13 4.91 0.65 3.10 0.10 5.49 0.61 sapiens cDNA: FLJ21715 fis, clone COL10287, highly similar to AF071569 Homo sapiens multifunction al calciumcalm odulin dependent protein kinase I delta2 isoform mRNA AF026219 Homo DLC1 1.16 0.07 2.28 1.13 0.61 0.09 3.52 0.84 sapiens HP protein (HP) mRNA, complete cds. /PROD=HP protein /FL=gb:AF02 6219.1 gb:AF03511 9.1 gb:NM_0060 94.2 AK024480 Homo LOC126917 1.64 0.11 2.86 0.24 1.19 0.06 2.58 0.25 sapiens mRNA for FLJ00074 protein, partial cds. /PROD=FLJ 00074 protein N29837 ESTs LIX1 -1.43 0.15 -0.11 0.33 -1.50 0.45 -0.22 0.22 AK001022 Homo 1SL2 0.41 0.34 2.14 0.39 0.32 0.08 1.57 0.49 168 sapiens cDNA FLJ10160 fis, clone HEMBA1003 545, highly similar to INSULIN GENE ENHANCER PROTEIN ISL-2. NM_000047 Homo ARSE 1.37 0.11 2.45 1.03 0.59 0.05 3.18 1.23 sapiens arylsulfatase E (chondrodys plasia punctata 1) (ARSE), mRNA. /PROD=aryls ulfatase E precursor /FL=gb:X835 73.1 gb:NM_0000 47.1 NM_006379 Homo SEMA3C 0.24 0.25 1.08 0.00 -0.34 0.05 0.86 0.18 sapiens sema domain, immunoglob ulin domain (Ig), short basic domain, secreted, (semaphorin) 3C (SEMA3C), mRNA. /PROD=sem a domain, immunoglob ulin domain (Ig), shortbasic 169 domain, secreted, (semaphorin) 3C /FL=gb:NM_ 006379.1 gb:AB00022 0.1 NM_007127 Homo VIL1 031 0.30 1.92 0.49 0.02 0.22 2.54 0.68 sapiens villin 1 (VIL1), mRNA. /PROD=villin 1 /FL=gb:NM_ 007127.1 U76549 Human KRT8 5.41 0.16 5.87 0.56 3.79 0.05 6.34 0.57 cytokeratin 8 mRNA, complete cds. /PROD=cyto keratin 8 /FL=gb:BC00 0654.1 gb:U76549.1 gb:NM_0022 73.1 gb:M26324.1 gb:M34225.1 NM_004904 Homo CREB5 0.92 0.23 1.84 0.37 0.00 0.06 1.21 0.80 sapiens cAMP response element binding protein CRE BPa (H_GS165LI 5.1), mRNA. /PROD=cAM P response element binding protein CRE BPa /FL=gb:NM_ 004904.1 170 gb:L05911.1 AW082836 ESTs, WNK4 -1.17 0.26 0.98 0.38 -0.97 0.20 0.05 0.86 Weakly similar to B34087 hypothetical protein (H.sapiens) BE568134 death TNFRSF21 4.76 0.06 5.90 0.54 3.94 0.08 6.28 0.58 receptor 6 /FL=gb:NM_ 014452.1 gb:AF06886 8.1 NM_002845 Homo PTPRM 2.50 0.10 3.43 0.46 1.34 0.19 3.76 0.50 sapiens protein tyrosine phosphatase , receptor type, M (PTPRM), mRNA. /PROD=prot ein tyrosine phosphatase , receptor type, mupolypepti de /FL=gb:NM_ 002845.1 A1949419 ESTs - -0.11 0.21 1.72 0.64 -0.47 0.01 2.39 0.77 AK024680 Homo NRP2 0.42 0.02 2.65 0.17 0.98 0.09 2.86 0.17 sapiens cDNA: FLJ21027 fis, clone CAE071 10. /FL=gb:NM_ 018534.1 BE542563 ESTs LOC643277 2.20 0.10 0.54 1.49 -3.73 0.40 -1.74 1.96 AW005572 putative 47 ANKS1B -1.21 0.52 -0.24 0.82 -1.19 0.55 1.05 0.64 kDa protein AW665892 paternally MFAP5 -3.87 0.82 -1.56 1.24 -2.40 0.24 -3.49 2.10 expressed 3 NM_006206 Homo PDGFRA 0.92 0.18 2.34 0.74 0.72 0.09 3.18 0.62 sapiens 171 platelet derived growth factor receptor, alpha polypeptide (PDGFRA), mRNA. /PROD=plate let-derived growth factor receptor, alphapolype ptide /FL=gb:NM_ 006206.1 gb:M21574.1 NM_002425 Homo MMPIO -1.21 0.70 1.21 0.88 -0.37 0.28 0.52 0.45 sapiens matrix metalloprotei nase 10 (stromelysin 2) (MMP10), mRNA. /PROD=matr ix metalloprote nase 10 preproprotei n /FL=gb:BCOO 2591.1 gb:NM_0024 25.1 NM_004338 Homo C18orfl -0.79 0.22 -0.09 0.39 -1.57 0.43 0.50 002 sapiens chromosome 18 open reading frame 1 (CI80RF1), mRNA. /PROD=chro mosome 18 open reading frame 1 /FL=gb:NM_ 172 004338.1 gb:AF00942 6.1 AF052094 Homo EPASI 0.75 0.12 2.28 0.19 0.42 0.21 1.74 033 sapiens done 23698 mRNA sequence. /FL=gb:U516 26.1 gb:U81984.1 gb:NM_0014 30.1 BF126155 ESTs S10OA10 -0.32 0.25 1.24 0.28 -0.65 0.33 1.02 0.44 A1860212 phosphoprot PAGI -0.17 0.22 1.37 0.28 -0.40 0.23 1.25 0.13 ein associated with GEMs /FL=gb:AF24 0634.1 gb:NM_0184 40.1 AL110298 Homo SLC2A14 5.13 0.06 6.03 0.58 3.97 0.24 6.33 0.73 sapiens mRNA; cDNA DKFZp564K 1672 (from done DKFZp564K 1672); partial cds. /PROD=hypo thetical protein AY048775 Homo MANEA -0.47 0.40 0.71 0.90 -0.69 0.35 1.23 0.81 sapiens mandaselin long form mRNA, complete cds. /PROD=man daselin long form /FL=gb:AY04 8775.1 M99436 Cluster ind. TLE2 2.65 0.07 4.05 0.66 1.95 0.13 4.76 0.61 173 M99436:Hu man transducin like enhancer protein (TLE2) mRNA, complete cds /cds=(25,225 6) /gb=M99436 /gi=307511 /ug=Hs.1730 63 /len=2271 NM_014061 Homo MAGEHI 2.04 0.23 3.84 1.17 1.08 0.24 4.86 1.12 sapiens APR-1 protein (APR-1), mRNA. /PROD=APR -1 protein /FL=gb:AF32 0912.1 gb:AF14323 5.3 gb:NM_0140 61.1 AL577531 caldesmon I CALD1 5.79 0.06 6.06 0.75 4.07 0.06 5.13 0.77 /FL=gb:M641 10.1 gb:NM_0043 42.2 A1082237 proprotein TAGLN 1.38 0.21 3.20 0.33 1.55 0.15 2.74 0.44 convertase subtilisinkexi n type 7 BF055171 acyl- ACOX3 0.88 0.22 2.52 0.83 1.27 0.06 3.73 0.81 Coenzyme A oxidase 3, pristanoyl /FL=gb:NM_ 003501.1 AF231124 Homo SPOCKI 2.84 0.09 4.17 0.95 2.71 0.07 5.38 1.00 sapiens testican-1 mRNA, 174 complete cds. /PROD=test can-1 /FL=gb:NM_ 004598.1 gb:AF23112 4.1 AA588092 ESTs SLC40A1 -1.53 0.23 -0.94 0.51 -2.42 0.33 0.27 0.27 AK094809 Homo RASGRF2 3.20 0.05 3.64 0.77 1.95 0.24 2.95 0.74 sapiens cDNA FLJ37490 fis, clone BRAWH201 4934, highly similar to GUANINE NUCLEOTID E RELEASING PROTEIN. NM_013959 Homo NRG1 1.50 0.20 3.22 0.68 1.34 0.13 3.78 0.75 sapiens neuregulin I (NRG1), transcript variant SMDF, mRNA. IPROD=neur egulin I isoform SMDF IFL=gb:L418 27.1 gb:NM_0139 59.1 NM_004887 Homo CXCL14 0.70 0.07 1.70 0.37 -0.15 0.11 2.36 0.63 sapiens small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK) (SCYB14), 175 mRNA. /PROD=smal I inducible cytokine subfamily B(Cys-X Cys), member 14 (BRAK) /FL=gb:AF14 4103.1 gb:AF10691 1.1 gb:AF07395 7.1 gb:BC00351 3.1 gb:NM_0048 87.1 T77995 Homo - -0.20 0.16 0.82 0.50 -1.70 0.24 1.17 0.06 sapiens cDNA FLJ13392 fis, clone PLACE1001 280 NM_030971 Homo SFXN3 -0.43 0.59 -0.01 0.78 -1.92 0.17 -1.25 0.43 sapiens similar to rat tricarboxylat e carrier-like protein (BA108L7.2), mRNA. /PROD=simil ar to rat tricarboxylat e carrier likeprotein /FL=gb:NM_ 030971.1 H25097 KIAA1350 USP53 3.25 0.05 4.57 0.20 2.96 0.04 4.47 0.13 protein NM_004932 Homo CDH6 -3.58 1.16 -1.12 0.51 -2.14 0.63 -0.88 0.39 sapiens cadherin 6, type 2, K cadherin 176 (fetal kidney) (CDH6), mRNA. /PROD=cadh erin 6, type 2, K cadherin (fetal kidney) /FL=gb:D317 84.1 gb:NM_0049 32.1 N21426 hypothetical SYTL2 2.41 0.09 3.44 1.22 1.70 0.06 2.02 1.21 protein FLJ20163 AA234096 KIAA0963 MGC16121 0.38 0.16 1.74 0.63 -0.13 0.04 1.10 0.65 protein AV734843 hypothetical OBFC2A 0.62 0.06 1.62 0.79 0.09 0.02 1.25 0.73 protein FLJ22833 AL519710 immunoglob IGSF4 3.86 0.02 4.95 0.26 3.22 0.12 4.66 0.27 ulin superfamily, member 4 /FL=gb:NM_ 014333.1 gb:AF13281 1.1 N32834 HIV-1 rev - -0.28 0.36 1.58 0.97 -0.23 0.18 0.33 1.17 binding protein 2 AF132811 Homo IGSF4 2.23 0.07 3.85 0.28 2.17 0.10 3.58 0.34 sapiens nectin-like protein 2 (NECL2) mRNA, complete cds. /PROD=nect n-like protein 2 /FL=gb:NM_ 014333.1 gb:AF13281 1.1 J04177 Clusterincl. COL11AI 3.28 0.22 4.44 1.22 2.32 0.03 3.03 1.31 J04177:Hum 177 an alpha-i type x collagen (COL1 A1) mRNA, complete cds /cds=(161,55 81) /gb=J04177 /gi=l 79729 /ug=Hs.8277 2 /len=6158 A1982754 clusterin CLU 0.17 0.14 1.86 0.94 0.39 0.13 0.97 0.83 (complement lysis inhibitor, SP 40,40, sulfated glycoprotein 2, testosterone repressed prostate message 2, apolipoprotei n J) NM_003501 Homo ACOX3 0.43 0.32 2.10 0.91 0.79 0.08 3.19 0.95 sapiens acyl Coenzyme A oxidase 3, pristanoyl (ACOX3), mRNA. /PROD=acyl Coenzyme A oxidase 3, pristanoyl /FL=gb:NM_ 003501.1 AF144103 Homo CXCL14 1.69 0.13 2.16 0.55 0.40 0.21 2.73 0.69 sapiens NJAC protein (NJAC) mRNA, complete cds. /PROD=NJA 178 C protein /FL=gb:AF14 4103.1 gb:AF10691 1.1 gb:AF07395 7.1 gb:BC00351 3.1 gb:NM_0048 87.1 NM_005451 Homo PDLIM7 2.58 0.12 3.12 0.50 1.30 0.16 2.65 0.37 sapiens enigma (LIM domain protein) (ENIGMA), mRNA. /PROD=enig ma protein /FL=gb:BCOO 1093.1 gb:NM_0054 51.2 gb:AF26520 9.1 NM_004472 Homo FOXD1 -0.85 0.80 2.04 0.55 0.71 0.23 1.70 0.74 sapiens forkhead box D1 (FOXD1), mRNA. /PROD=fork head box DI /FL=gb:U598 32.1 gb:NM_0044 72.1 AF332197 Homo SIX2 0.36 0.24 0.72 0.12 -0.44 0.35 1.05 0.15 sapiens adult SIX2 (SIX2) mRNA, complete cds. /PROD=SIX2 /FL=gb:AF33 2197.1 gb:NM_0169 32.1 179 gb:AF13694 0.1 AB046817 Homo SYTL2 2.88 0.17 4.09 1.09 2.50 0.05 3.12 1.03 sapiens mRNA for KIAA1597 protein, partial cds. /PROD=KIA Al 597 protein AK093435 Homo FU36116 4.75 0.02 4.59 1.53 2.46 0.18 6.15 1.46 sapiens cDNA FLJ36116 fis, clone TEST120223 38. NM_004815 Homo ARHGAP29 2.18 0.02 3.18 0.82 1.69 0.03 4.15 0.69 sapiens PTPL1 associated RhoGAP 1 (PARG), mRNA. IPROD=PTP L1 associated RhoGAP 1 /FL=gb:U909 20.1 gb:NM_0048 15.1 BG028597 ESTs COL11A1 0.19 0.02 1.61 1.02 -0.11 0.38 0.48 1.09 AB019562 Homo SPP1 0.58 0.14 2.79 1.07 1.10 0.02 1.21 1.06 sapiens mRNA expressed only in placental villi, clone SMAP41. NM_002346 Homo LY6E 3.54 0.06 3.92 1.16 1.81 0.23 4.93 1.39 sapiens lymphocyte antigen 6 complex, locus E 180 (LY6E), mRNA. /PROD=Iymp hocyte antigen 6 complex, locus E IFL=gb:U423 76.1 gb:NM_0023 46.1 gb:U56145.1 BF589515 ESTs TMEM16D 0.63 0.24 1.94 0.85 0.90 0.20 1.47 0.75 AL037401 nuclear NR2F2 -2.00 0.30 0.58 0.67 -2.19 0.13 0.82 0.66 receptor subfamily 2, group F, member 2 /FL=gb:M644 97.1 NM_000783 Homo CYP26AI 3.92 0.27 6.28 1.06 6.29 0.09 7.31 0.98 sapiens cytochrome P450, subfamily XXVIA, polypeptide 1 (CYP26AI), mRNA. /PROD=cyto chrome P450, subfamily XXVIA, polypeptide I /FL=gb:NM_ 000783.1 gb:AF00541 8.1 U16307 Human GLIPRI -0.11 0.03 1.16 0.95 -0.46 0.77 0.35 0.77 glioma pathogenesis s-related protein (GliPR) mRNA, 181 complete cds. /PROD=glio ma pathogenesis s-related protein /FL=gb:NM_ 006851.1 gb:U16307.1 NM_001233 Homo CAV2 4.07 0.07 4.42 0.90 2.82 0,08 3.44 0.85 sapiens caveolin 2 (CAV2), mRNA. /PROD=cave olin 2 /FL=gb:AF03 5752.1 gb:BC00525 6.1 gb:NM_0012 33.1 AA211909 ESTs C200rf100 0.62 0.17 1.93 1.00 -0.21 0.11 0.72 0.99 AK057525 Homo - 2.17 0.13 2.97 0.77 0.97 0.08 3.68 0.60 sapiens cDNA FU32963 fis, clone TEST120084 05. BF344237 Homo - -2.82 0.20 -0.92 0.64 -0.73 0.67 -1.25 1.03 sapiens mRNA; cDNA DKFZp564N 1116 (from clone DKFZp564N 1116) NM_014481 Homo APEX2 2.76 0.15 3.18 0.80 1.57 0.11 3.91 0.93 sapien, apurinicapyri midinic endonucleas e(APEX nuclease) like 2 protein 182 (APEXL2), mRNA. /PROD=apur inicapyrimidi nic endonucleas e(APEXnucI ease)-like 2 protein /FL=gb:AB04 9211.1 gb:NM_0144 81.1 gb:BC00295 9.1 gb:AB02126 0.1 gb:AF1 1904 6.1 A1912583 HIV-1 rev KRR1 1.10 0.23 2.68 1.04 1.31 0.06 1.53 1.01 binding protein 2 B1254089 Homo ADAMTS5 -1.40 0.26 -0.01 0.31 -1.71 0.64 -0.79 0.52 sapiens full length insert cDNA clone ZD50E03 BF197655 caveolin 2 CAV2 3.51 0.10 3.54 0.94 2.32 0.09 2.70 0.85 /FL=gb:AF03 5752.1 gb:BC00525 6.1 gb:NM_0012 33.1 NM_001955 Homo EDN1 2.84 0.15 2.97 0.95 1.01 0.14 1.75 1.03 sapiens endothelin I (EDN1), mRNA. /PROD=end othelin 1 /FL=gb:NM_ 001955.1 NM_003319 Homo TTN 1.28 0.19 0.62 0.86 -0.92 0.42 2.00 0.55 sapiens titin (TTN), mRNA. /PROD=titin 183 /FL=gb:NM_ 003319.1 BE965029 Homo MICAL2 0.60 0.21 1.95 0.64 0.21 0.19 0.83 0.78 sapiens cDNA: FLJ22463 fis, clone HRC10126 A1452457 ESTs Clorf168 -1.48 0.53 0.02 0.93 -1.87 0.07 1.05 0.94 A1733465 collagen, COL9A2 0.96 0.13 1.99 1.00 1.17 0.14 2.94 0.86 type IX, alpha2 /FL=gb:NM_ 001852.1 NM_006103 Homo WFDC2 4.02 0.11 5.11 1.05 3.39 0.04 6.19 1.10 sapiens epididymis specific, whey-acidic protein type, four-disulfide core; putative ovarian carcinoma marker (HE4), mRNA. /PROD=epidi dymis specific, whey-acidic protein type,four disulfide core; putative ovarian carcinoma marker /FL=gb:NM_ 00610 NM_017540 Homo GALNTIO 1.46 0.18 2.68 0.78 0.97 0.23 3.47 0.82 sapiens hypothetical protein DKFZp586H 0623 184 (DKFZp586H 0623), mRNA. /PROD=hypo thetical protein DKFZp586H 0623 /FL=gb:NM_ 017540.1 W72527 phosphoseri SLC1A4 -0.65 0.09 0.38 0.80 -0.63 0.62 -0.72 0.09 ne aminotransfe rase NM_003468 Homo FZD5 1.35 0.26 3.43 1.21 1.45 0.10 4.43 1.16 sapiens frizzled (Drosophila) homolog 5 (FZD5), mRNA. /PROD=frizzl ed5 /FL=gb:NM_ 003468.1 gb:U43318.1 H15920 ESTs, MRGPRF 2.34 0.18 3.62 1.02 2.11 0.11 2.87 0.84 Weakly similar to RTA RAT PROBABLE G PROTEIN COUPLED RECEPTOR RTA (R.norvegicu s) U83508 Human ANGPT1 1.06 0.11 1.49 0.44 -0.32 0.27 0.32 0.79 angiopoletin 1 mRNA, complete cds. /PROD=angi opoletin-1 /FL=gb:NM_ 001146.1 gb:D13628.1 gb:U83508.1 185 AF043179 Homo PRSS1 2.42 0.12 3.07 0.81 1.71 0.10 2.30 0.60 sapiens T cell receptor beta chain (TCRBV13S 1 TCRBJ2SI) mRNA, complete cds. /PROD=T cell receptor beta chain /FL=gb:AF04 3179.1 AU157541 hypothetical - 1.39 0.08 2.12 0.42 0.55 0.18 1.41 0.77 protein FLJ22833 /FL=gb:NM_ 022837.1 AF114264 Homo NEXN 1.37 0.21 2.86 0.51 1.72 0.16 1.96 0.76 sapiens clone HH409 unknown mRNA. /PROD=unkn own BE965029 Homo MICAL2 1.58 0.19 2.58 0.51 1.32 0.13 1.40 0.74 sapiens cDNA FLJ22463 fis, clone HRC10126 AB028976 Homo SAMD4A 2.89 0.08 3.65 0.66 2.04 0.17 2.78 0.81 sapiens mRNA for KIAA1053 protein, partial cds. /PROD=KIA A1053 protein A1670862 ESTs, FOSL2 0.17 0.21 2.05 0.57 0.45 0.16 1.18 0.65 Weakly similar to A49134 Ig kappa chain V-1 region 186 (H.sapiens) L03203 Human PMP22 0.37 0.24 1.95 0.84 0.31 0.26 2.77 0.91 peripheral myelin protein 22 (GAS3) mRNA, complete cds. /PROD=peri pheral myelin protein 22 /FL=gb:L032 03.1 A1571798 Rho GDP ARHGDIA 0.89 0.06 -0.54 0.26 -3.00 0.89 -2.58 0.87 dissociation inhibitor (GDI) alpha X57348 Cluster Incl. - 2.94 0.04 4.07 0.41 2.70 0.08 3.69 0.41 X57348:H.sa piens mRNA (clone 9112) /cds=(165,91 1) /gb=X57348 /gi=23939 /ug=Hs.1845 10 /len=1407 AF051851 Homo SVIL 2.03 0.18 2.28 0.62 1.13 0.20 1.71 0.69 sapiens supervillin mRNA, complete cds. /PROD=supe rvillin /FL=gb:AF05 1851.1 gb:NM_0031 74.2 gb:AF05185 0.1 M95929 Human - 0.07 0.43 1.27 0.58 -0.02 0.19 0.64 0.61 homeobox protein (PHOXI) mRNA, 3 187 end. /PROD=hom eobox protein BG251266 FOS-like FOSL1 1.94 0.06 2.41 0.46 1.25 0.05 1.93 0.36 antigen-1 /FL=gb:NM_ 005438.1 AW298375 ESTs - -0.40 0.30 0.46 0.63 -0.09 0.20 -0.58 1.07 NM_004362 Homo CLGN 0.90 0.30 1.95 0.96 0.69 0.11 3.11 1.01 sapiens calmegin (CLGN), mRNA. /PROD=calm egin /FL=gb:NM_ 004362.1 gb:D86322.1 AF001540 calcineurin- - 0.10 0.15 2.84 0.70 0.42 0.44 1.64 0.39 binding protein calsarcin-1 NM_001191 Homo BCL2L1 1.21 0.22 0.58 0.35 -1.89 0.35 -1.09 1.03 sapiens BCL2-like 1 (BCL2L1), mRNA. /PROD=BCL 2-like 1 /FL=gb:NM_ 001191.1 NM_003316 Homo TTC3 3.90 0.15 5.15 0.98 3.68 0.12 6.19 0.97 sapiens tetratricopept ide repeat domain 3 (TTC3), mRNA. /PROD=tetra tricopeptide repeat domain 3 /FL=gb:D842 95.1 gb:NM_0033 16.1 L16895 Human lysyl - -0.66 0.24 0.53 0.14 -0.63 0.15 0.14 0.19 188 oxidase (LOX) gene, exon 7 A1912976 ESTs RASGRF2 3.13 0.08 4.05 0.56 2.66 0.16 3.54 0.64 NM_012242 Homo DKKI 0.47 0.29 0.73 0.04 0.49 0.51 1.09 0.23 sapiens dickkopf (Xenopus laevis) homolog 1 (DKK1), mRNA. /PROD=dick kopf (Xenopus laevis) homolog 1 /FL=gb:AF17 7394.1 gb:NM_0122 42.1 gb:AF12756 3.1 AL096776 Human DNA - 1.94 0.07 3.41 0.16 2.40 0.07 3.40 0.14 sequence from clone RP4-646112 on chromosome 1q42.1 1 42.3. Contains an FTH1 (ferritin, heavy polypeptide 1) (FTHL6) pseudogene, the gene for a novel Ras family protein, ESTs, STSs, GSSs and a putative CpG island /FL=gb:AF28 2258.1 189 gb:NM_0212 BC005997 Homo - 1.12 0.25 0.95 0.44 2.04 0.07 1.51 0.22 sapiens, done MGC:14801, mRNA, complete cds. /PROD=Unk known (protein for MGC:14801) /FL=gb:BCOO 5997.1 AF074979 Homo RGS20 -0.52 0.18 -0.04 0.38 -1.30 0.09 -0.34 0.13 sapiens regulator of G protein signaling-Z (RGSZ1) mRNA, complete cds. /PROD=regu lator of G protein signaling /FL=gb:AF06 0877.2 gb:AF07497 9.1 gb:NM_0037 02.2 BF060767 ESTs ADAMTS5 -0.36 0.15 0.80 0.33 0.22 0.14 0.40 0.56 AU151151 Homo LEPR 1.72 0.18 2.38 0.80 1.85 0.10 1.71 0.69 sapiens cDNA FLJ13536 fis, clone PLACE1006 521 L27624 Homo TFP12 3.77 0.06 3.57 0.77 2.59 0.11 2.44 0.89 sapiens tissue factor pathway inhibitor-2 mRNA, complete 190 cds. /PROD-tissu e factor pathway inhibitor-2 /FL=gb:D299 92.1 gb:L27624.1 gb:NM_0065 28.1 gb:BC00533 0.1 NM_003174 Homo SVIL 3.15 0.09 3.68 0.44 2.91 0.01 3.27 0.46 sapiens supervillin (SVIL), transcript variant 1, mRNA. /PROD=supe rvillin, isoform 1 /FL=gb:AFO5 1851.1 gb:NM_0031 74.2 gb:AF05185 0.1 AF052127 Homo RELN -3.13 1.04 -1.36 0.26 -0.88 0.17 -0.40 0.11 sapiens clone 23850 mRNA sequence. AL031290 Human DNA - 0.38 0.06 1.39 0.46 0.40 0.05 0.95 0.44 sequence from clone 774124 on chromosome 1 q24.1-24.3 Contains protein similar to pregnancy associated plasma protein A precursor neuronal 191 migration protein astrotactin, ESTs, STS and GSS A1129628 ESTs SAMD3 -0.30 0.18 -0.01 0.25 0.72 0.06 0.17 021 NM_016206 Homo VGLL3 -0.39 0.36 0.05 1.03 -0.31 0.29 -1.05 1.01 sapiens colon carcinoma related protein (LOC51159), mRNA. /PROD=colo n carcinoma related protein /FL=gb:NM_ 016206.1 gb:AF09950 5.1 BE348291 ESTs - 1.62 0.06 -0.19 0.98 -3.65 0.10 -2.75 1.84 AW242720 Homo LOC143381 -1.62 0.34 -1.20 0.94 -0.08 0.24 -0.08 0.77 sapiens cDNA FLJ10561 fis, clone NT2RP2002 672 NM_001146 Homo ANGPT1 1.86 0.06 2.09 0.81 1.10 0.16 0.87 1.05 sapiens angiopoietin 1 (ANGPT1), mRNA. /PROD=angi opoietin 1 /FL=gb:NM_ 001146.1 gb:D13628.1 gb:U83508.1 AU152579 Homo PCSK5 2.41 0.14 2.47 0.86 2.04 0.15 1.11 1.20 sapiens cDNA FLJ13034 fis, clone NT2RP3001 232 192 NM_006200 Homo PCSKS 3.01 0.21 2.88 0.92 2.28 0.11 1.52 1.25 sapiens proprotein convertase subtilisinkexi n type 5 (PCSK5), mRNA. IPROD=prop rotein convertase subtilisinkexi n type 5 /FL=gb:U563 87.2 gb:NM_0062 00.1 BF342661 KIAA0036 MAP2 -0.77 0.30 -0.19 0.44 0.12 0.17 -2.21 1.64 gene product AF063824 Homo TRPC4 -3.03 0.39 0.05 0.49 1.28 0.17 0.21 0.92 sapiens trp related protein 4 truncated variant delta mRNA, complete cds. /PROD=trp related protein 4 truncated variant delta /FL=gb:AF06 3824.1 AA723810 cDNA for LY6K 0.07 0.20 -0.13 1.23 0.15 0.14 -0.38 1.27 differentially expressed C016 gene /FL=gb:BCOO 1291.1 N29877 interleukin - 1.94 0.13 0.51 0.48 0.78 0.64 -1.57 0.65 14 NM_007287 Homo MME 2.59 0.03 1.81 0.40 1.89 0.21 2.14 0.30 sapiens membrane metallo endopeptida 193 se (neutral endopeptida se, enkephalinas e, CALLA, CD1O) (MME), transcript variant Ibis, mRNA. /PROD=me mbrane metallo endopeptida se /FL=gb:NM_ 007288.1 gb:NM_0072 87.1 gb:J03779.1 AB050856 Homo B3GALNT1 1.39 0.05 0.20 0.22 -0.13 0.21 -0.10 0.17 sapiens beta3GaNA cT-1 mRNA for globoside synthase, complete cds, clone:type 2. /PROD=glob oside synthase /FL=gb:AB05 0856.1 A1827455 Homo BCL6B 0.65 0.31 0.62 0.21 1.07 0.24 0.90 0.29 sapiens cDNA FLJ21042 fis, clone CAE11204 AF017987 Homo SFRPI 4.15 0.22 4.37 1.24 6.02 0.06 5.74 1.01 sapiens secreted apoptosis related protein 2 (SARP2) mRNA, 194 complete cds. /PROD=secr eted apoptosis related protein 2 /FL=gb:AF05 6087.1 gb:NM_0030 12.2 gb:AF01798 7.1 gb:AF00190 0.1 AL117451 Homo Clor108 -0.73 0.20 0.68 0.24 1.06 0.05 0.82 0.21 sapiens mRNA; cDNA DKFZp586E 2317 (from clone DKFZp586E 2317). AW268357 ESTs, Highly USP32 0.73 0.20 0.36 0.19 0.70 0.03 0.09 0.18 similar to AF155116 I NY-REN-60 antigen (H.sapiens) BE465243 ESTs ARFGEF1 0.50 0.23 0.16 0.32 1.03 0.08 0.47 0.06 AA993400 ESTs ADAL 0.89 0.22 0.48 0.28 0.83 0.10 0.29 0.43 A1970898 Cluster Incl. ACACB 0.69 0.15 0.51 0.53 1.46 0.11 -0.87 0.83 A[970898:wr 21 c03.x1 Homo sapiens cDNA, 3 end /done=MAG E-2488324 /doneend= 3 /gb=A197089 8 /gi=5767724 /ug=Hs.2348 98 /len=382 195 BG026457 ESTs, KIAA1909 0.60 0.07 0.23 0.59 0.98 0.03 -2.11 1.28 Weakly similar to ALU5_HUM AN ALU SUBFAMILY SC SEQUENCE CONTAMIN ATION WARNING ENTRY (H.sapiens) BC041933 Homo UBE3C 0.83 0.23 0.11 0.51 0.55 0.05 0.41 0.92 sapiens, clone IMAGE:5300 703, mRNA. A1638611 KIAA1373 STAMBPLI 2.20 0.17 1.37 0.58 2.32 0.08 -0.39 1.24 protein A1341686 ESTs, Highly MTRF1 1.36 0.14 0.45 0.48 1.43 0.09 -1.09 0.99 similar to RF1M_HUM AN MITOCHON DRIAL PEPTIDE CHAIN RELEASE FACTOR 1 PRECURSO R (H.sapiens) NM_003182 Homo TACI 1.89 0.20 1.65 0.13 2.46 0.09 1.48 0.26 sapiens tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin alpha, neuropeptide K,neuropepti de gamma) 196 (TAC1), transcript variant beta, mRNA. /PROD=tach ykinin 2 precursor, isoform beta /FL=gb:U3 M80634 Human FGFR2 3.63 0.06 2.25 0.39 2.79 0.19 2.07 0.84 keratinocyte growth factor receptor mRNA, complete cds. /PROD=kera tinocyte growth factor receptor /FL=gb:M806 34.1 gb:NM_0229 69.1 gb:M97193.1 AK021452 Homo ZNF521 -0.20 0.16 -1.15 1.12 1.31 0.05 0.36 0.18 sapiens cDNA FLJ11390 fis, clone HEMBA1000 561, weakly similar to ZINC FINGER PROTEIN 91. AA541622 ESTs SYNPO2 -0.49 0.30 -0.90 0.06 0.35 0.09 -2.58 0.93 N50714 ESTs - -1.13 0.13 -1.34 0.52 0.10 0.12 -0.21 0.28 NM_002674 Homo PMCH 0.62 0.24 1.10 0.48 1.64 0.03 0.09 0.80 sapiens pro melanin concentratin g hormone (PMCH), mRNA. /PROD=pro melanin 197 concentratin g hormone /FL=gb:NM_ 002674.1 gb:M57703.1 BM666010 Homo LOC200169 1.36 0.16 0.45 0.74 1.49 0.12 -1.65 1.41 sapiens cDNA FLJ23803 fis, clone HEP22811. Al343467 Homo - -0.44 0.08 -1.50 0.82 1.11 0.19 -0.64 0.20 sapiens cDNA FLJ 1041 fis, clone PLACE1004 405 AA046424 ESTs, ACOT4 0.58 0.27 -0.94 0.66 -1.08 0.38 -1.09 0.25 Weakly similar to YZ28_HUMA N HYPOTHET CAL PROTEIN ZAP128 (H.sapiens) R38389 olfactomedin OLFM1 4.27 0.11 3.02 0.76 4.53 0.07 2.17 0.96 related ER localized protein BF724270 ESTs - 2.03 0.22 0.72 0.42 2.36 0.06 0.01 0.97 NM_001819 Homo CHGB 1.40 0.18 0.50 0.75 1.66 0.05 -0.74 1.03 sapiens chromograni n B (secretograni n 1) (CHGB), mRNA. /PROD=chro mogranin B precursor /FL=gb:BCOO 0375.1 gb:NM_0018 19.1 AK026387 Homo - 0.03 0.28 -0.05 0.52 1.23 0.26 0.52 0.67 198 sapiens cDNA' FLJ22734 fis, clone HUVO0109. BF062139 polymerase - 5.23 0.06 4.31 0.74 5.80 0.07 3.37 0.86 (RNA) Ill (DNA directed) (32kD) /FL=gb:NM_ 006467.1 gb:U93868.1 BG540454 ESTs SCGB3A2 4.64 0.02 2.91 0.84 4.13 0.07 1.72 0.83 A1659533 ArgAbl- SORBS2 0.02 0.12 1.12 0.71 2.17 0.05 -1.08 1.48 interacting protein ArgBP2 AA531287 ESTs - 2.94 0.27 1.32 0.72 2.57 0.04 0.22 0.90 NM_013243 Homo SCG3 3.30 0.20 2.13 0.95 3.67 0.19 0.87 1.06 sapiens secretograni n Ill (SCG3), mRNA. /PROD=secr etogranin Ill /FL=gb:AF07 8851.1 gb:NM_0132 43.1 A1307586 Homo ClOorf95 0.34 0.22 -1.15 0.24 -0.49 0.16 -3.61 0.99 sapiens mRNA; cDNA DKFZp566H 0124 (from done DKFZp566H 0124) BC032004 Homo GRIA3 -0.02 0.23 -0.15 0.33 0.47 0.04 0.17 0.07 sapiens, Similar to glutamate receptor, ionotrophic, AMPA 3, clone IMAGE:4753 199 474, mRNA. AW205739 ESTs, TYW3 0.47 0.01 0.81 1.35 3.72 0.18 2.46 1.15 Weakly similar to ORF YGL050w (S.cerevisiae NM_153262 Homo SYT14 -0.01 0.17 -0.84 0.51 0.00 0.18 -3.88 1.64 sapiens hypothetical protein FLJ34198 (FLJ34198), mRNA. /FL=gb:NM_ 153262.1 AA156873 albumin PELO 0.77 0.12 -0.23 0.93 0.65 0.14 -2.33 1.01 BC012375 Homo ARSG -0.46 0.48 -0.78 0.42 0.57 0.22 -0.41 0.55 sapiens, Similar to KIAA1001 protein, clone MGC:8996 IMAGE:3882 163, mRNA, complete cds. /PROD=Simil ar to KIAA1001 protein /FL=gb:AB02 3218.1 gb:NM_0149 60.1 gb:BC01237 5.1 AA843242 ESTs BNC2 2.12 0.37 1.03 0.47 2.89 0.06 0.43 0.80 BF792954 ESTs HDLBP -1.53 1.04 -2.75 0.91 0.30 0.16 -0.72 0.26 AA780067 heparan HS3ST3B1 0.41 0.19 0.30 0.61 2.61 0.18 0.78 0.60 sulfate (glucosamin e) 3-0 sulfotransfer ase 3B1 AA909330 ESTs RPI-32F7.2 0.98 0.17 -1.67 0.51 0.79 0.02 -0.38 0.12 200 AF141339 Homo ZNF521 -0.41 0.12 -0.97 0.93 1.67 0.11 -0.31 0.80 sapiens

LYST

interacting protein LIP3 mRNA, partial cds. /PROD=LYS T-interacting protein LIP3 BF435123 bromodomai - 2.28 0.17 1.31 0.51 2.70 0.12 1.30 1.00 n and PHD finger containing, 3 AK056212 Homo - 1.03 0.14 0.14 0.27 1.10 0.07 -1.41 0.51 sapiens cDNA FU31650 fis, done NT2R120040 79. NM_001446 Homo FABP7 2.07 0.15 0.74 0.29 2.20 0.04 1.08 0.16 sapiens fatty acid binding protein 7, brain (FABP7), mRNA. /PROD=fatty acid binding protein 7, brain /FL=gb:U812 35.1 gb:D88648.1 gb:U51338.1 gb:NM_0014 46.1 gb:D50373.1 AW051591 ESTs, RNF175 1.41 0.32 0.22 0.10 2.60 0.06 0.96 0.20 Moderately similar to unnamed protein product (H.sapiens) BC041970 Homo C9orf122 0.74 0.03 -0.35 0.49 0.76 0.06 -2.31 1.25 sapiens, 201 done IMAGE:5302 687, mRNA. BC013077 Homo 2.51 0.11 0.80 1.15 2.85 0.06 0.08 0.89 sapiens, done IMAGE:3459 334, mRNA AW572379 ESTs - 1.80 0.03 0.60 0.84 1.45 0.07 1.88 0.53 BE644917 nuclear XIST -3.88 1.26 -0.54 1.28 1.94 0.13 -0.20 1.94 receptor subfamily 1, group 1, member 3 NM_171999 Homo SALL3 2.97 0.18 2.04 0.71 3.79 0.08 1.02 0.74 sapiens sal like 3 (Drosophila) (SALL3), mRNA. /PROD=sal like 3 /FL=gb:NM_ 171999.1 A1654224 ESTs - 0.46 0.36 0.14 0.44 1.03 0.07 -0.81 0.85 AA167449 nuclear XIST -3.08 0.10 -0.47 2.59 4.59 0.07 2.80 1.86 receptor subfamily 1, group I, member 3 BF977837 KIAA0527 SUSD5 1.64 0.02 0.50 0.68 1.96 0.16 -1.52 1.66 protein BC029425 Homo FILIPI -0.83 0.45 -0.03 0.62 0.76 0.20 -0.29 0.44 sapiens, Similar to KIAA1275 protein, done IMAGE:4616 553, mRNA A1978754 ESTs - 2.76 0.14 1.54 0.57 3.57 0.06 2.31 0.69 AA628440 nuclear XIST 0.18 0.13 1.42 1.52 4.80 0.02 3.01 1.50 receptor subfamily 1, group 1, member 3 L36861 L36861 - 2.75 0.17 2.01 0.82 3.63 0.09 3.00 0.97 /FEATURE= 202 expanded-c ds /DEFINITIO N=HUMGCA PB Homo sapiens guanylate cyclase activating protein (GCAP) gene exons 1-4, complete cds AW023227 ESTs MKX -0.91 0.60 -1.31 0.06 0.27 0.13 -2.90 0.52 NM_021614 Homo KCNN2 3.45 0.13 2.52 0.83 4.40 0.14 1.54 0.80 sapiens potassium intermediate small conductance calcium activated channel, subfamily N, member 2 (KCNN2), mRNA. /PROD=pota ssium intermediate small conductance calcium activated channel, subfamily N, member 2 /FL=gb:NM_ 021614.1 gb:AF23961 3.1 NM_000956 Homo PTGER2 -0.71 0.71 -0.73 0.57 0.63 0.33 -2.38 0.61 sapiens prostaglandi n E receptor 2 (subtype EP2), 53kD 203 (PTGER2), mRNA. IPROD=pros taglandin E receptor 2 (subtype EP2), 53kD /FL=gb:U194 87.1 gb:NM_0009 56.1 NM_013381 Homo TRHDE 1.96 0.16 0.25 0.36 1.81 0.03 0.82 0.23 sapiens thyrotropin releasing hormone degrading ectoenzyme (TRHDE), mRNA. /PROD=thyr otropin releasing hormone degradingect oenzyme /FL=gb:AF12 6372.1 gb:NM_0133 81.1 NM_016354 Homo SLCO4A1 2.18 0.06 1.01 0.37 2.35 0.05 -0.91 1.23 sapiens solute carrier family 21 (organic anion transporter), member 12 (SLC21A12), mRNA. /PROD=orga nic anion transporter OATP-E /FL=gb:AB03 1051.1 gb:NM_0163 54.1 204 gb:AF20507 2.1 gb:AF18781 7.1 BC028359 Homo ZNF141 -1.05 0.39 -0.59 0.65 1.25 0.17 -1.48 0.72 sapiens, done IMAGE:4828 836, mRNA. A1193252 ESTs, LRRN6A 4.38 0.11 247 0.43 4.23 0.11 1.90 0.37 Weakly similar to AF133270 1 SLIT2 (H.sapiens) H09780 Human - 2.04 0.19 0.56 0.07 2.50 0.11 0.12 0.40 (clone CTG A4) mRNA sequence BC040605 Homo - 2.64 0.16 1.61 1.08 3.59 0.09 0.45 1.14 sapiens, done IMAGE:5271 039, mRNA AW057589 ESTs - -0.96 0.26 -2.77 0.81 0.25 0.24 -1.21 0.35 M31213 Human RET 0.42 0.10 -1.86 0.83 1.77 0.12 -0.64 0.15 papillary thyroid carcinoma encoded protein mRNA, complete cds. /FL=gb:M312 13.1 Z92546 Human DNA - 0.58 0.13 -1.16 0.54 1.07 0.12 -1.27 0.14 sequence from clone CTA-65A6 on chromosome 22q11-12 Contains the 3 part of the gene for the ortholog of rat CAIN 205 (KIAA0330), the gene for a novel Sushi domain (SCR repeat) containing protein similar to Mucins, ESTs, an STS, GSSs and two... AA974416 protein PPP2R2B 4.02 0.16 3.52 0.23 5.22 0.07 3.12 0.15 phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform AW138143 ESTs SORBS2 3.44 0.16 2.89 0.88 4.47 0.10 1.88 1.15 NM_014862 Homo ARNT2 1.29 0.08 -0.68 0.97 2.00 0.08 0.02 0.24 sapiens KIAA0307 gene product (KIAA0307), mRNA. IPROD=KIA A0307 gene product /FL=gb:AB00 2305.1 gb:NM_0148 62.1 A1765540 ESTs - 1.28 0.22 0.07 0.39 1.50 0.07 -0.11 0.26 NM_018013 Homo FLJ10159 1.30 0.21 0.38 0.39 2.89 0.02 0.62 0.21 sapiens hypothetical protein FLJ10159 (FLJ10159), mRNA. IPROD=hypo thetical protein FLJ10159 /FL=gb:NM_ 206 018013.1 BF382322 ESTs, - -0.40 0.09 -2.09 0.67 -0.12 0.08 -1.73 0.50 Weakly similar to unnamed protein product (H.sapiens) AV699347 nuclear XIST -1.37 0.38 0.45 1.69 4.28 0.02 2.25 1.53 receptor subfamily 1, group 1, member 3 BC011549 Homo ATP5S 0.69 0.19 0.96 0.68 2.57 0.29 -0.02 0.52 sapiens, clone MGC:19945 IMAGE:4554 461, mRNA, complete cds. /PROD=Unk nown (protein for MGC:19945) /FL=gb:BC01 1549.1 NM_001889 Homo CRYZ -1.68 0.26 0.23 1.38 3.75 0.07 1.78 1.11 sapiens crystallin, zeta (quinone reductase) (CRYZ), mRNA. /PROD=cryst allin, zeta (quinone reductase) /FL=gb:NM_ 001889.1 gb:L13278.1 gb:S58039.1 BC002665 Homo PLP1 4.57 0.15 2.95 0.64 4.70 0.06 2.32 0.52 sapiens, proteolipid protein (Pelizaeus 207 Merzbacher disease, spastic paraplegia 2, uncomplicate d), clone MGC:3940, mRNA, complete cds. /PROD=prot eolipid protein (Pelizaeus Merzbacherd isease, spastic paraplegia 2, uncomplicate d) /FL=gb:BCOO 2665.1 NM_001243 Homo TNFRSF8 3.75 0.03 1.45 0.35 3.24 0.11 0.89 0.46 sapiens tumor necrosis factor receptor superfamily, member 8 (TNFRSF8), mRNA. /PROD=CD3 0 antigen (Ki-1 antigen) /FL=gb:NM_ 001243.1 gb:D86042.1 gb:M83554.1 NM_001195 Homo BFSP1 0.57 0.33 -1.65 1.30 0.60 0.14 -0.86 0.73 sapiens beaded filament structural protein 1, filensin (BFSP1), 208 mRNA. /PROD=filen sin /FL=gb:AF03 9655.1 gb:NM_0011 95.2 gb:Y16717.2 NM_024582 Homo FAT4 2.16 0.27 -0.49 0.30 1.54 0.28 -1.35 1.01 sapiens hypothetical protein FLJ23056 (FLJ23056), mRNA. /PROD=hypo thetical protein FLJ23056 /FL=gb:NM_ 024582.1 NM_000767 Homo CYP2B6 2.60 0.18 0.87 0.96 1.47 0.12 -0.69 1.03 sapiens cytochrome P450, subfamily 11 (phenobarbit al-inducible), polypeptide 6 (CYP2B6), mRNA. /PROD=cyto chrome P450, subfamily llB(phenobar bital inducible), polypeptide 6 /FL=gb:NM_ 000767.2 gb:AF18227 7.1 gb:M29874.1 AW665509 ESTs MGC42174 -0.10 0.33 -0.87 0.72 1.20 0.08 -2.60 1.40 NM_001104 Homo ACTN3 2.12 0.13 1.64 0.28 3.35 0.03 1.67 0.36 sapiens 209 actinin, alpha 3 (ACTN3), mRNA. /PROD=skel etal muscle specific actinin, alpha 3 /FL=gb:M864 07.1 gb:NM_0011 04.1 NM_021069 Homo SORBS2 -0.49 0.43 0.30 1.36 2.03 0.07 -1.13 1.15 sapiens ArgAbi interacting protein ArgBP2 (ARGBP2), transcript variant 2, mRNA. /PROD=Arg Abl interacting protein 2, isoform 2 /FL=gb:ABO1 8320.1 gb:NM_0210 69.1 T65020 ESTs - 0.51 0.16 -0.84 0.26 1.10 0.15 -1.50 0.38 NM_152647 Homo GALK2 0.08 0.56 -1.42 0.52 0.03 0.17 -2.34 0.91 sapiens hypothetical protein FLJ32800 (FLJ32800), mRNA. /FL=gb:NM_ 152647.1 BC036917 Homo C6orf141 -0.82 0.30 -1.18 0.40 0.88 0.11 -2.18 0.62 sapiens, clone MGC:46457 IMAGE:5201 433, mRNA, complete 210 cds. /PROD=Unk known (protein for MGC:46457) /FL=gb:BC03 6917.1 Al969112 Homo PHIP -1.07 0.13 -2.88 0.91 -0.37 0.02 -2.23 0.33 sapiens, done IMAGE:5260 603, mRNA, partial cds AW449813 KIAA0918 SLITRK5 0.32 0.26 -1.89 0.50 0.46 0.10 -0.57 0.13 protein AW044658 ESTs - 0.16 0.16 -1.47 0.25 0.90 0.14 -0.89 0.16 A1694300 ESTs - -0.52 0.02 -1.34 0.52 0.27 0.08 -1.00 0.08 NM_017631 Homo FLJ20035 1.35 0.13 0.05 0.19 1.51 0.17 0.32 0.15 sapiens hypothetical protein FLJ20035 (FLJ20035), mRNA. /PROD=hypo thetical protein FLJ20035 /FL=gb:NM_ 017631.1 AF298547 Homo NALP2 1.54 0.08 1.22 1.61 5.04 0.05 3.23 1.36 sapiens nucleotide binding site protein I mRNA, complete cds. IPROD=nuc eotide binding site protein 1 /FL=gb:AF29 8547.1 NM_030631 Homo SLC25A21 1.96 0.25 0.33 0.81 2.47 0.11 -0.28 0.63 sapiens oxodicarboxy late carrier 211 (ODC1), mRNA. /PROD=oxod icarboxylate carrier /FL=gb:NM_ 030631.1 BF196255 ESTs 2.94 005 1.18 0.43 3.15 0.08 0.54 0.57 NM_003247 Homo THBS2 2.62 0.20 1.04 0.28 2.70 0.04 0.27 0.45 sapiens thrombospon din2 (THBS2), mRNA. /PROD--thro mbospondin 2 /FL=gb:NM_ 003247.1 gb:L12350.1 NM_001446 Homo FABP7 0.95 0.09 -0.75 0.37 0.20 0.22 -1.73 0.99 sapiens fatty acid binding protein 7, brain (FABP7), mRNA. /PROD=fatty acid binding protein 7, brain IFL=gb:U812 35.1 gb:D88648.1 gb:U51338.1 gb:NM_0014 46.1 gb:D50373.1 AW004016 ESTs ST6GAL2 1.57 0.14 0.89 0.32 3.30 0.07 1.48 0.43 AW072790 contactin I CNTN1 0.50 0.20 0.18 0.98 1.84 0.10 1.01 1.39 AL512686 Homo GNAOI 2.16 0.50 -0.28 1.03 1.67 0.18 -1.12 0.37 sapiens mRNA; cDNA DKFZp761 11 77 (from clone DKFZp761 11 212 77). Al638063 ESTs CBX5 0.49 0.16 -0.34 0.34 0.98 0.11 -2.71 1.22 AU157049 Homo LOC153346 2.24 0.20 0.34 0.47 2.24 0.09 -0.44 0.96 sapiens cDNA FLJ14284 fis, clone PLACE1005 898 NM_002738 Homo PRKCB1 0.99 0.28 -0.15 0.45 1.42 0.08 -1.02 1.04 sapiens protein kinase C, beta I (PRKCB1), mRNA. /PROD=prot ein kinase C, beta 1 /FL=gb:NM_ 002738.1 A1185136 ESTs DYDC2 0.12 0.31 -0.80 0.08 0.72 0.08 -0.60 0.09 Al928037 ESTs RPIB9 -0.55 0.55 -2.71 0.74 0.49 0.12 -0.89 0.27 NM_016179 Homo TRPC4 -1.51 0.85 -1.87 1.42 1.71 0.11 -0.13 1.23 sapiens transient receptor potential channel 4 (TRPC4), mRNA. /PROD=tran sient receptor potential 4 /FL=gb:NM_ 016179.1 gb:AF1 7540 6.1 AW138143 ESTs SORBS2 3.29 0.13 2.35 1.05 4.28 0.10 1.32 1.07 NM_001876 Homo CPTIA 1.63 0.18 -0.15 0.21 1.32 0.07 -0.20 0.33 sapiens camitine palmitoyltran sferase 1, liver (CPT1A), nuclear gene 213 encoding mitochondria I protein, mRNA. /PROD=Iiver carnitine palmitoyltran sferase I /FL=gb:L392 11.1 gb:NM_0018 76.1 AA903862 ESTs C20orf54 1.61 0.15 -1.17 0.30 0.68 0.21 -1.49 0.23 A1670947 phosphatidyli - 3.91 0.05 0.55 1.54 3.33 0.10 1.17 0.68 nositol-4 phosphate 5 kinase, type 1, beta AV648405 polymerase - -0.01 0.11 0.23 0.52 1.73 0.14 -1.23 1.15 (RNA) III (DNA directed) (32kD) SF435123 bromodomai - 1.80 0.13 -1.35 1.01 1.14 0.03 0.37 0.24 n and PHD fnger containing, 3 NM_016582 Homo SLC15A3 1.77 0.16 -0.88 1.35 1.30 0.23 -2.04 1.23 sapiens peptide transporter 3 (LOC51296), mRNA. /PROD=pepti de transporter 3 /FL=gb:NM_ 016582.1 gb:AB02059 8.1 A1830490 glycerol GK 0.61 0.01 -0.65 0.79 1.25 0.20 -0.38 0.33 kinase AW134979 HSPCI56 STXBP6 2.28 0.03 0.55 0.28 2.05 0.03 0.30 0.44 protein A1354636 ESTs - 2.81 0.11 0.68 1.17 3.02 0.20 0.19 0.76 BE672659 ESTs - 0.20 0.64 -0.43 0.61 1.98 0.12 -0.69 0.45 AF284095 Homo ADRA2A 0.63 0.21 -0.74 0.98 1.85 0.03 0.55 0.31 sapiens 214 alpha-2A adrenergic receptor mRNA, complete cds. /PROD=alph a-2A adrenergic receptor /FL=gb:AF28 4095.1 gb:NM_0006 81.1 NM_021136 Homo RTN1 -0.30 0.03 -1.39 0.35 0.80 0.07 -1.23 0.39 sapiens reticulon 1 (RTN1), mRNA. /PROD=retic ulon 1 /FL=gb:L1 03 33.1 gb:L10334.1 gb:NM_0211 36.1 NM_014729 Homo TOX 0.34 0.03 -0.46 0.12 0.90 0.18 -1.86 0.40 sapiens KIAA0808 gene product (KIAA0808), mRNA. /PROD=KIA A0808 gene product /FL=gb:ABOI 8351.1 gb:NM_0147 29.1 BE674118 ESTs - 0.78 0.07 -1.32 0.73 0.28 0.19 -0.96 0.74 BC026969 Homo WDR67 2.95 0.11 0.75 0.92 3.08 0.08 0.45 0.61 sapiens, done IMAGE:5116 073, mRNA, partial cds. AF131783 Homo PAP2D -0.42 0.26 -2.00 1.05 0.31 0.22 -1.56 0.70 sapiens 215 done 25181 mRNA sequence. U11058 Homo KCNMAI 1.56 0.09 -0.16 1.08 2.29 0.18 -0.79 0.86 sapiens large conductance calcium- and voltage dependent potassium channel alpha subunit (MaxiK) mRNA, complete cds. /PROD=larg e conductance calcium- and voltage dependentpo tassium channel alpha subunit IFL=gb:U237 67.1 gb:NM_0022 47.1 gb:AF02599 9 BF510715 fibroblast - 2.67 0.27 0.84 0.17 3.29 0.01 0.64 0.51 growth factor 4 (heparin secretory transforming protein 1, Kaposi sarcoma oncogene) /FL=gb:M174 46.1 gb:NM_0020 07.1 BE897866 ESTs ACADSB 1.41 0.23 0.08 0.34 3.10 0.10 -0.27 0.88 216 A1735586 ESTs LOC152573 0.60 0.13 0.00 1.14 2.84 0.07 1.12 1.30 AL573058 complement CIR 0.92 0.14 -1.67 0.38 0.73 0.02 -0.96 0.77 component 1, r subcompone nt AF429305 Homo RMST -0.48 0.03 -2.49 0.51 -0.25 0.20 -1.89 0.27 sapiens C23up NCRMS mRNA, partial sequence; alternatively spliced. BF195118 ESTs, ATP5J 0.09 0.13 -0.92 0.42 1.57 0.16 -0.53 0.08 Weakly similar to ALU7_HUM AN ALU SUBFAMILY SQ SEQUENCE CONTAMIN ATION WARNING ENTRY (H.sapiens) NM_005460 Homo SNCAIP 1.76 0.16 -0.84 0.52 1.61 0.19 -0.92 0.88 sapiens synuclein, alpha interacting protein (synphilin) (SNCAJP), mRNA. /PROD=synu ciein alpha interacting protein /FL=gb:AF07 6929.1 gb:NM_0054 60.1 NM_024893 Homo C200rf39 1.16 0.29 -0.56 0.42 2.36 0.15 -0.06 0.17 sapiens hypothetical 217 protein FLJ14220 (FLJ14220), mRNA. /PROD=hypo thetical protein FLJ14220 /FL=gb:NM_ 024893.1 NM_022034 Homo CUZD1 1.31 0.08 0.80 0.28 2.78 0.07 0.24 0.58 sapiens estrogen regulated gene I (ERG-1), mRNA. /PROD=estr ogen regulated gene 1 /FL=gb:AF30 5835.1 gb:NM_0220 34.1 NM_014788 Homo TRIM14 3.12 0.09 1.22 0.59 3.54 0.08 1.02 0.45 sapiens KIAA0129 gene product (KIAA0129), mRNA. /PROD=KIA A0129 gene product /FL=gb:D509 19.1 gb:NM_0147 88.1 AV646597 ESTs, XIST -0.77 0.18 0.06 1.55 3.78 0.25 2.28 0.98 Weakly similar to ALU7_HUM AN ALU SUBFAMILY SQ SEQUENCE CONTAMIN ATION 218 WARNING ENTRY (H.sapiens) BF062629 DKFZP586E TMEM158 4.00 0.19 2.41 0.27 4.87 0.00 1.93 0.19 1621 protein AW440492 ATPase, ATP1A2 1.33 0.07 -2.12 1.07 1.27 0.06 -0.53 0.11 Na+K+ transporting, alpha 2 (+) polypeptide /FL=gb:NM_ 000702.1 AF283777 Homo CD72 -0.08 0.45 -1.88 1.19 0.41 0.24 -1.42 1.13 sapiens clone TCBAP0702 mRNA sequence. NM_005375 Homo MYB 2.11 0.17 -0.52 0.18 2.24 0.03 0.10 0.08 sapiens v myb avian myeloblastos is viral oncogene homolog (MYB), mRNA. /PROD=v myb avian myeloblastos is viral oncogeneho molog /FL=gb:NM_ 005375. 1 gb:AF10486 3.1 gb:M15024.1 NM_017671 Homo C20orf42 3.19 0.12 0.97 0.70 3.26 0.07 0.16 0.94 sapiens hypothetical protein FLJ20116 (FLJ20116), mRNA. /PROD=hypo thetical protein 219 FLJ20116 /FL=gb:NM_ 017671.1 BG283790 ESTs MATR3 2.27 0.11 0.95 0.57 3.53 0.04 0.89 0.51 NM_000702 Homo ATP1A2 2.12 0.17 0.76 0.38 2.93 0.16 0.51 0.12 sapiens ATPase, Na+K+ transporting, alpha 2 (+) polypeptide (ATPIA2), mRNA. /PROD=ATP ase, Na+K+ transporting, alpha2 (+)polypeptid e /FL=gb:NM_ 000702.1 NM_025135 Homo FHOD3 1.02 0.18 0.80 0.40 2.34 0.10 -0.77 0.72 sapiens hypothetical protein FLJ22297 (KIAA1695), mRNA. /PROD=hypo thetical protein KIAA1695 /FL=gb:NM_ 025135.1 NM_012281 Homo KCND2 1.67 0.30 0.05 0.15 2.70 0.09 -0.26 0.38 sapiens potassium voltage gated channel, Shal-related subfamily, member 2 (KCND2), mRNA. /PROD=pota ssium voltage 220 gated channel, Shal relatedsubfa mily, member 2 /FL=gb:NM_ 012281.1 gb:AB02896 7.1 gb:AF12110 4.1 BF449063 collagen, COL14A1 1.61 0.15 0.30 0.38 2.68 0.17 -0.33 0.68 type XIV, alpha 1 (undulin) AA280904 ESTs C9orf39 0.23 0.21 -1.58 1.26 1.13 0.14 -0.78 0.42 NM_022467 Homo CHST8 2.11 0.20 -0.51 0.30 2.17 0.10 0.48 0.02 sapiens N acetylgalacto samine-4-O sulfotransfer ase (GALNAC-4 ST1), mRNA.

/PROD=N

acetylgalacto samine-4-0 sulfotransfer ase /FL=gb:NM_ 022467.1 gb:AF30061 2.1 BE468066 ESTs RMST 3.26 0.09 1.49 0.10 3.80 0.09 1.63 0.08 AL120674 ESTs - 1.00 0.11 -1.35 1.73 1.55 0.15 -2.20 0.86 NM_133329 Homo KCNG3 2.18 0.27 0.74 0.29 3.67 0.01 0.26 0.28 sapiens potassium voltage gated channel, subfamily G, member 3 (KCNG3), transcript variant 1, 221 mRNA. /PROD=pota ssium voltage gated channel, subfamily G,member 3 isoform I /FL=gb:AF45 4548.1 gb:AF34898 2.1 gb:AB07060 4.1 gb:NM_1333 29.4 A1742043 ESTs - 0.94 0.34 -0.76 0.37 1.77 0.10 -1.45 0.52 NM_005103 Homo FEZI 2.80 0.11 2.08 0.25 4.98 0.06 2.20 0.26 sapiens fasciculation and elongation protein zeta 1 (zygin 1) (FEZ1), transcript variant 1, mRNA. /PROD=zygi n 1, isoform 1 /FL=gb:U600 60.1 gb:U69139.1 gb:NM_0051 03.2 NM_000277 Homo PAH 0.65 0.11 -1.08 0.08 1.46 0.18 -0.42 0.12 sapiens phenylalanin e hydroxylase (PAH), mRNA. /PROD=phe nylalanine hydroxylase /FL=gb:U498 222 97.1 gb:NM_0002 77.1 BF698797 ESTs - 0.93 0.10 -0.74 0.11 2.07 0.10 -0.40 0.44 BF437747 ESTs, C20orfl18 4.26 0.07 1.99 0.45 4.57 0.09 1.75 0.39 Weakly similar to ALU7_HUM AN ALU SUBFAMILY SQ SEQUENCE CONTAMIN ATION WARNING ENTRY (H.sapiens) NM_003020 Homo SCG5 4.03 0.14 2.53 0.32 5.01 0.12 3.11 0.24 sapiens secretory granule, neuroendocri ne protein 1 (7B2 protein) (SGNE1), mRNA. /PROD=secr etory granule, neuroendocri ne protein 1 (7B2protein) /FL=gb:BCOO 5349.1 gb:NM_0030 20.1 NM_002800 Homo PSMB9 1.38 0.10 0.27 0.34 2.05 0.07 -1.43 1.14 sapiens proteasome (prosome, macropain) subunit, beta type, 9 (large multifunction a protease 2) (PSMB9), mRNA. /PROD=prot 223 easome (prosome, macropain) subunit, betatype, 9 (large multifunction al protease 2) /FL=gb:U010 25.1 gb:NM_0028 00.1 BE972639 ESTs LOC646326 0.00 0.15 -2.71 0.55 0.33 0.22 -2.24 0.61 BC044830 Homo Cl0orf96 1.38 0.12 -0.32 0.82 2.28 0.06 -1.39 0.90 sapiens, Similar to RIKEN cDNA 1700011F14 gene, clone MGC:35062 IMAGE:5166 167, mRNA, complete cds. /PROD=Simil ar to RIKEN cDNA 1700011F14 gene /FL=gb:BC04 4830.1 A1961231 KIAA0808 TOX 3.28 0.13 1.23 0.06 4.00 0.01 1.13 0.37 gene product /FL=gb:AB01 8351.1 gb:NM_0147 29.1 U17496 Human PSMB8 3.43 0.21 0.46 1.17 3.30 0.06 0.09 0.64 proteasome subunit LMP7 (allele LMP7B) mRNA, complete cds. /PROD=prot 224 easome subunit LMP7 /FL=gb:U174 97.1 gb:U17496.1 N23651 ESTs SDK2 -1.16 0.31 -2.65 0.42 1.27 0.09 -207 0.75 NM_007015 Homo LECTI 4.83 0.12 2.27 0.84 5.36 0.09 1.83 0.69 sapiens chondromod ulin I precursor (CHM-1), mRNA. /PROD=chon dromodulin I precursor /FL=gb:NM_ 007015.1 gb:AB00600 0.1 NM_015474 Homo SAMHDI 2.63 0.17 0.57 0.33 2.89 0.09 0.29 0.22 sapiens DKFZP564A 032 protein (DKFZP564 A032), mRNA. /PROD=DKF ZP564A032 protein /FL=gb:AF22 8421.1 gb:AL05026 7.1 gb:AB01384 7.1 gb:NM_0154 74.1 AF147427 Homo SAMHD1 1.33 0.03 -0.99 0.88 1.35 0.08 -2.30 0.97 sapiens full length insert cDNA clone YP80A10. NM_004688 Homo NMI 3.54 0.04 0.96 0.07 3.80 0.07 1.13 0.34 sapiens N myc (and STAT) 225 interactor (NMI), mRNA.

/PROD=N

myc and STAT interactor /FL=gb:BCOO 1268.1 gb:NM_0046 88.1 gb:U32849.1 AB040812 Homo PAK7 -1.37 0.60 -3.89 1.62 -0.49 0.07 -4.18 0.12 sapiens mRNA for protein kinase PAK5, complete cds. /PROD=prot ein kinase PAK5 IFL=gb:AB04 0812.1 A1985987 ESTs, SCNN1G -0.28 0.31 -0.99 0.35 0.12 0.19 -2.70 0.59 Moderately similar to ALU1_HUM AN ALU SUBFAMILY J SEQUENCE CONTAMIN ATION WARNING ENTRY (H.sapiens) NM_001877 Homo CR2 1.50 0.13 -0.43 1.05 2.35 0.14 -1.44 1.51 sapiens complement component (3dEpstein Barr virus) receptor 2 (CR2), mRNA. /PROD=com 226 plement component (3dEpstein Barr virus)recepto r2 /FL=gb:NM_ 001877.1 gb:M26004.1 NM_001351 Homo DAZL 1.69 0.24 -0.81 0.76 1.93 0.12 -0.73 0.06 sapiens deleted in azoospermia -like (DAZL), mRNA. /PROD=delet ed in azoospermia -like /FL=gb:U667 26.2 gb:NM_0013 51.1 gb:U65918.1 gb:U66078.1 NM_022168 Homo IFIHI -2.03 1.08 -2.76 0.83 -0.10 0.15 -2.15 0.40 sapiens melanoma differentiatio n associated protein-5 (MDA5), mRNA. /PROD=mela noma differentiatio n associated protein-5 /FL=gb:AY01 7378.1 gb:NM_0221 68.1 gb:AF09584 4.1 AF052108 Homo LOC157627 1.49 0.33 0.22 1.02 2.26 0.40 -1.33 1.19 sapiens clone 23687 mRNA 227 sequence. A1056877 Human DNA LOC200230 0.11 0.30 -2-37 0.94 1.15 0.18 -1.35 0.75 sequence from clone RP4-53011 5 on chromosome 20. Contains the 3 end of the PTPN1 gene for protein tyrosine phosphatase ,non receptor type 1 (EC 3.1.3.48), the gene for a novel protein similar to placental protein DIFF40, an RPL36 (60S Ribos NM_002522 Homo NPTX1 2.35 0.25 -0.48 0.19 2.17 0.09 -1.19 0.83 sapiens neuronal pentraxin I (NPTX1), mRNA. /PROD=neur onal pentraxin I precursor /FL=gb:NM_ 002522.1 gb:U61849.1 N21096 ESTs STXBP6 2.42 0.16 0.99 0.08 3.69 0.09 1.14 0.04 A1693516 ESTs COL14A1 0.39 0.23 -1.63 0.96 0.96 0.17 -1.81 0.67 NM_018043 Homo TMEM16A -0.90 0.37 -1.93 0.70 0.25 0.43 -3.93 0.49 sapiens hypothetical protein FLJ10261 (FLJ10261), mRNA. 228 /PROD=hypo thetical protein FLJ10261 /FL=gb:NM_ 018043.1 AF110400 Homo FGF19 2.12 014 -0.08 0.34 2.18 0.04 -0.91 0.18 sapiens fibroblast growth factor 19 (FGF19) mRNA, complete cds. /PROD-fibro blast growth factor 19 /FL=gb:AF1 1 0400.1 gb:NM_0051 17.1 gb:ABO1812 2.1 AK098525 Homo HHIP 1.76 0.14 -0.57 0.63 3.32 0.06 -0.11 0.15 sapiens cDNA FLJ25659 fis, clone TST00427, highly similar to Mus musculus hedgehog interacting protein (Hip) mRNA. AV715309 ESTs, C200rf118 4.28 0.13 1.89 0.39 4.76 0.10 1.48 0.42 Weakly similar to ALU7_HUM AN ALU SUBFAM ILY SQ SEQUENCE CONTAMIN ATION WARNING ENTRY 229 (H.sapiens) U96136 Homo CTNND2 0.78 0.11 -1.33 0.87 1.18 0.12 -1.17 0.67 sapiens delta-catenin mRNA, complete cds. /PROD=delta -catenin /FL=gb:NM_ 001332.1 gb:U72665.1 gb:ABO1380 5.1 gb:U96136.1 gb:AF03530 2.1 NM_002590 Homo PCDH8 -0.80 0.34 -0.83 0.82 2.18 0.02 0.12 0.33 sapiens protocadheri n8 (PCDH8), mRNA. /PROD=prot ocadherin 8 /FL=gb:NM_ 002590.2 gb:AF06157 3.2 AF107846 Homo - 0.44 0.20 -0.25 0.12 2.12 0.14 -2.56 0.81 sapiens neuroendocri ne-specific Golgi protein p55 (XLalphas) gene, exon XL2 and complete cds BG169832 adenylate AK5 0.62 0.36 -2.79 0.50 1.03 0.36 -1.94 0.32 kinase 5 /FL=gb:NM_ 012093.1 gb:AF06259 5.1 BE968806 ESTs, ATP5S -1.15 0.14 -3.03 0.71 -0.34 0.15 -4.73 0.74 Weakly similar to 230 ALU4_HUM AN ALU SUBFAMILY SB2 SEQUENCE CONTAMIN ATION WARNING ENTRY (H.sapiens) BU729850 hypothetical JAKMIP2 2.30 0.07 0.43 1.78 3.86 0.04 -1.56 1.92 protein LOC153469 AL832535 Homo LOC157627 2.25 0.18 -0.04 1.00 3.14 0.25 -1.50 1.19 sapiens mRNA; cDNA DKFZp547J1 816 (from clone DKFZp547J1 816). NM_000439 Homo PCSK1 -0.63 0.18 -2.68 0.53 0.69 0.30 -3.19 1.03 sapiens proprotein convertase subtilisinkexi n type 1 (PCSK1), mRNA. /PROD=prop rotein convertase subtilisinkexi n type 1 /FL=gb:NM_ 000439.2 gb:M90753.1 M34455 Human INDO 4.39 0.23 1.58 0.09 5.44 0.08 1.69 0.13 interferon gamma inducible indoleamine 2,3 dioxygenase (IDO) mRNA, complete 231 cds. /FL=gb:NM_ 002164.1 gb:M34455.1 AB014737 Homo SMOC2 1.25 0.12 -2.04 0.48 1.94 0.06 -2.27 1.12 sapiens mRNA for SMAP-2b, complete cds. /PROD=SMA P-2b /FL=gb:ABOI 4737.1 BM682352 Homo HCN1 -0.41 0.14 -4.38 1.19 0.35 0.31 -2.88 0.32 sapiens cDNA FLJ37204 fis, clone BRALZ2006 976. 232 TABLE V: RELATIVE EXPRESSION OF DEFINITE ENDODERM MARKERS FOR CONDITIONS OUTLINED IN EXAMPLE 10. ALL VALUES WERE NORMALIZED TO GROUP 1 (CONTROL). Sox17 CXCR4 Goosecoid HNF-3B SOX-2 Oct-4 Group I- 1 1 1 1 1 1 control Group 2 45 19.5 2.8 0.64 0.91 1.1 Group 3 45 30 2.9 0.74 0.70 0.76 Group 4 8 14 2.7 1.11 0.18 0.36 Group 5 23 16 3.1 1.76 0.16 0.41 Group 6 41 5.8 3.0 1.87 0.61 0.57 Group 7 25 19.5 2.7 0.62 0.34 0.48 Group 8 6 15.9 2.9 2.0 0.13 0.43 Group 9 1 1.4 0.9 0.89 1.2 0.85 Group 10 22 1.5 1.4 1.20 1.36 0.68 Group 11 54 23 2.5 0.71 0.66 0.65 Group 12 68 0.7 0.9 1.51 0.02 0.30 Group 13 13.9 12.7 3.0 2.1 0.11 0.30 Group 14 52.6 20.6 2.9 0.82 0.69 0.70 Group 15 68 27.7 2.9 0.68 0.68 0.85 Group 16 13.9 21 2.4 0.79 0.46 0.72 Group 17 52 14.9 3.5 2.12 0.22 0.44 233 TABLE VI: MEAN NORMALIZED INTENSITY VALUES (IN LOG FORMAT) OF GENES FOR H9 EMBRYONIC STEM CELLS DERIVED DEFINITIVE ENDODERM STAGE CELLS CULTURED ON EITHER MATRIGELT" OR MEFS +/- WNT-3A. Gene Title DE treatment DE DE Benjamini in low serum treatment in treatme and + AA on low serum + nt in low Hochberg MATRIGEL AA + Wnt- serum + P-value 3A on AA on MATRIGEL MEFS ESTs 4.82708 2.63968 -4.26995 8.62E-05 microfibrillar-associated protein 4 0.063791 5.16358 -0.60091 3.48E-03 Homo sapiens, alpha-1 (VI) collagen -3.66187 2.36459 -2.26934 1.45E-04 ESTs -3.43712 2.14508 -2.6475 0.00E+00 Homo sapiens cystatin SN (CST1), 0.072931 7.53908 4.63955 4.46E-03 mRNA. /PROD=cystatin SN /FL=gb:J03870.1 gb:NM_001898.1 solute carrier family 16 (monocarboxylic -0.066405 5.23572 0.279005 4.27E-04 acid transporters), member 3 /FL=gb:U81800.1 gb:NM_004207.1 Homo sapiens fibroblast growth factor -0.894644 5.75417 2.4872 4.93E-03 17 (FGF17), mRNA. /PROD=fibroblast growth factor 17 /FL=gb:NM_003867.1 gb:AB009249.1 Human link protein mRNA, complete -1.93991 3.31348 -1.26346 1.14E-02 cds. /PROD=link protein /FL=gb:NM_001884.1 gb:U43328.1 Homo sapiens solute carrier family 16 0.710321 6.12971 1.72403 0.OOE+00 (monocarboxylic acid transporters), member 3 (SLC16A3), mRNA. /PROD=solute carrier family 16 (monocarboxylic acidtransporters), member 3 /FL=gb:U81800.1 gb:NM_004207.1 Homo sapiens apolipoprotein A-1 -1.47073 5.37558 2.46891 5.07E-03 (APOA1), mRNA. /PROD=apolipoprotein 234 A-I precursor /FL=gb:M27875.1 gb:M11791.1 gb:NM_000039.1 gb:BC005380.1 Homo sapiens cytidine deaminase -3.89129 2.05822 -1.67035 2.23E-03 (CDA), mRNA. /PROD=cytidine deaminase /FL=gb:L27943.1 gb:NM_001785.1 ESTs, Moderately similar to JE0284 -2.37712 5.75671 4.22227 2.56E-02 Mm-1 cell derived transplantability associated protein lb (H.sapiens) ESTs -0.04716 5.28231 0.966974 0.OOE+00 glycophorin B (includes Ss blood group) -2.85201 3.32812 -0.12969 1.45E-04 Homo sapiens homeobox protein -4.42042 3.55326 1.89424 2.50E-02 goosecoid mRNA, complete cds. /PROD=homeobox protein goosecoid /FL=gb:AY177407.1 gb:NM_173849.1 MCP-1=monocyte chemotactic protein -2.27571 5.13499 2.95543 2.92E-02 (human, aortic endothelial cells, mRNA, 661 nt). /PROD=MCP-1 Homo sapiens Mix-like homeobox -1.54648 4.47601 0.921971 2.01E-02 protein 1 (MILDI) mRNA, complete cds. /PROD=Mix-like homeobox protein I /FL=gb:AF211891.1 ESTs -4.93603 2.17917 -0.23735 1.12E-04 Homo sapiens lumican (LUM), mRNA. -4.05726 3.21064 0.948822 3.39E-02 /PROD=lumican /FL=gb:NM_002345.1 gb:U18728.1 gb:U21128.1 Homo sapiens HNF-3beta mRNA for -2.71785 4.68666 2.82506 3.71 E-02 hepatocyte nuclear factor-3 beta, complete cds. /PROD=hepatocyte nuclear factor-3 beta /FL=gb:AB028021.1 gb:NM_021784.1 Homo sapiens reserved (KCNK12), -0.468745 6.28184 3.77969 1.97E-02 mRNA. /PR OD=tandem pore domain potassium channel THIK-2 /FL=gb:NM_022055.1 gb:AF287302.1 Homo sapiens atrophin-1 interacting -4.30828 1.80825 -1.32021 9.63E-03 protein 1; activin receptor interacting 235 protein I (KIAA0705), mRNA. /PROD=atrophin-1 interacting protein 1; activinreceptor interacting protein I /FL=gb:NM_012301.1 gb:AF038563.1 ESTs -2.33636 2.25176 -2.32124 5.26E-04 Homo sapiens glutamate decarboxylase -2.424 2.31908 -1.87965 4.07E-04 1 (brain, 67kD) (GAD1), transcript variant GAD25, mRNA. /PROD=glutamate decarboxylase 1, isoform GAD25 /FL=gb:NM_013445.1 gb:AF178853.1 gb:BC002815.1 Homo sapiens cardiac ventricular -0.549728 4.89072 1.4377 2.99E-03 troponin C mRNA, complete cds. /PROD=cardiac ventricular troponin C /FL=gb:NM_003280.1 gb:AF020769.1 ESTs -2.89554 3.42817 0.926036 2.62E-02 Homo sapiens fibroblast growth factor 8 -4.32791 2.19561 0.015827 5.91 E-03 (androgen-induced) (FGF8), mRNA. /PROD=fibroblast growth factor 8 (androgen-induced) /FL=gb:U36223.1 gb:U46212.1 gb:NM_006119.1 ESTs -3.09818 1.66254 -2.20564 8.62E-05 Homo sapiens haptoglobin-related -2.6068 2.38009 -1.19632 6.95E-03 protein (HPR), mRNA. /PROD=haptoglobin-related protein /FL=gb:NM_020995.1 collagen, type VI, alpha 1 -1.418 3.85952 0.604245 1.21 E-02 Human (clone 8B1) Br-cadherin mRNA, -2.17941 2.59894 -1.02624 1.24E-02 complete cds. /PROD=Br-cadherin /FL=gb:L34057.1 gb:L33477.1 gb:NM_004061.1 ESTs -1.40092 2.57297 -1.82509 1.45E-04 Homo sapiens cystatin SA (CST2), -0.102178 5.21645 2.1671 2.40E-02 mRNA. /PROD=cystatin SA /FL=gb:NM_001322.1 Human mRNA for apolipoprotein Al (apo 0.215086 5.51109 2.49684 9.57E-03 AI)=. /PROD=preproapolipoprotein Al Homo sapiens MLL septin-like fusion -3.29221 1.70902 -1.49951 2.25E-03 236 (MSF), mRNA. /PROD=MLL septin-like fusion /FL=gb:AF123052.1 gb:NM_006640A Homo sapiens cystatin S (CST4), 0.92448 6.48842 3.87036 7.20E-03 mRNA. /PROD=cystatin S /FL=gb:NM_001899.1 Homo sapiens phorbolin-like protein -1.11883 4.73391 2.40782 7.86E-03 MDS019 (MDS019), mRNA. /PROD=phorbolin-like protein MDS019 /FL=gb:AF182420.1 gb:NM_021822.1 Homo sapiens apolipoprotein A-Il -1.03333 5.80468 4.46856 3.23E-02 (APOA2), mRNA. /PROD=apolipoprotein A-Il precursor /FL=gb:M29882.1 gb:NM_001643.1 gb:BC005282.1 ESTs -1.55475 3.48278 0.420447 2.50E-02 Homo sapiens glutamate decarboxylase -3.86752 1.56384 -1.08675 2.52E-02 I (brain, 67kD) (GAD1), transcript variant GAD67, mRNA. /PROD=glutamate decarboxylase 1, isoform GAD67 /FL=gb:NM_000817.1 gb:M81883.1 gb:L16888.1 ESTs -0.731491 5.43249 3.52168 1.60E-02 ESTs -2.03591 3.38924 0.760984 2.34E-03 Homo sapiens retinoid X receptor, -2.37496 2.62934 -0.32035 8.83E-04 gamma (RXRG), mRNA. /PROD=retinoid X receptor, gamma /FL=gb:NM_006917.1 gb:U38480.1 ESTs -0.648552 4.30576 1.43266 2.19E-03 Homo sapiens cDNA FLJ11550 fis, -1.22228 5.37746 4.21644 1.68E-02 clone HEMBA1002970 ESTs -1.782 3.50391 1.0501 1.85E-02 Homo sapiens haptoglobin (HP), mRNA. -1.10114 3.5449 0.477027 8.13E-03 /PROD=haptoglobin /FL=gb:K00422.1 gb:L29394.1 gb:NM_005143.1 Homo sapiens hypothetical protein -0.431989 5.14497 3.02045 2.62E-02 FLJ10970 (FLJ10970), mRNA. /PROD=hypothetical protein FLJ10970 /FL=gb:NM_018286.1 237 Homo sapiens beta-site APP cleaving -2.0354 3.70648 1.75385 8.00E-03 enzyme (BACE) mRNA, complete cds. /PROD=beta-site APP cleaving enzyme /FL=gb:AF200343.1 gb:AF204943.1 gb:AF190725.1 gb:AF201468.1 gb:NM_012104.1 Homo sapiens hypothetical protein 1.36784 6.82571 4.5979 2.10E-02 FLJ22252 similar to SRY-box containing gene 17 (FLJ22252), mRNA. /PROD=hypothetical protein FLJ22252 similar to SRY-boxcontaining gene 17 /FL=gb:NM_022454.1 Cluster Incl. AB028021:Homo sapiens -1.5339 5.12418 4.11704 4.47E-02 HNF-3beta mRNA for hepatocyte nuclear factor-3 beta, complete cds /cds=(196,1569) /gb=AB028021 /gi=4958949 /ug=Hs.155651 /len=1944 Homo sapiens gastrin-releasing peptide -2.74071 2.70077 0.509757 2.49E-04 (GRP), mRNA. /PROD=gastrin-releasing peptide /FL=gb:NM_002091.1 gb:K02054.1 gb:BC004488.1 Homo sapiens sema domain, seven -1.53335 3.78503 1.48732 4.71 E-02 thrombospondin repeats (type 1 and type I -like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A (SEMA5A), mRNA. /PROD=sema domain, seven thrombospondin repeats typel and type 1-like), transmem Homo sapiens mRNA; cDNA -0.835182 5.22406 3.69882 2.08E-02 DKFZp586J0624 (from clone DKFZp586J0624); complete cds. /PROD=hypothetical protein /FL=gb:AF215636.1 gb:NM_014585.1 gb:AF231121.1 gb:AF226614.1 gb:AL136944.1 Human mRNA for alpha-I type II -2.8736 2155 -0.38021 5.70E-03 collagen. 238 Rho GDP dissociation inhibitor (GDI) -1.54385 1.7147 -2.58241 1.71 E-02 alpha neuropilin 1 /FL=gb:AF016050.1 -1.62253 1.95432 -1.9667 8.83E-04 gb:NM_003873.1 gb:AF018956.1 Human DNA sequence from clone RP1 - -3.72313 1.68755 -0.37308 1.38E-03 181C24 on chromosome 6p11.1-12.2. Contains the 3 end of the BMP5 gene for bone morphogenetic protein 5, ESTs, STSs and GSSs /FL=gb:M60314.1 gb:NM_021073.1 myristoylated alanine-rich protein kinase -0.71724 3.51728 0.335725 4.29E-03 C substrate (MARCKS, 80K-L) /FL=gb:M68956.1 gb:DI0522.1 gb:NM_002356.4 hypothetical protein FLJ23403 -1.45618 1.81423 -2.31327 1.20E-02 /FL=gb:NM_022068.1 hepatocyte nuclear factor 4, alpha -4.26574 1.7879 0.445241 3.25E-02 Homo sapiens cell adhesion molecule -0.541188 2.1751 -2.5002 1.16E-03 with homology to L1CAM (close homologue of LI) (CHLI), mRNA. /PROD=cell adhesion molecule with homology to L1CAM(close homologue of LI) /FL=gb:AF002246.1 gb:NM_006614.1 matrix metalloproteinase 14 (membrane- -2.05734 2.36236 -0.5185 1.66E-02 inserted) /FL=gb:U41078.1 gb:NM_004995.2 Homo sapiens glycophorin B (includes -0.947308 3.26089 0.180293 4.83E-04 Ss blood group) (GYPB), mRNA. /PROD=glycophorin B precursor /FL=gb:J02982.1 gb:NM_002100.2 WAS protein family, member 2 -2.18746 1.99129 -1.05968 4.OOE-03 /FL=gb:NM_006990.1 gb:AB026542.1 Homo sapiens frizzled-related protein 0.56502 5.7261 3.67629 1.75E-02 (FRZB), mRNA. /PROD=frizzled-related protein /FL=gb:U24163.1 gb:U68057.1 gb:NM_001463.1 gb:U91903.1 Homo sapiens glutamate decarboxylase -1.68495 2.27067 -0.96944 8.02E-03 239 I (brain, 67kD) (GAD1), transcript variant GAD25, mRNA. /PROD=glutamate decarboxylase 1, isoform GAD25 /FL=gb:NM_013445.1 gb:AF178853.1 gb:BC002815.1 ESTs 0.812766 5.93144 3.91314 4.15E-02 Homo sapiens clone 23736 mRNA -0.047182 5.79006 4.50744 1.74E-02 sequence Homo sapiens glycophorin E (GYPE), -2.01601 1.79002 -1.50134 1.97E-02 mRNA. /PROD=glycophorin E /FL=gb:NM_002102.1 gb:M29610.1 ESTs 1.06767 5.63319 3.12487 2.00E-02 ESTs -1.41162 2.5396 -0.57029 1.29E-02 Human Fritz mRNA, complete cds. 0.436589 5.69814 3.91514 1.99E-02 /PROD=Fritz /FL=gb:U24163.1 gb:U68057.1 gb:NM_001463.1 gb:U91903.1 Homo sapiens, clone MGC:4655, 2.3772 5.9184 2.47596 1.20E-02 mRNA, complete cds. /PROD=Unknown (protein for MGC:4655) /FL=gb:BC004908.1 KIAA0878 protein /FL=gb:NM_014899.1 1.1189 6.41747 4.78882 2.01 E-02 gb:AB020685.1 Homo sapiens sema domain, -0.785987 3.69668 1.27624 2.10E-02 immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E (SEMA3E), mRNA. /PROD=sema domain, immunoglobulin domain (Ig), shortbasic domain, secreted, (semaphorin) 3E /FL=gb:NM_012431.1 gb:AB002329.1 ESTs 1.48084 6.59709 4.81395 1.36E-02 noggin /FL=gb:NM_005450.1 -1.63627 3.28161 1.32958 2.53E-02 Homo sapiens hypothetical protein -0.904749 3.35854 0.755319 1.12E-04 FLJ11316 (FLJ11316), mRNA. /PROD=hypothetical protein FLJ 1316 /FL=gb:NM_018388.1 Homo sapiens angiopoietin 2 (ANGPT2), -2.93044 2.23779 0.59685 3.43E-02 240 mRNA. /PROD=angiopoietin 2 /FL=gb:AB009865.1 gb:AF004327.1 gb:NM_001147.1 Homo sapiens matrix metalloproteinase -0.723489 2.97262 -0.09689 5.44E-03 14 (membrane-inserted) (MMP14), mRNA. /PROD=matrix metalloproteinase 14 preproprotein /FL=gb:U41078.1 gb:NM_004995.2 G protein-coupled receptor 1.50709 6.65228 5.05327 2.OOE-02 collagen, type IX, alpha 2 1.27026 5.4659 2.93507 3.19E-03 /FL=gb:NM_001852.1 ESTs 0.521638 3.93176 0.620223 0.OOE+00 KIAA1462 protein -3.84563 1.65452 0.437064 3.27E-02 Homo sapiens cartilage linking protein 1 -1.31515 2.27271 -0.80521 2.22E-02 (CRTL1), mRNA. /PROD=cartilage linking protein 1 /FL=gb:NM_001884.1 gb:U43328.1 Homo sapiens solute carrier family 21 0.711428 4.89808 2.43304 6.84E-03 (prostaglandin transporter), member 2 (SLC21A2), mRNA. /PROD=solute carrier family 21 (prostaglandintransporter), member 2 /FL=gb:U70867.1 gb:NM_005630.1 ESTs 0.307173 4.78515 2.65653 1.72E-02 6-phosphofructo-2-kinasefructose-2,6- -0.242865 3.97929 1.59985 5.28E-03 biphosphatase 4 Homo sapiens dual specificity 0.953857 5.82811 4.12159 4.OOE-03 phosphatase 4 (DUSP4), mRNA. /PROD=dual specificity phosphatase 4 /FL=gb:NM_001394.2 gb:BC002671.1 gb:U48807.1 gb:U21108.1 ESTs, Weakly similar to T00331 -1.57372 2.70797 0.443622 6.74E-03 hypothetical protein KIAA0555 (H.sapiens) ESTs -3.57414 3.15167 3.37198 8.82E-03 ESTs, Highly similar to IHHHUMAN -0.653989 3.22059 0.590533 5.18E-03 INDIAN HEDGEHOG PROTEIN PRECURSOR (H.sapiens) 241 ESTs, Weakly similar to FCE2 MOUSE 0.494192 5.22522 3.48031 1.97E-02 LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR (M.musculus) homeo box HB9 /FL=gb:NM_005515.1 -1.65563 3.2238 1.63092 5.58E-03 Homo sapiens arylsulfatase E 0.283004 4.95903 3.18424 9.22E-03 (chondrodysplasia punctata 1) (ARSE), mRNA. /PROD=arylsulfatase E precursor /FL=gb:X83573.1 gb:NM_000047.1 ESTs -0.05909 3.0455 -0.29817 1.47E-02 Homo sapiens hypothetical protein -1.48452 1.97473 -1.00431 5.72E-03 FLJ23403 (FLJ23403), mRNA. /PROD=hypothetical protein FLJ23403 /FL=gb:NM_022068.1 ESTs -0.182403 3.01548 -0.18954 3.72E-03 hypothetical protein FLJ23091 0.323388 5.25192 3.77987 3.57E-02 Human dipeptidyl peptidase IV (CD26) -3.61145 0.760585 -1.25595 3.07E-02 mRNA, complete cds. /PROD=dipeptidyl peptidase IV /FL=gb:M74777.1 hypothetical protein FLJ21032 0.355672 4.67756 2.61753 4.59E-02 Homo sapiens Kell blood group (KEL), -2.20519 1.89439 -0.38393 1.91 E-02 mRNA. /PROD=Kell blood group antigen /FL=gb:BC003135.1 gb:NM_000420.1 splicing factor, arginineserine-rich 5 0.7481 5.68934 4.27169 2.97E-03 Human prostatic secretory protein 57 -3.01313 1.46338 -0.40767 1.97E-02 mRNA, complete cds. /PROD=PSP57 /FL=gb:U22178.1 Homo sapiens KIAA0878 protein 2.0265 7.00937 5.65368 2.85E-02 (KIAA0878), mRNA. /PROD=KIAA0878 protein /FL=gb:NM_014899.1 gb:AB020685.1 Homo sapiens cryptic mRNA, complete 0.104874 2.87319 -0.67353 1.61 E-03 cds. /PROD=cryptic /FL=gb:AF312769.1 Homo sapiens cDNA FLJ13221 fis, 0.355743 3.98782 1.30963 1.38E-03 clone NT2RP4002075 phorbolin-like protein MDS019 -1.11756 2.83853 0.503523 1.59E-02 Homo sapiens mRNA for KIAA1409 0.368334 2.8009 -1.03191 1.78E-02 protein, partial cds. /PROD=KIAA1409 242 protein Homo sapiens mRNA; cDNA -2.63427 1.64513 -0.3056 2.52E-02 DKFZp434D0818 (from clone DKFZp434DO818) ESTs 0.35393 5.14775 3.74875 3.16E-02 Homo sapiens TBX3-iso protein (TBX3- -2.34566 2.45238 1.07038 1.31 E-02 iso), mRNA. /PROD=TBX3-iso protein /FL=gb:NM_016569.1 gb:AF216750.1 Homo sapiens chromosome 19, cosmid -0.258871 3.0636 0.223926 1.58E-03 R31181 Homo sapiens mRNA for GATA-6, 2.21862 6.8609 5.34263 4.29E-02 complete cds. /PROD=GATA-6 /FL=gb:U66075.1 gb:NM_005257.1 gb:D8781 1.1 Homo sapiens ankyrin-like with -1.10879 3.93484 2.81939 1.29E-02 transmembrane domains 1 (ANKTMI1), mRNA G protein-coupled receptor 49 0.265509 4.46257 2.50537 2.19E-02 Homo sapiens growth differentiation 1.67253 5.34944 2.87486 8.62E-05 factor 3 (GDF3), mRNA. /PROD=growth differentiation factor 3 precursor /FL=gb:NM_020634.1 gb:AF263538.1 Human (clone HSY3RR) neuropeptide Y 1.77461 6.70301 5.47995 3.OOE-02 receptor (NPYR) mRNA, complete cds. /PROD=neuropeptide Y receptor /FL=gb:L06797.1 gb:NM_003467.1 gb:AF025375.1 gb:AF147204.1 gb:M99293.1 gb:LO1639.1 Homo sapiens type VI collagen alpha 2 1.7011 5.33126 2.84458 5.91 E-03 chain precursor (COL6A2) mRNA, complete cds, alternatively spliced. /PROD=type VI collagen alpha 2 chain precursor /FL=gb:AY029208.1 ESTs -0.349726 3.29119 0.824929 4.11E-03 ESTs -0.903317 1.89777 -1.36429 6.84E-03 Homo sapiens hypothetical protein 2.60483 7.10633 5.55242 1.41 E-02 FLJ10718 (FLJ10718), mRNA. /PROD=hypothetical protein FLJ10718 243 /FL=gb:NM_018192.1 Homo sapiens Rho GTPase activating -1.10389 1.83053 -1.28521 1.28E-02 protein 6 (ARHGAP6), transcript variant 2, mRNA. /PROD=Rho GTPase activating protein 6 isoform 2 /FL=gb:AF022212.2 gb:NM_001174.2 stanniocalcin 1 /FL=gb:U25997.1 2.41135 7.29563 6.14284 2.51 E-02 gb:NM_003155.1 gb:U46768.1 Human glycophorin HeP2 mRNA, partial -0.843493 2.71108 0.233547 2.98E-04 cds. /PROD=glycophorin HeP2 Homo sapiens cDNA FLJ12993 fis, 0.147259 4.12241 2.06949 6.84E-03 clone NT2RP3000197 Homo sapiens presenilin stabilization -0.86173 2.85614 0.56745 6.09E-03 factor b (PSF) mRNA, complete cds; alternatively spliced. /PROD=presenilin stabilization factor b /FL=gb:AY1 13699.1 Homo sapiens glycophorin Erik STA -1.19362 2.17108 -0.45439 1.45E-04 (GPErik) gene complete cds. /PROD=glycophorin Erik (STA) /FL=gb:U00178.1 bromodomain and PHD finger -2.8472 1.75573 0.369397 8.62E-05 containing, 3 ESTs 0.784344 4.74104 2.71543 7.55E-03 ESTs -1.26251 3.4693 2.27614 3.80E-03 ESTs -1.71713 1.23763 -1.71122 2.99E-02 Homo sapiens microsomal glutathione 2.06233 6.81536 5.6918 3.79E-02 S-transferase 2 (MGST2), mRNA. /PROD=microsomal glutathione S transferase 2 /FL=gb:NM_002413.1 gb:U77604.1 Homo sapiens eomesodermin (Xenopus 2.65926 6.71627 4.89839 2.76E-02 laevis) homolog (EOMES), mRNA. /PROD=eomesodermin (Xenopus laevis) homolog /FL=gb:AB031038.1 gb:NM_005442.1 Homo sapiens mRNA for MSX-2, 0.407211 4.11145 1.94529 1.35E-02 complete cds. /PROD=MSX-2 /FL=gb:D89377.1 244 Homo sapiens apolipoprotein A-Il -1.10237 5.10066 4.75899 1.34E-02 (APOA2), mRNA. /PROD=apolipoprotein A-Il precursor /FL=gb:M29882.1 gb:NM_001643.1 gb:BC005282.1 Homo sapiens adenylate cyclase 8 -1.3408 1.12773 -2.26149 1.07E-02 (brain) (ADCY8), mRNA. /PROD=adenylate cyclase 8 /FL=gb:NM_001 115.1 Homo sapiens glucose-6-phosphate -0.193516 3.03064 0.407738 1.38E-03 transporter (G6PT) gene, G6PT-Dt allele, complete cds Homo sapiens glutathione S-transferase -3.10645 1.11704 -0.4221 5.37E-04 A2 (GSTA2), mRNA. /PROD=glutathione S-transferase A2 /FL=gb:BC002895.1 gb:M25627.1 gb:M16594.1 gb:M14777.1 gb:M15872.1 gb:M21758.1 gb:NM_000846.1 Homo sapiens sodium dependent -0.397133 2.78341 0.231961 1.11E-02 phosphate transporter isoform NaPi-Ilb mRNA, complete cds. /PROD=sodium dependent phosphate transporter isoformNaPi-Ilb /FL=gb:AFI 11856.1 gb:NM_006424.1 gb:AF146796.1 ESTs 2.77413 7.19192 5.906 3.17E-02 Homo sapiens partial LHX9 gene for -2.2486 1.64952 -0.13424 7.89E-03 LIM-homeobox 9, 3UTR. Homo sapiens LYST-interacting protein -0.682149 2.34271 -0.31253 9.87E-03 LIP3 mRNA, partial cds. /PROD=LYST interacting protein LIP3 putative 47 kDa protein -0.123937 3.2914 1.05247 3.72E-03 Homo sapiens protein S (alpha) 0.577604 4.00035 1.7883 7.89E-03 (PROS1), mRNA. /PROD=protein S (alpha) /FL=gb:M15036.1 gb:NM_000313.1 ESTs -1.63711 0.915477 -2.15328 1.83E-02 protocadherin 10 1.76718 5.1503 2.98569 2.52E-02 KIAA1511 protein 0.620278 3.86886 1.57543 1.86E-03 Homo sapiens cDNA FLJ13221 fis, 0.282785 3.44178 1.08178 1.31E-03 245 clone NT2RP4002075 Homo sapiens fibroblast growth factor -1.72385 2.26674 0.747239 6.86E-03 receptor 4, soluble-form splice variant (FGFR4) mRNA, complete cds. /PROD=fibroblast growth factor receptor 4,soluble-form splice variant /FL=gb:NM_022963.1 gb:AF202063.1 X75208 /FEATURE=cds -1.36729 2.60456 1.08204 1.58E-02 /DEFINITION=HSPTKR H.sapiens HEK2 mRNA for protein tyrosine kinase receptor Homo sapiens chemokine receptor 2.30557 6.72969 5.66933 3.31 E-02 CXCR4 mRNA, complete cds. /PROD=chemokine receptor CXCR4 /FL=gb:AF348491.1 KIAA1415 protein 0.185854 3.70346 1.74255 7.78E-04 ESTs -0.048335 3.11786 0.836448 1.29E-02 Homo sapiens stanniocalcin 1 (STC1), 2.39435 6.55737 5.28007 2.19E-02 mRNA. /PROD=stanniocalcin I /FL=gb:U25997.1 gb:NM_003155.1 gb:U46768.1 Homo sapiens high mobility group 1.04695 3.2786 0.095286 2.11 E-02 protein-R mRNA, complete cds. /PROD=high mobility group protein-R /FL=gb:AF176039.1 ESTs, Moderately similar to -1.10358 1.66331 -0.98371 3.37E-02 ALU4_HUMAN ALU SUBFAMILY SB2 SEQUENCE CONTAMINATION WARNING ENTRY (H.sapiens) Homo sapiens arrestin, beta 1 (ARRB1), -0.158844 2.41791 -0.40915 1.12E-02 transcript variant 1, mRNA. /PROD=arrestin beta 1, isoform A /FL=gb:BC003636.1 gb:AF084040.1 gb:NM_004041.2 ESTs -1.34399 1.80279 -0.44529 1.60E-03 Human mRNA for pro-alpha 1 (II) 0.85982 4.1935 2.15657 1.09E-02 collagen 3end C-term. triple helical and C-terminal non-helical domain. 246 /PROD=pro-alpha 1 (11) collagen (313 AA; AA 975-271 c) /FL=gb:NM_001844.2 Homo sapiens hypothetical protein 1.47773 4.42479 2.00326 1.16E-03 DKFZp564BO52 (DKFZp564B052), mRNA. /PROD=hypothetical protein DKFZp564B052 /FL=gb:NM_030820.1 testis enhanced gene transcript (BAX -0.695228 2.99328 1.31679 1.17E-03 inhibitor 1) Homo sapiens fasciculation and 1.86433 4.71354 2.20315 8.62E-05 elongation protein zeta 1 (zygin I) (FEZ1), transcript variant 1, mRNA. /PROD=zygin 1, isoform 1 /FL=gb:U60060.1 gb:U69139.1 gb:NM_005103.2 Homo sapiens matrix metalloproteinase -0.298504 3.44582 1.8336 4.80E-03 15 (membrane-inserted) (MMP15), mRNA. /PROD=matrix metalloproteinase 15 preproprotein /FL=gb:D86331.1 gb:NM_002428.1 heparan sulfate proteoglycan 2 -2.53327 0.924726 -0.97212 4.31 E-02 (perlecan) /FL=gb:M85289.1 gb:NM_005529.2 Homo sapiens dickkopf (Xenopus laevis) 0.981469 3.70716 1.09014 1.76E-03 homolog 1 (DKK1), mRNA. /PROD=dickkopf (Xenopus laevis) homolog I /FL=gb:AF177394.1 gb:NM_012242.1 gb:AF127563.1 ESTs -0.801487 3.37342 2.21393 1.22E-02 ESTs -2.57626 1.40231 0.050493 6.60E-03 ESTs 0.499579 4.10541 2.39934 4.29E-03 Homo sapiens bone morphogenetic 2.04506 6.19114 5.02927 4.98E-02 protein 2 (BMP2), mRNA. /PROD=bone morphogenetic protein 2 precursor /FL=gb:NM_001200.1 Human extracellular matrix protein 1 0.634778 3.65829 1.37564 6.11E-04 (ECMI1) mRNA, complete cds. /PROD=extracellular matrix protein 1 /FL=gb:NM 004425.2 gb:U65932.1 247 gb:U68186.1 Homo sapiens nuclear receptor -1.92783 2.32456 1.27907 2.99E-02 subfamily 0, group B, member I (NROB1), mRNA. /PROD=adrenal hypoplasia protein /FL=gb:NM_000475.2 Homo sapiens cDNA: FLJ23067 fis, -2.25626 1.95987 0.882498 6.62E-03 clone LNG04993. Homo sapiens ADP-ribosylation factor 4- 1.63466 5.70351 4.48037 1.90E-02 like (ARF4L), mRNA. /PROD=ADP ribosylation factor 4-like /FL=gb:U25771.1 gb:L38490.1 gb:NM_001661.1 gb:BC000043.1 Homo sapiens HTO16 mRNA, complete 0.218762 3.97514 2.45222 3.37E-02 cds. /PROD=HT016 /FL=gb:AF225426.1 Homo sapiens, tropomodulin, clone 0.348796 3.54199 1.46427 1.29E-03 MGC:3643, mRNA, complete cds. /PROD=tropomodulin /FL=gb:NM_003275.1 gb:M77016.1 gb:BC002660.1 Homo sapiens hypothetical protein 0.903825 4.65366 3.1349 2.48E-02 FLJ22471 (FLJ22471), mRNA. /PROD=hypothetical protein FLJ22471 /FL=gb:NM_025140.1 ESTs -0.120583 2.94229 0.738304 7.20E-03 ESTs, Moderately similar to JC4969 pig- -2.39713 0.906454 -1.04495 1.69E-02 c protein (H.sapiens) Homo sapiens LIM homeobox protein 1 -0.77166 2.27746 0.085559 4.26E-02 (LHX1), mRNA. /PROD=LIM homeobox protein 1 /FL=gb:NM_005568.1 gb:U14755.1 Homo sapiens, hypothetical protein -2.43105 0.646883 -1.50617 8.27E-03 MGC2865, clone MGC:20246 IMAGE:4635389, mRNA, complete cds. /FL=gb:BC016043.1 ESTs -2.01523 2.16773 1.12403 1.99E-02 Homo sapiens oxoglutarate -0.032595 2.3997 -0.38533 1.45E-02 dehydrogenase (lipoamide) (OGDH), mRNA. /PROD=oxoglutarate 248 dehydrogenase (lipoamide) /FL=gb:D10523.1 gb:BC004964.1 gb:NM_002541.1 ESTs, Weakly similar to T32252 2.20966 5.35974 3.33255 1.12E-04 hypothetical protein T15B7.2 Caenorhabditis elegans (C.elegans) Homo sapiens, cleft lip and palate 1.31578 3.52357 0.556735 2.92E-03 associated transmembrane protein 1, clone MGC:10593, mRNA, complete cds. /PROD=cleft lip and palate associated transmembraneprotein 1 /FL=gb:BC004865.1 Homo sapiens clone TUA8 Cri-du-chat 0.09218 3.37126 1.49746 6.46E-03 region mRNA Homo :;apiens transcriptional activator of 0.666391 4.50481 3.22532 5.80E-03 the c-fos promoter (CROC4), mRNA. /PROD=transcriptional activator of the c fos promoter /FL=gb:NM_006365.1 gb:U49857.1 Homo sapiens hypothetical protein -1.38519 2.23626 0.763963 7.36E-03 FLJ21195 similar to protein related to DAC and cerberus (FLJ21195), mRNA. /PROD=hypothetical protein FLJ21195 similar to proteinrelated to DAC and cerberus /FL=gb:NM_022469.1 ras homolog gene family, member B -0.123101 2.52093 0.071885 1.86E-02 /FL=gb:AF498971.1 gb:NM_004040.1 cartilage linking protein 1 0.879449 3.47789 0.987243 1.03E-03 Homo sapiens BCL2adenovirus E1B 3.30506 6.91803 5.44746 1.79E-03 19kD-interacting protein 3 (BNIP3) mRNA, complete cds. /PROD=BCL2adenovirus E1B 19kD interacting protein 3 /FL=gb:AF002697.1 gb:NM_004052.2 gb:U15174.1 Homo sapiens polycythemia rubra vera -1.19629 2.40987 0.93741 9.40E-03 1; cell surface receptor (PRV1), mRNA. /PROD=polycythemia rubra vera 1; cell surfacereceptor /FL=gb:NM_020406.1 249 gb:AF146747.1 Homo sapiens hypothetical protein -0.044112 3.42017 1.80688 3.77E-03 FLJ11560 (FLJ11560), mRNA. /PROD=hypothetical protein FLJ 1560 /FL=gb:NM_025182.1 plexin A2 0.930527 4.36203 2.74167 1.52E-02 Homo sapiens mRNA; cDNA 1.37193 4.24502 2.08129 5.37E-04 DKFZp547H236 (from clone DKFZp547H236). /PROD=hypothetical protein Homo sapiens cystatin C (amyloid 2.08601 5.30525 3.51965 2.20E-03 angiopathy and cerebral hemorrhage) (CST3), mRNA. /PROD=cystatin C (amyloid angiopathy and cerebralhemorrhage) /FL=gb:NM_000099.1 ESTs, Moderately similar to NFY-C -0.749407 2.00148 -0.24268 2.34E-03 (H.sapiens) ESTs 2.54243 5.75201 3.97307 2.60E-02 Homo sapiens sialyltransferase (STHM), -0.68709 2.89586 1.50348 3.70E-02 mRNA. /PROD=sialyltransferase /FL=gb:U14550.1 gb:NM_006456.1 Homo sapiens SG2NA beta isoform -1.15566 1.13989 -1.53439 1.55E-02 mRNA, partial cds. /PROD=SG2NA beta isoform Homo sapiens hypothetical protein 1.49091 4.80138 3.15205 2.63E-02 FLJ12838 (FLJ12838), mRNA. /PROD=hypothetical protein FLJ12838 /FL=gb:NM_024641.1 Homo sapiens solute carrier 0.403706 2.12385 -1.10043 1.78E-02 (SLC25AI8) mRNA, complete cds; nuclear gene for mitochondrial product. /PROD=solute carrier /FL=gb:AY008285.1 KIAA0346 protein -1.34736 2.49605 1.41497 3.90E-03 Human clone 23826 mRNA sequence 1.80782 4.07112 1.44315 2.28E-04 Homo sapiens receptor tyrosine kinase- 1.53333 4.73839 3.05612 1.63E-02 like orphan receptor 2 (ROR2), mRNA. 250 /PROD=receptor tyrosine kinase-like orphan receptor 2 /FL=gb:M97639.1 gb:NM_004560.1 Homo sapiens MYC-associated zinc -0.055569 2.67075 0.511292 2.63E-02 finger protein (purine-binding transcription factor) (MAZ), mRNA. /PROD=MYC-associated zinc finger protein(purine-binding transcription factor) /FL=gb:D85131.1 gb:NM_002383.1 Homo sapiens cDNA FLJ30081 fis, 0.677905 3.33728 1.12499 1.12E-04 clone BGGI 12000693, weakly similar to POLYHOMEOTIC-PROXIMAL CHROMATIN PROTEIN. Homo sapiens elongation of very long 0.099979 3.23372 1.50802 2.59E-03 chain fatty acids (FENI Elo2, SUR4EIo3, yeast)-like 2 (ELOVL2), mRNA. /PROD=elongation of very long chain fatty acids(FENI Elo2, SUR4Elo3, yeast)-like 2 /FL=gb:NM_017770.1 Homo sapiens thyrotropin-releasing -1.65672 1.46994 -0.25839 3.02E-02 hormone (TRH), mRNA. /PROD=thyrotropin-releasing hormone /FL=gb:NM_007117.1 ESTs, Weakly similar to A46302 PTB- 0.894051 4.21835 2.69535 1.57E-02 associated splicing factor, long form (H.sapiens) Human MLC1emb gene for embryonic 1.3489 5.11354 4.03961 1.61 E-02 myosin alkaline light chain, promoter and exon 1 Homo sapiens microseminoprotein, -2.37904 1.3101 0.169915 2.46E-02 beta- (MSMB), mRNA. /PROD=microseminoprotein, beta /FL=gb:NM_002443.1 Homo sapiens cDNA FLJ11390 fis, -1.12944 2.02889 0.364373 0.OOE+00 clone HEMBA1000561, weakly similar to ZINC FINGER PROTEIN 91. ESTs, Weakly similar to ALU8_HUMAN 2.76608 6.07949 4.57766 1.93E-02 251 ALU SUBFAMILY SX SEQUENCE CONTAMINATION WARNING ENTRY (H.sapiens) Homo sapiens cDNA FLJ13810 fis, -2.92389 0.51764 -0.85322 8.08E-03 clone THYRO1000279 Homo sapiens, aminolevulinate, delta-, 1.3099 4.44525 2.76918 7.69E-03 dehydratase, clone MGC:5057, mRNA, complete cds. /PROD=aminolevulinate, delta-, dehydratase /FL=gb:BC000977.1 gb:M13928.1 gb:NM_000031.1 Homo sapiens kidney-specific 1.91929 5.08917 3.44968 6.91E-03 membrane protein NX-17 mRNA, complete cds. /PROD=kidney-specific membrane protein NX-17 /FL=gb:AF229179.1 Homo sapiens alpha 2,8- -1.10548 2.36359 1.05469 4.63E-03 sialyltransferase mRNA, complete cds. /PROD=alpha 2,8-sialyltransferase /FL=gb:L43494.1 gb:D26360.1 gb:L32867.1 gb:NM_003034.1 tyrosine 3-monooxygenasetryptophan 5- 2.98486 6.17918 4.60758 8.01E-03 monooxygenase activation protein, eta polypeptide Homo sapiens cardiac ankyrin repeat -0.002291 3.35645 1.98688 3.44E-02 protein (CARP), mRNA. /PROD=cardiac ankyrin repeat protein /FL=gb:NM_014391.1 Homo sapiens porcupine (MG61), 1.51754 4.96311 3.68103 9.86E-03 mRNA. /PROD=porcupine /FL=gb:AF317059.1 gb:AF317058.1 gb:NM_022825.1 collagen, type V, alpha 1 1.5875 3.98844 1.66569 1.17E-03 /FL=gb:D90279.1 gb:NM_000093.1 gb:M76729.1 Homo sapiens forkhead box F2 -1.54469 1.02305 -1.11517 6.95E-03 (FOXF2), mRNA. /PROD=forkhead box F2/FL=gb:U13220.1 gb:NM_001452.1 PTPRF interacting protein, binding -1.92021 3.74378 2.77277 2.10E-02 252 protein 2 (liprin beta 2) Homo sapiens PRO1957 mRNA, 1.68941 5.30311 4.22705 1.43E-02 complete cds. /PROD=PRO1957 /FL=gb:AFI 16676.1 Homo sapiens hypothetical protein 0.564613 5.98527 5.24692 2.85E-02 FLJ23514 (FLJ23514), mRNA. /PROD=hypothetical protein FLJ23514 /FL=gb:NM_021827.1 Homo sapiens mRNA; cDNA -1.80897 1.69722 0.523009 2.47E-02 DKFZp586G2120 (from clone DKFZp586G2120); complete cds. /PROD=hypothetical protein /FL=gb:AL1 36924.1 Cluster Incl. L37033:Human FK-506 0.615619 3.478 1.66132 1.54E-02 binding protein homologue (FKBP38) mRNA, complete cds /cds=(140,1207) /gb=L37033 /gi=965469 /ug=Hs.173464 /len=1613 ESTs -0.004009 3.63657 2.61352 4.29E-02 Homo sapiens apolipoprotein C-I 3.24954 6.71073 5.50997 2.16E-02 (APOC), mRNA. /PROD=apolipoprotein C-I precursor /FL=gb:NM_001645.2 ESTs 1.38635 4.93112 3.83641 1.39E-02 Homo sapiens cDNA FLJ34035 fis, -3.58002 -0.48718 -2.00751 1.46E-02 clone FCBBF2004788. Homo sapiens, clone IMAGE:3509274, 0.493686 2.94923 0.794513 1.82E-02 mRNA, partial cds Homo sapiens putative sterol reductase 1.66857 4.3767 2.47833 5.37E-04 SR-1 (TM7SF2) mRNA, complete cds. /PROD=putative sterol reductase SR-1 /FL=gb:AF096304.1 nuclear factor of kappa light polypeptide 2.91463 6.48938 5.47812 1.97E-02 gene enhancer in B-cells inhibitor, alpha /FL=gb:NM_020529.1 gb:BC002601.1 gb:BC004983.1 gb:M69043.1 hypothetical protein FLJ12666 0.215767 3.10249 1.40459 1.91 E-02 Homo sapiens ectodermal dysplasia 1, 0.796627 4.22895 3.07833 1.01 E-02 anhidrotic (ED1), mRNA. 253 /PROD=ectodermal dysplasia 1, anhidrotic /FL=gb:AF060999.1 gb:NM_001399.1 gb:AF040628.1 gb:AF061189.1 glycoprotein M6A /FL=gb:D49958.1 0.274378 3.59045 2.3278 2.64E-02 ESTs 1.04714 3.87608 2.12752 3.75E-02 ESTs -1.48489 1.371 -0.35043 1.88E-03 ESTs, Weakly similar to KIAA1 330 -0.925232 2.41149 1.18187 2.65E-03 protein (H.sapiens) putative 47 kDa protein 0.156484 2.78771 0.861726 2.60E-02 Homo sapiens hypothetical protein -0.595622 4.84785 3.94683 3.34E-02 FLJ32835 (FLJ32835), mRNA. /FL=gb:NM_152506.1 Homo sapiens GS1999full mRNA, 0.137029 2.75189 0.849942 0.OOE+00 complete cds. /FL=gb:AB048286.1 Homo sapiens hexabrachion (tenascin 3.96862 5.66572 2.85391 1.39E-02 C, cytotactin) (HXB), mRNA. /PROD=hexabrachion (tenascin C, cytotactin) /FL=gb:M55618.1 gb:NM_002160.1 Homo sapiens Pig1O (PIG10) mRNA, 0.129454 2.86013 1.09765 1.16E-03 complete cds. /PROD=PigIO /FL=gb:AF059611.1 gb:AF010314.1 gb:NM_003633.1 gb:BC000418.1 gb:AF005381.1 Homo sapiens annexin A6 (ANXA6), 3.89026 6.43752 4.49981 8.81 E-04 transcript variant 1, mRNA. /PROD=annexin VI isoform 1 /FL=gb:D00510.1 gb:J03578.1 gb:NM_001155.2 Homo sapiens c-mer proto-oncogene 1.78994 4.92901 3.61665 1.84E-02 tyrosine kinase (MERTK), mRNA. /PROD=c-mer proto-oncogene tyrosine kinase /FL=gb:NM_006343.1 gb:U08023.1 Homo sapiens caspase-like apoptosis 0.434199 5.04863 5.2167 2.46E-02 regulatory protein 2 (clarp) mRNA, alternatively spliced, complete cds. 254 /PROD=caspase-like apoptosis regulatory protein 2 /FL=gb:AF005775.1 Human embryonic myosin alkali light 1.94171 5.24959 4.11475 2.11E-02 chain (MLC1) mRNA, complete cds. /FL=gb:M36172.1 gb:M24121.1 gb:NM_002476.1 Homo sapiens phosphatidylinositol-4- 1.34876 4.12788 2.46657 3.66E-03 phosphate 5-kinase, type 1, beta (PIP5K1 B), mRNA. /PROD=phosphatidylinositol-4 phosphate 5-kinase, typel, beta /FL=gb:NM_003558.1 Homo sapiens mRNA; cDNA 1.36443 4.34866 2.94283 2.92E-03 DKFZp434EO82 (from clone DKFZp434EO82) Homo sapiens dystrophin (muscular 1.40427 4.41881 3.04441 1.83E-02 dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272 (DMD), transcript variant Dp427p2, mRNA. /PROD=dystrophin Dp427p2 isoform /FL=gb:NM_004010.1 Homo sapiens, clone MGC:14801, 2.03928 3.96694 1.51059 5.65E-04 mRNA, complete cds. /PROD=Unknown (protein for MGC:14801) /FL=gb:BC005997.1 Homo sapiens hypothetical protein -0.290244 2.2418 0.40157 6.04E-03 BC017868 (LOC159091), mRNA. /FL=gb:BC017868.1 gb:NM_138819.1 ESTs, Highly similar to AF229172 1 -0.475471 1.94826 0.002417 5.28E-03 class IlIl myosin (H.sapiens) Homo sapiens solute carrier family 9 0.047487 2.80601 1.19645 2.80E-03 (sodiumhydrogen exchanger), isoform 5 (SLC9A5), mRNA. /PROD=solute carrier family 9 (sodiumhydrogenexchanger), isoform 5 IFL=gb:AF1 11173.1 gb:NM_004594.1 255 Homo sapiens F37Esophageal cancer- -0.128814 3.17069 2.10422 1.54E-02 related gene-coding leucine-zipper motif (FEZ1), mRNA. /PROD=F37Esophageal cancer-related gene-codingleucine zipper motif /FL=gb:AF123659.1 gb:NM_021020.1 Homo sapiens deiodinase, -0.136937 5.08366 4.22897 1.41 E-02 iodothyronine, type IIl (DIO3), mRNA. /PROD=thyroxine deiodinase type III /FL=gb:NM_001362.1 gb:S79854.1 Homo sapiens insulin-like growth factor 2.6126 5.13945 3.30402 9.72E-04 binding protein 6 (IGFBP6), mRNA. /PROD=insulin-like growth factor binding protein 6 /FL=gb:BC005007.1 gb:M62402.1 gb:BC003507.1 gb:NM_002178.1 Homo sapiens U2 small nuclear -0.821533 1.81533 0.096512 4.72E-02 ribonucleoprotein auxiliary factor (65kD) (U2AF65), mRNA. /PROD=U2 small nuclear ribonucleoprotein auxiliaryfactor (65kD) /FL=gb:NM_007279.1 Homo sapiens hypothetical protein -1.11464 1.81375 0.394686 9.09E-03 DKFZp434F0318 (DKFZP434FO318), mRNA. /PROD=hypothetical protein DKFZp434FO318 /FL=gb:NM_030817.1 Homo sapiens BACE mRNA for beta- 0.48553 3.13284 1.44588 4.99E-04 site APP cleaving enzyme 1-476, complete cds. /PROD=beta-site APP cleaving enzyme 1-476 /FL=gb:AB050436.1 ESTs, Weakly similar to ALUCHUMAN 1.07951 4.06134 2.7193 2.11E-02 !!!! ALU CLASS C WARNING ENTRY M! (H.sapiens) Homo sapiens mRNA for KIAA0876 -0.432037 1.97736 0.073246 3.37E-02 protein, partial cds. /PROD=KIAA0876 protein Homo sapiens mRNA for protein- 0.160986 2.75713 1.04172 2.11E-02 tyrosine kinase, complete cds. 256 /PROD=protein-tyrosine kinase /FL=gb:U05682.1 gb:D17517.1 gb:D50479.1 KIAA0418 gene product -0.677643 1.83134 0.034385 1.45E-04 Homo sapiens phosphofructokinase, 2.039 4.51747 2.70388 1.28E-03 liver (PFKL), mRNA. /PROD=phosphofructokinase, liver /FL=gb:NM_002626.1 gb:BC004920.1 gb:X1 5573.1 Homo sapiens enolase 2, (gamma, 2.60624 5.37458 3.92621 3.17E-03 neuronal) (ENO2), mRNA. /PROD=enolase 2, (gamma, neuronal) /FL=gb:NM_001975.1 gb:BC002745.1 gb:M22349.1 Homo sapiens AD036 mRNA, complete -0.503334 2.65787 1.60278 3.61 E-02 cds. /PROD=AD036 /FL=gb:AF260333.1 ESTs -2.07933 1.00157 -0.1307 2.39E-02 Homo sapiens keratin 19 (KRT19), 3.80582 6.96535 5.91937 2.11E-02 mRNA. /PROD=keratin 19 /FL=gb:NM_002276.1 gb:BC002539.1 pleiomorphic adenoma gene-like 1 -0.646793 1.88692 0.221481 4.21 E-03 /FL=gb:U72621.3 Homo sapiens, Similar to lipase protein, -1.16073 1.9994 0.961706 1.89E-02 clone MGC:2843, mRNA, complete cds. /PROD=Similar to lipase protein /FL=gb:NM_020676.1 gb:BC001698.1 Cluster Incl. AB002344:Human mRNA 2.15679 4.91332 3.47797 7.39E-03 for KIAA0346 gene, partial cds /cds=(0,4852) /gb=AB002344 /gi=2280479 /ug=Hs. 103915 /len=6121 Cluster Incl. N80935:zbO7gO6.s1 Homo 2.12419 4.48236 2.66555 1.50E-02 sapiens cDNA, 3 end /clone=IMAGE 301402 /cloneend=3 /gb=N80935 /gi=1243636 /ug=Hs.22483 /len=527 tryptase, alpha 2.99108 5.46095 3.76442 1.31 E-03 ESTs, Weakly similar to Z132_HUMAN 1.04865 3.65906 2.12166 2.43E-02 ZINC FINGER PROTEIN 13 (H.sapiens) Homo sapiens core histone 1.67293 4.73906 3.66212 3.62E-02 257 macroH2A2.2 (MACROH2A2), mRNA. /PROD=core histone macroH2A2.2 /FL=gb:AF151534.1 gb:NM_018649.1 ESTs -0.146413 2.69334 1.39451 1.02E-02 Human rho GDI mRNA, complete cds. 0.019358 1.75075 -0.65155 1.85E-02 /PROD=human rho GDI /FL=gb:M97579.1 gb:D13989.1 gb:NM_004309.1 heat shock 9OkD protein 1, alpha 1.69225 4.20576 2.60887 2.10E-02 Homo sapiens BTB (POZ) domain 1.10085 3.7628 2.32464 1.85E-02 containing 2 (BTBD2), mRNA. /PROD=BTB (POZ) domain containing 2 /FL=gb:NM_017797.1 Homo sapiens mandaselin long form -0.148053 2.58361 1.2296 1.57E-02 mRNA, complete cds. /PROD=mandaselin long form /FL=gb:AY048775.1 signal transducer and activator of -0.837261 1.90254 0.560225 8.83E-04 transcription 3 (acute-phase response factor) Homo sapiens lymphocyte antigen 6 0.866364 4.91832 4.92642 2.78E-02 complex, locus E (LY6E), mRNA. /PROD=lymphocyte antigen 6 complex, locus E /FL=gb:U42376.1 gb:NM_002346.1 gb:U56145.1 ESTs -1.24632 1.09042 -0.61316 4.05E-02 Homo sapiens, clone IMAGE:4047715, -2.50816 1.81 1.52693 2.63E-02 mRNA. Cluster Incl. AB002344:Human mRNA 1.89578 4.61333 3.31717 1.12E-02 for KIAA0346 gene, partial cds /cds=(0,4852) /gb=AB002344 /gi=2280479 /ug=Hs.103915 /len=6121 Homo sapiens singed (Drosophila)-like 4.23317 6.74774 5.25403 5.12E-03 (sea urchin fascin homolog like) (SNL), mRNA. /PROD=singed (Drosophila)-like (sea urchin fascinhomolog like) /FL=gb:BC000521.1 gb:NM_003088.1 gb:U03057.1 gb:U09873.1 258 Homo sapiens mRNA; cDNA -2.72593 1.58998 1.27994 4.54E-02 DKFZp586L0120 (from clone DKFZp586LO120). Homo sapiens mitogen-activated protein 0.647994 3.46459 2.28644 6.65E-03 kinase 10 (MAPK10), mRNA. /PROD=mitogen-activated protein kinase 10 /FL=gb:U07620.1 gb:U34819.1 gb:U34820.1 gb:NM_002753.1 Homo sapiens transmembrane tyrosine -0.006089 2.96035 1.93237 7.69E-03 kinase mRNA, complete cds. /PROD=tyrosine kinase /FL=gb:L08961.1 Homo sapiens mRNA; cDNA 2.83663 5.30784 3.79206 6.22E-03 DKFZp762H185 (from clone DKFZp762H185) tyrosine 3-monooxygenasetryptophan 5- 3.48271 619368 4.92556 2.11E-02 monooxygenase activation protein, eta polypeptide Homo sapiens mRNA; cDNA 0.581419 3.38088 2.21428 3.89E-02 DKFZp434K0621 (from clone DKFZp434KO621); partial cds ESTs, Weakly similar to ALUF_HUMAN -1.03247 1.75349 0.587598 2.11E-02 !!!! ALU CLASS F WARNING ENTRY ! (H.sapiens) tudor repeat associator with PCTAIRE 2 2.15771 4.69127 3.27451 2.63E-02 Homo sapiens mRNA; cDNA 4.49405 7.38448 6.33474 1.39E-02 DKFZp564KI672 (from clone DKFZp564K1672); partial cds. /PROD=hypothetical protein ESTs -0.184212 2.15367 0.554696 1.15E-02 Homo sapiens bHLH factor Hes4 0.47816 3.40725 2.40001 3.16E-02 (LOC57801), mRNA. /PROD=bHLH factor Hes4 /FL=gb:NM_021170.1 gb:AB048791.1 Homo sapiens guanylate cyclase -0.714216 1.95339 0.684983 3.38E-03 activator 1 B (retina) (GUCA1 B), mRNA. IPROD=guanylate cyclase activator 1 B (retina) /FL=gb:M95174.1 259 gb:NM_002098.1 gb:M97496.1 KIAA0918 protein -1.39708 0.961939 -0.57499 1.40E-02 Homo sapiens mRNA for KIAA1 161 0.781796 3.32846 1.98143 6.60E-03 protein, partial cds. /PROD=KIAA1 161 protein Homo sapiens, Similar to B9 protein, 1.43881 3.80457 2.29205 8.62E-05 clone MGC: 11339, mRNA, complete cds. /PROD=Similar to B9 protein /FL=gb:BC002944.1 hypothetical protein FLJ12666 2.34087 5.11201 4.02837 1.97E-02 Homo sapiens FLICE-like inhibitory 0.135783 4.45631 4.92758 1.96E-02 protein short form mRNA, complete cds. /PROD=FLICE-like inhibitory protein short form /FL=gb:U97075.1 Homo sapiens olfactory receptor, family -0.309574 2.08723 0.636487 4.36E-03 52, subfamily A, member I (OR52A1), mRNA. /PROD=olfactory receptor, family 52, subfamily A,member 1 /FL=gb:NM_012375.1 Human DNA sequence from clone RP4- 2.82768 5.54517 4.43909 2.04E-03 781L3 on chromosome 1p34.3-36. 11 Contains a pseudogene similar to IFITM3 (interferon inducedntransmembrane protein 3 (1 8U)), STSs and GSSs Homo sapiens KIAA01 27 gene product 2.05236 4.43794 3.00216 3.12E-02 (KIAAO 127), mRNA. /PROD=KIAA0127 gene product /FL=gb:D50917.1 gb:NM_014755.1 Homo sapiens clone HB-2 mRNA -0.503949 2.27896 1.25171 3.01 E-02 sequence hypothetical protein FLJ23091 -0.76092 3.70916 3.04154 2.45E-02 ESTs -0.403665 2.01868 0.643615 5.11E-04 ESTs 2.14401 4.70353 3.47114 3.15E-03 Homo sapiens regulator of G protein 3.0091 5.37511 3.95132 1.29E-03 signalling 5 (RGS5) mRNA, complete cds. /PROD=regulator of G protein signalling 5 /FL=gb:AF493929.1 260 endothelin receptor type A -1.83423 2.54948 1.95432 1.51 E-02 /FL=gb:NM_001957.1 gb:L06622.1 H.sapiens skeletal embryonic myosin 0.690058 3.3896 2.36018 3.27E-02 light chain 1 (MLCI) mRNA. /PROD=myosin light chain 1 Homo sapiens Kruppel-like factor 8 0.326119 2.825 1.63929 3.92E-02 (KLF8), mRNA. /PROD=Kruppel-like factor 8 /FL=gb:U28282.1 gb:NM_007250.1 hypothetical protein DKFZp434F2322 0.070576 2.58185 1.42121 5.81 E-03 Homo sapiens transcription factor 2, -1.12537 3.45355 2.54347 1.1 5E-02 hepatic; LF-B3; variant hepatic nuclear factor (TCF2), transcript variant a, mRNA. /PROD=transcription factor 2, isoform a /FL=gb:NM_000458.1 H2A histone family, member X 1.37085 2.48515 -0.04057 1.34E-02 Homo sapiens HI histone family, 3.21701 5.68105 4.50969 4.29E-03 member X (H1 FX), mRNA. /PROD=H1 histone family, member X /FL=gb:D64142.1 gb:BC000426.1 gb:NM_006026.1 ESTs, Weakly similar to KIAA1399 -0.831241 2.82364 2.79997 4.18E-02 protein (H.sapiens) Homo sapiens PNAS-145 mRNA, 2.84962 5.38084 4.2868 8.61 E-03 complete cds. /PROD=PNAS-145 /FL=gb:U03105.1 gb:NM_006813.1 gb:AF279899.1 Homo sapiens erythrocyte membrane -0.306603 2.11391 0.923806 4.81E-03 protein band 4.9 (dematin) (EPB49), mRNA. /PROD=erythrocyte membrane protein band 4.9 (dematin) /FL=gb:NM_001978.1 gb:U28389.1 ESTs 0.783545 3.23146 2.07738 2.13E-02 ESTs 1.17515 3.61815 2.46265 1.56E-03 nudix (nucleoside diphosphate linked 2.09472 5.82355 5.68859 3.63E-02 moiety X)-type motif 4 Novel human mRNA from chromosome -0.533665 3.44679 3.05803 3.99E-02 22. /PROD=hypothetical protein 261 Homo sapiens partial mRNA for putative 1.55224 3.89366 2.67866 1.53E-03 nuclear factor. /PROD=putative nuclear factor /FL=gb:NM_017688.1 Homo sapiens BCL2adenovirus E1B 4.51142 6.99506 5.92755 2.25E-03 19kD-interacting protein 3 (BNIP3), nuclear gene encoding mitochondrial protein, mRNA. /PROD=BCL2adenovirus E1B 19kD interacting protein 3 /FL=gb:AF002697.1 gb:NM_004052.2 gb:U15174.1 Homo sapiens bone morphogenetic -0.6099 1.76351 0.614791 6.46E-03 protein 5 (BMP5), mRNA. /PROD=bone morphogenetic protein 5 /FL=gb:M60314.1 gb:NM_021073.1 Homo sapiens nuclear receptor -0.213822 4.14059 3.29782 3.42E-02 subfamily 0, group B, member 1 (NROB1), mRNA. /PROD=adrenal hypoplasia protein /FL=gb:NM_000475.2 Homo sapiens mRNA; cDNA 1.76846 4.196 3.11284 1.23E-02 DKFZp434P228 (from clone DKFZp434P228) Homo sapiens pilin-like transcription 3.14467 5.51066 4.38212 3.80E-03 factor (PILB), mRNA. /PROD=pilin-like transcription factor /FL=gb:AF1 22004.1 gb:NM_012228.1 Homo sapiens complement component -1.89639 1.65637 1.59643 1.74E-02 5 (C5), mRNA. /PROD=complement component 5 /FL=gb:M57729.1 gb:NM_001735.1 Homo sapiens adaptor-related protein -0.208283 2.17404 1.07398 1.39E-02 complex 3, beta 2 subunit (AP3B2), mRNA. /PROD=adaptor-related protein complex 3, beta 2subunit /FL=gb:AF022152.1 gb:NM_004644.1 gb:U37673.1 Homo sapiens dynein, axonemal, light 0.458271 2.88755 1.8494 3.66E-03 polypeptide 4 (DNAL4), mRNA. /PROD=dynein, axonemal, light 262 polypeptide 4 /FL=gb:BC002968.1 gb:NM_005740.1 Homo sapiens, Similar to RIKEN cDNA 0.087468 245867 1.42701 3.35E-03 C330013D18 gene, clone MGC:11226, mRNA, complete cds Homo sapiens cDNA: FLJ22731 fis, -2.30948 1.62817 2.24143 4.15E-02 clone HS115841. ESTs 0.532996 4.6172 3.79228 2.76E-02 Homo sapiens CXCR4 gene encoding 3.11086 7.24917 6.36084 3.13E-02 receptor CXCR4 stanniocalcin 1 2.48686 6.20245 5.70081 4.94E-02 KIAA0761 protein -2.09591 1.57935 1.05907 1.86E-02 ESTs -1.16374 2.24964 2.52108 3.83E-02 Homo sapiens cDNA FLJ36116 fis, 3.02587 6.7146 6.15456 3.88E-02 clone TEST12022338. Homo sapiens, clone MGC:24252 -1.53346 2.53854 1.59251 3.91 E-03 IMAGE:3932604, mRNA, complete cds. /PROD=Unknown (protein for MGC:24252) /FL=gb:BC014364.1 Homo sapiens cDNA FLJ13392 fis, -1.90184 1.76129 1.16856 1.47E-02 clone PLACE1001280 Homo sapiens hypothetical protein 1.70617 5.11419 4.73391 2.71 E-02 FLJ 12538 similar to ras-related protein RAB17 (FLJ12538), mRNA. /PROD=hypothetical protein FLJ12538 similar toras-related protein RAB17 /FL=gb:AL136645.1 gb:NM_022449.1 Human DNA sequence from clone -0.889422 2.90076 2.11955 3.52E-02 RPI 1-446H13 on chromosome 10. Contains the 3 end of the gene for a novel protein similar to KIAAI 059 (ortholog of mouse VPS10 domain receptor protein SORCS), an RPL23A (60S ribosmal protein 23A) pseudogene, ESTs, STSs an Homo sapiens calmegin (CLGN), -0.104278 2.97817 3.11092 1.89E-02 mRNA. /PROD=calmegin /FL=gb:NM_004362.1 gb:D86322.1 263 Homo sapiens testican 3 (HSAJ1454), -2.81226 0.7939 1.55068 3.99E-02 mRNA. /PROD=testican 3 /FL=gb:NM_016950.1 gb:BC000460.1 gb:BC003017.1 Homo sapiens gelsolin (amyloidosis, 1.6198 4.54047 4.45008 1.07E-02 Finnish type) (GSN), mRNA. /PROD=gelsolin (amyloidosis, Finnish type) /FL=gb:NM_000177.1 Homo sapiens endothelin receptor type 0.763007 4.05983 3.55203 3.99E-02 A (EDNRA), mRNA. /PROD=endothelin receptor type A /FL=gb:NM_001957.1 gb:L06622.1 Homo sapiens cDNA: FLJ22808 fis, -0.367449 2.7584 2.41394 4.31E-02 clone KAIA2925. Homo sapiens hypothetical protein 1.59498 4.6335 4.89157 4.85E-02 FLJ10312 (FLJ10312), mRNA. /PROD=hypothetical protein FLJ10312 /FL=gb:NM_030672.1 Homo sapiens lipase mRNA, complete -2.2131 1.0208 0.55849 3.57E-02 cds. /PROD=lipase /FL=gb:AF225418.1 Homo sapiens clone FLC1492 PR03121 -0.300037 -0.46894 -3.39203 1.80E-02 mRNA, complete cds. /PROD=PRO3121 /FL=gb:AF130082.1 protease, serine, 4 (trypsin 4, brain) -0.345569 2.86256 3.35886 4.65E-02 Homo sapiens ret finger protein-like 2 -2.15511 1.1797 0.503917 1.94E-02 (RFPL2), mRNA. /PROD=ret finger protein-like 2 /FL=gb:NM_006605.1 Homo sapiens beta3GaNAcT-1 mRNA -2.73257 0.21269 -0.0984 2.48E-02 for globoside synthase, complete cds, clone:type 2. /PROD=globoside synthase /FL=gb:AB050856.1 Homo sapiens hypothetical protein -3.34565 -0.42738 -0.71255 3.07E-02 FLJ11155 (FLJ11155), mRNA. /PROD=hypothetical protein FLJ 11155 /FL=gb:NM_018342.1 Homo sapiens, dual specificity 2.11487 5.16681 5.60057 3.11 E-02 phosphatase 4, clone MGC:3713, mRNA, complete cds. /PROD=dual 264 specificity phosphatase 4 /FL=gb:NM_001394.2 gb:BC002671.1 gb:U48807.1 gb:U21108.1 Homo sapiens MAD (mothers against 0.917516 4.29847 3.5309 2.44E-02 decapentaplegic, Drosophila) homolog 6 (MADH6), mRNA. /PROD=MAD (mothers against decapentaplegic,Drosophila) homolog 6 /FL=gb:U59914.1 gb:NM_005585.1 secreted frizzled-related protein 1 1.64933 4.41286 4.21799 4.12E-02 /FL=gb:AF056087.1 gb:NM_003012.2 gb:AF017987.1 gb:AF001900.1 Homo sapiens secreted apoptosis 3.18446 5.9316 5.74251 3.31 E-02 related protein 2 (SARP2) mRNA, complete cds. /PROD=secreted apoptosis related protein 2 /FL=gb:AF056087.1 gb:NM_003012.2 gb:AF017987.1 gb:AF001900.1 KIAA0882 protein 2.05587 4.63577 4.67451 4.89E-02 Homo sapiens nudix (nucleoside 3.91519 6.54632 6.42767 4.63E-02 diphosphate linked moiety X)-type motif 4 (NUDT4), mRNA. /PROD=nudix (nucleoside diphosphate linked moietyX)-type motif 4 /FL=gb:NM_019094.1 gb:AF191653.1 gb:AF191649.1 gb:AF191650.1 Homo sapiens cDNA FLJ31061 fis, -1.30452 2.06218 1.20749 1.72E-02 clone HSYRA2000927. Homo sapiens diphosphoinositol 2.62612 5.53515 5.12935 3.96E-02 polyphosphate phosphohydrolase type 2 beta (NUDT4) mRNA, complete cds. /PROD=diphosphoinositol polyphosphate phosphohydrolasetype 2 beta /FL=gb:NM_019094.1 gb:AF191653.1 gb:AF191649.1 gb:AF191650.1 Homo sapiens titin (TTN), mRNA. -0.466154 2.46856 2.00309 4.18E-03 /PROD=titin /FL=gb:NM_003319.1 265 carboxypeptidase E 2.72316 5.80072 5.15668 2.99E-02 /FL=gb:NM_001873.1 ESTs -1.80443 0.692933 0.613229 1.46E-03 Homo sapiens hypothetical protein -1.60435 1.6149 2.4204 2.10E-02 FLJ39502 (FLJ39502), mRNA. /FL=gb:NM_173648.1 Homo sapiens renal tumor antigen -0.305406 2.4556 2.09136 3.30E-02 (RAGE), mRNA. /PROD=renal tumor antigen /FL=gb:NM_014226.1 gb:AB022694.1 T-box 3 (ulnar mammary syndrome) -1.70952 1.31576 0.679584 1.29E-02 Homo sapiens mitogen-activated protein -1.14241 1.82177 1.23928 2.48E-02 kinase kinase kinase 8 (MAP3K8), mRNA. /PROD=mitogen-activated protein kinase kinase kinase8 /FL=gb:NM_005204.1 gb:D14497.1 Homo sapiens enoyl-Coenzyme A, 0.226733 3.18231 2.59938 6.22E-03 hydratase3-hydroxyacyl Coenzyme A dehydrogenase (EHHADH), nuclear gene encoding mitochondrial protein, mRNA. /PROD=enoyl-Coenzyme A, hydratase3-hydroxyacylCoenzyme A dehydrogenase /FL=gb:NM_001966.1 gb:L07077.1 ESTs 1.65525 3.9984 3.98375 1.97E-02 Homo sapiens secreted frizzled-related 3.91678 7.18429 6.24313 2.35E-02 protein I (SFRP1), mRNA. /PROD=secreted frizzled-related protein 1 /FL=gb:AF056087.1 gb:NM_003012.2 gb:AF017987.1 gb:AF001900.1 ESTs 2.28659 5.21675 4.59884 3.11E-02 Homo sapiens selenoprotein P, plasma, 2.73332 5.13625 5.04138 1.75E-02 1 (SEPPI), mRNA. /PROD=selenoprotein P precursor /FL=gb:NM_005410.1 hypothetical protein FU12838 2.21522 5.4785 4.50835 4.55E-02 /FL=gb:NM_024641.1 Homo sapiens mRNA; cDNA -2.59761 0.092924 -0.31569 4.19E-02 266 DKFZp761M1216 (from clone DKFZp761M1216) Homo sapiens KPLI (KPL1) mRNA, -0.08886 2.51294 2.15967 1.97E-02 complete cds. /PROD=KPLI /FL=gb:AF081583.1 gb:U89715.1 gb:NM_021200.1 Homo sapiens, synovial sarcoma, X -1.57209 1.39869 2.12662 6.84E-03 breakpoint 1, clone MGC:5162, mRNA, complete cds. /PROD=synovial sarcoma, X breakpoint 1 /FL=gb:BC001003.2 gb:NM_005635.1 Homo sapiens, Similar to testican 3, -2.778 0.563149 1.66935 1.87E-02 clone MGC:8506, mRNA, complete cds. /PROD=Similar to testican 3 /FL=gb:NM_016950.1 gb:BC000460.1 gb:BC003017.1 ESTs 0.502949 3.0682 2.72874 2.02E-02 Homo sapiens cDNA FLJ32963 fis, 1.49644 3.87336 3.68478 6.89E-03 clone TEST12008405. triadin /FL=gb:U18985.1 -1.61408 0.713083 0.566175 1.87E-02 gb:NM_006073.1 Homo sapiens adlican mRNA, complete 0.872786 3.20404 3.02406 4.21 E-02 cds. /PROD=adlican /FL=gb:AF245505.1 Human midkine mRNA, complete cds. 3.55275 5.93819 5.68363 1.89E-02 /PROD=midkine /FL=gb:NM_002391.1 gb:M69148.1 Homo sapiens, synovial sarcoma, X -0.806785 1.90972 2.5215 4.17E-02 breakpoint 4, clone MGC:12411, mRNA, complete cds. /PROD=synovial sarcoma, X breakpoint 4 /FL=gb:BC005325.1 ESTs -3.61193 -0.9408 -1.53439 2.43E-03 ESTs -0.619714 1.93617 1.44843 4.14E-02 ESTs 0.446983 3.14315 2.48676 1.98E-02 Homo sapiens flavin containing -0.476203 1.99948 1.55491 3.73E-02 monooxygenase 5 (FMO5), mRNA. /PROD=flavin containing 267 monooxygenase 5 /FL=gb:L37080.1 gb:NM_001461.1 Homo sapiens aminopeptidase A -0.758987 2.07596 1.20831 3.OOE-02 mRNA, complete cds. /PROD=aminopeptidase A /FL=gb:L12468.1 gb:NM_001977.1 gb:L14721.1 Homo sapiens hypothetical protein -0.713164 2.03145 1.24823 2.17E-03 DKFZp761H1710 (DKFZP761H171O), mRNA. /PROD=hypothetical protein DKFZp761H1710 /FL=gb:NM_031297.1 ESTs -1.94194 0.608912 0.013238 1.72E-02 Homo sapiens sialyltransferase 8 (alpha- -1.07243 1.83889 0.855205 2.16E-02 2, 8-polysialytransferase) D (SIAT8D), mRNA. /PROD=sialyltransferase 8 (alpha-2,8-polysialytransferase) D /FL=gb:NM_005668.1 gb:L41680.1 Homo sapiens, clone IMAGE:5194204, -2.13256 0.383746 1.02639 4.55E-02 mRNA. hypothetical protein MGC4342 -0.403018 2.01722 1.41263 1.97E-02 /FL=gb:NM_024329.1 gb:BC003033.1 Homo sapiens PHD finger protein 1 0.620171 2.95191 2.42296 2.32E-02 (PHF1), transcript variant 2, mRNA. /PROD=PHD finger protein 1, isoform b /FL=gb:NM_024165.1 gb:AF052205.1 actinin, alpha 4 0.436893 3.11051 2.23625 5.44E-03 Homo sapiens PCTAIRE protein kinase 2.38171 4.87071 4.16957 2.90E-03 1 (PCTK1), mRNA. /PROD=PCTAIRE protein kinase 1 /FL=gb:NM_006201.1 Human DNA sequence from clone 0.167347 2.56439 1.93736 3.93E-02 RP1 1-165F24 on chromosome 9. Contains the 3 end of the gene for a novel protein (similar to Drosophila CG6630 and CG 11376, KIAA1 058, rat TRG), an RPL1 2 (60S ribosomal protein L12) pseudogene, ESTs, STSs, GSSs and a C... insulin-like growth factor binding protein 0.921068 3.60279 2.67905 4.80E-02 268 3 /FL=gb:NM_000598.1 Homo sapiens, clone IMAGE:3840937, 3.59778 6.12936 6.92649 8.62E-05 mRNA, partial cds. /PROD=Unknown (protein for IMAGE:3840937) Homo sapiens phosphoglucomutase 1 4.74364 7.09524 6.43056 2.21 E-02 (PGMI), mRNA. /PROD=phosphoglucomutase 1 /FL=gb:NM_002633.1 gb:BC001756.1 gb:M83088.1 apolipoprotein C-I 2.77701 5.23054 4.44049 3.39E-02 Homo sapiens insulin induced gene 1 2.11462 4.44128 3.77765 3.21 E-02 (INSIG1), mRNA. /PROD=insulin induced gene 1 /FL=gb:NM_005542.1 Human a6(IV) collagen (COL4A6) 0.798849 3.23623 2.41372 1.38E-03 mRNA, complete cds. /PROD=A type IV collagen /FL=gb:U04845.1 Homo sapiens mRNA for alpha 1,6- 1.31479 3.6699 2.90742 3.48E-02 fucosyltransferase, complete cds. /PROD=alpha 1,6-fucosyltransferase /FL=gb:AB049740.2 ESTs, Moderately similar to Six5 0.434259 2.81512 1.9556 1.23E-02 (M-musculus) solute carrier family 2 (facilitated glucose 5.23156 7.63734 6.74444 1.99E-02 transporter), member 3 /FL=gb:NM_006931.1 gb:M20681.1 Human acid sphingomyelinase (ASM) 1.03965 3.45689 2.52125 2.62E-02 mRNA, complete cds. /PROD=acid sphingomyelinase /FL=gb:NM_000543.1 gb:M59916.1 ESTs, Weakly similar to unnamed 3.0131 5.41021 4.46614 4.79E-03 protein product (H.sapiens) Homo sapiens cDNA FLJ33178 fis, 0.137476 -1.9718 -4.73502 2.23E-03 clone ADRGL2002753. Homo sapiens, parathyroid hormone-like 2.46289 -0.34647 -1.96791 3.05E-02 hormone, clone MGC:14611, mRNA, complete cds. /PROD=parathyroid hormone-like hormone /FL=gb:BC005961.1 269 Homo sapiens colon carcinoma related 2.50614 -0.01889 -1.04926 2.52E-02 protein (LOC51159), mRNA. /PROD=colon carcinoma related protein /FL=gb:NM_016206.1 gb:AF099505.1 KIAA0036 gene product 3.05174 -0.66523 -2.2068 2.62E-02 Homo sapiens cDNA FLJ 13536 fis, 4.27968 1.86625 1.70965 1.11E-02 clone PLACE1006521 Homo sapiens cDNA: FLJ22463 fis, 3.68063 1.24806 1.39728 1.42E-02 clone HRC10126 Homo sapiens UDP-N- 2.71164 0.270906 0.433883 1.98E-02 acetylglucosamine:a-1,3-D-mannoside beta-1,4-N acetylglucosaminyltransferase IV homolog (HGNT-IV-H), mRNA. /PROD=UDP-N-acetylglucosamine:a 1,3-D-mannosidebeta-1,4-N acetylglucosaminyltransferase IV homolog /FL=gb:AB024729.1 gb:NM_0 tissue factor pathway inhibitor 2 4.19529 1.63281 1.58393 7.53E-03 /FL=gb:D29992.1 gb:L27624.1 gb:NM_006528.1 gb:BC005330.1 ESTs 2.8924 0.521234 0.762594 2.82E-02 putative gene product -0.518738 -0.66615 1.82038 4.91E-02 Homo sapiens mRNA for KlAA1758 2.42082 -0.03923 0.213473 1.25E-02 protein, partial cds. /PROD=KIAA1758 protein prostaglandin E receptor 4 (subtype 2.58497 0.196846 0.527172 1.42E-02 EP4) /FL=gb:L25124.1 gb:D28472.1 gb:NM_000958.1 gb:L28175.1 Homo sapiens cDNA: FLJ22463 fis, 2.85068 0.473875 0.830447 1.97E-02 clone HRC10126 Homo sapiens heparan sulfate 3.18462 0.571052 0.709206 4.54E-02 (glucosamine) 3-0-sulfotransferase 2 (HS3ST2), mRNA. /PROD=heparan sulfate D-glucosaminyl3-O sulfotransferase 2 /FL=gb:AF105375.1 gb:AF105374.1 gb:NM_006043.1 Homo sapiens schwannomin interacting 5.5957 3.21054 3.57915 2.11E-02 270 protein I (SCHIP-1), mRNA. /PROD=schwannomin interacting protein 1 /FL=gb:AF145713.1 gb:NM_014575.1 Human lysyl oxidase (LOX) gene, exon 2.11886 -0.24936 0.138069 2.55E-03 7 Human nephropontin mRNA, complete 7.82555 5.27856 5.06542 4.61E-02 cds. /PROD=nephropontin /FL=gb:M83248.1 Human mRNA for KIAA0386 gene, 3.9213 1.56305 1.13663 1.93E-02 complete cds. /FL=gb:AB002384.1 ESTs 3.22146 0.851355 0.404487 3.41E-03 Human glioma pathogenesis-related 3.20187 0.502872 0.348681 1.34E-02 protein (GliPR) mRNA, complete cds. /PROD=glioma pathogenesis-related protein /FL=gb:NM_006851.1 gb:U16307.1 ESTs 2.96697 0.440894 0.773495 1.97E-02 Homo sapiens cDNA FLJ13384 fis, 5.9221 3.48419 3.9531 3.38E-02 clone PLACE1001062, highly similar to Homo sapiens mRNA for lysine ketoglutarate reductasesaccharopine dehydrogenase. Homo sapiens mRNA; cDNA 6.06894 3.31919 3.4798 4.97E-02 DKFZp76111912 (from clone DKFZp76111912) ESTs 4.12419 1.53997 1.88239 5.68E-03 Homo sapiens fibroblast growth factor 2 5.49297 2.64534 2.76054 4.71 E-02 (basic) (FGF2), mRNA. /PROD=fibroblast growth factor 2 (basic) /FL=gb:NM_002006.1 gb:M27968.1 ribosomal protein L34 pseudogene 1 3.45116 2.78236 5.10812 2.42E-02 HIV-1 rev binding protein 2 4.4245 1.47599 1.52824 2.10E-02 H.sapiens FGF gene, exon 3 2.04849 -0.34703 -0./5745 3.33E-02 /FL=gb:NM_000800.1 gb:M13361.1 ESTs 2.03304 -0.9164 -0.83676 4.19E-02 ESTs 2.87393 0.428858 1.02011 9.72E-04 Homo sapiens clone 23700 mRNA 4.60148 1.64243 1.72052 4.74E-02 sequence 271 ESTs, Highly similar to S21424 nestin 3.08579 0.725853 1.40345 1.99E-02 (H.sapiens) Homo sapiens actin, gamma 2, smooth 7.17155 4.15208 4.18551 4.72E-02 muscle, enteric (ACTG2), mRNA. /PROD=actin, gamma 2 propeptide /FL=gb:NM_001615.2 hypothetical protein FLJ22833 2.80785 0.480636 1.25154 2.43E-02 Homo sapiens LIM homeobox protein 6 2.52571 -0.06036 0.459727 4.37E-02 (LHX6), mRNA. /PROD=LIM homeobox protein 6 /FL=gb:AB031041.1 gb:NM_014368.1 gb:AL136570.1 Homo sapiens, clone IMAGE:5271039, 3.05576 0.189935 0.452681 4.05E-02 mRNA. Homo sapiens cAMP response element- 2.90971 0.487264 1.21334 4.24E-02 binding protein CRE-BPa (HGS165L15.1), mRNA. /PROD=cAMP response element-binding protein CRE BPa /FL=gb:NM_004904.1 gb:L0591 1.1 G protein-coupled receptor 1 1.15804 -1.24345 -0.49352 2.28E-03 /FL=gb:NM_005279.1 Homo sapiens neuropilin (NRP) and 3.25525 0.20233 0.301354 2.83E-02 tolloid (TLL)-like 1 (NETO1), transcript variant 3, mRNA. /PROD=neuropilin and tolloid-like protein 1 isoform 3precursor /FL=gb:AF448838.1 gb:NM_1 38966.2 Homo sapiens mRNA for KIAA0559 2.37088 -0.29358 0.199028 2.81E-02 protein, partial cds. /PROD=KIAA0559 protein Human 65-kilodalton phosphoprotein 3.25522 0.620942 1.15317 2.88E-02 (p65) mRNA, complete cds. /PROD=phosphoprotein p65 /FL=gb:M22300.1 gb:NM_002298.2 gb:J02923.1 Human DNA sequence from clone 4.77522 2.18971 2.77459 4.04E-02 RP1 1-31 KI 6 on chromosome 9. Contains a snoRNA binding domain pseudogene, the ELAVL2 gene for 272 ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2, ESTs, STSs, GSSs and a CpG island hypothetical protein FLJ 11006 1.75389 -0.66646 0.100591 7.78E-04 Homo sapiens mRNA; cDNA 3.97344 1.32598 1.8683 3.19E-02 DKFZp566A1046 (from clone DKFZp566A1 046) ESTs 4.13356 1.60769 2.27415 1.85E-02 H.sapiens gene from PAC 106H8. 3.05906 -0.08711 -0.13845 4.34E-02 Human T-cell receptor rearranged beta- 3.43862 0.94127 1.64514 5.31 E-03 chain V-region (V-D-J) mRNA, complete cds. /FL=gb:M15564.1 peptidylprolyl isomerase A (cyclophilin 1.76352 0.908832 3.26124 2.19E-02 A) Homo sapiens mRNA for KIAA1597 6.20675 3.06104 3.12403 1.78E-02 protein, partial cds. /PROD=KIAA1597 protein HIV-1 rev binding protein 2 3.54001 0.617783 0.325316 3.52E-02 Homo sapiens nidogen 2 (NID2), mRNA. 3.39549 0.915898 1.65422 4.70E-03 /PROD=nidogen 2 /FL=gb:NM_007361.1 gb:D86425.1 Homo sapiens mRNA; cDNA 3.49826 0.859233 1.46022 3.01E-02 DKFZp566A1 046 (from clone DKFZp566AI 046) Homo sapiens muscleblind (Drosophila)- 3.53962 0.508166 0.298438 3.90E-02 like (MBNL), mRNA. /PROD=muscleblind (Drosophila)-like /FL=gb:NM_021038.1 gb:AB007888.1 hypothetical protein FLJ20163 5.26708 2.17148 2.01643 3.33E-02 KIAA0455 gene product 3.25374 0.057742 -0.01612 2.66E-02 hypothetical protein FLJ22833 2.93229 0.533105 1.40606 3.19E-02 /FL=gb:NM_022837.1 ESTs 2.19313 -0.32822 0.427128 1.87E-02 Homo sapiens NADPH oxidase 4 5.57794 2.61602 2.28462 4.04E-02 (NOX4), mRNA. /PROD=NADPH oxidase 4 /FL=gb:AF261943.1 gb:NM_016931.1 gb:AF254621.1 gb:ABO41035.1 273 ESTs 3.3266 0.840887 1.69605 0.00E+00 ESTs 1.99635 -0.56359 0.236236 1.39E-02 Homo sapiens serumglucocorticoid 4.81433 2.46478 3.47797 2.02E-02 regulated kinase (SGK), mRNA. /PROD=serumglucocorticoid regulated kinase /FL=gb:BC001263.1 gb:NM_005627.1 gb:AF153609.1 A kinase (PRKA) anchor protein 2 6.03149 3.65135 4.63469 1.17E-02 ESTs 3.8522 1.17894 0.483367 3.08E-02 Homo sapiens similar to rat 1.74077 -1.45032 -1.24979 5.69E-04 tricarboxylate carrier-like protein (BA108L7.2), mRNA. /PROD=similar to rat tricarboxylate carrier-likeprotein /FL=gb:NM_030971.1 Homo sapiens, lectin, galactoside- 4.53668 1.85893 2.59596 3.84E-03 binding, soluble, 3 (galectin 3), clone MGC:2058, mRNA, complete cds. /PROD=lectin, galactoside-binding, soluble, 3(galectin 3) /FL=gb:NM_002306.1 gb:M35368.1 gb:BC001 120.1 gb:M36682.1 gb:M57710.1 gb:AB006780.1 ESTs 1.06738 -1.51321 -0.67814 7.68E-03 Homo sapiens heptacellular carcinoma 5.55437 3.02649 3.91576 2.22E-02 novel gene-3 protein (LOC51339), mRNA. /PROD=heptacellular carcinoma novel gene-3 protein /FL=gb:NM_016651.2 gb:AF251079.2 Homo sapiens, Similar to transforming 4.82642 2.07249 2.74019 1.03E-02 growth factor beta 1 induced transcript 1, clone MGC:4078, mRNA, complete cds. /PROD=Similar to transforming growth factor beta induced transcript 1 /FL=gb:NM_015927.1 gb:BC001830.1 gb:AFI 16343.1 ESTs, Highly similar to FXD3_HUMAN 3.81523 1.18624 1.98102 4.17E-02 FORKHEAD BOX PROTEIN D3 (H.sapiens) 274 ESTs 4.52094 1.70664 2.3196 2.78E-02 Homo sapiens potassium 3.68048 0.897369 1.5433 1.32E-02 intermediatesmall conductance calcium activated channel, subfamily N, member 2 (KCNN2), mRNA. /PROD=potassium intermediatesmall conductancecalcium activated channel, subfamily N, member 2 /FL=gb:NM_021614.1 gb:AF239613.1 Homo sapiens transporter similar to 5.68324 3.35483 4.46553 3.OOE-03 yeast MRS2 (MRS2L), mRNA. /PROD=transporter similar to yeast MRS2 /FL=gb:AF288288.1 gb:NM_020662.1 Homo sapiens a disintegrin-like and 4.54713 2.07152 1.10726 5.91 E-03 metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2) (ADAMTS5), mRNA. /PROD=a disintegrin and metalloprotease withthrombospondin motifs-5 preproprotein /FL=gb:NM_007038.1 gb:AF14209 HIV-1 rev binding protein 2 3.85003 0.823769 0.407316 3.76E-02 Human, parathyroid-like protein 1.73564 -1.5631 -1.41799 4.04E-02 (associated with humoral hypercalcemia of malignancy) mRNA, complete cds. /FL=gb:J03580.1 ESTs 5.27633 2.76577 3.71542 1.39E-02 ESTs 1.7022 -1.29085 -0.81236 1.72E-02 pyruvate dehydrogenase phosphatase 6.62966 4.26189 5.37384 1.04E-03 /FL=gb:NM_018444.1 gb:AF155661.1 ESTs 3.90566 1.11378 1.80307 1.57E-02 Homo sapiens DRM (DRM) mRNA, 6.16645 3.12369 3.57831 1.59E-02 complete cds. /PROD=DRM /FL=gb:NM01 3372.1 gb:AF1 10137.2 gb:AF045800.1 gb:AF154054.1 Homo sapiens cDNA: FLJ22769 fis, 2.36483 -0.5543 0.025213 1.45E-04 clone KAIA1316 ESTs 4.31647 1.44801 2.11226 2.19E-02 275 ESTs 1.24891 -1.42983 -0.57145 1.29E-02 Homo sapiens mRNA; cDNA 2.85031 0.231102 1.16439 1.08E-02 DKFZp586N012 (from clone DKFZp586NO12) jagged 1 (Alagille syndrome) 2.54951 0.151382 1.31733 4.46E-03 ESTs, Weakly similar to 138588 reverse 1.16209 -1.26828 -0.1187 3.40E-02 transcriptase homolog (H.sapiens) KIAA 339 protein 4.41803 2.09451 3.35786 3.90E-02 ESTs 3.83407 0.892884 1.56759 8.98E-03 DKFZP434D1 56 protein 4.42983 2.05154 3.28988 1.60E-02 Homo sapiens mRNA expressed only in 3.84408 0.705031 1.20856 2.25E-02 placental villi, clone SMAP41. RAS guanyl releasing protein 2 (calcium 2.7724 0.235409 1.34452 1.96E-02 and DAG-regulated) KIAA0164 gene product 4.99867 2.5327 3.72535 2.85E-02 /FL=gb:NM_014739.1 gb:D79986.1 Homo sapiens mRNA; cDNA 5.14752 2.61217 3.76652 3.78E-02 DKFZp761 MOI 11 (from clone DKFZp761M01 11) Homo sapiens NPDO09 mRNA, 2.15383 -0.27664 0.990295 2.09E-03 complete cds. /PROD=NPDO09 /FL=gb:NM_020686.1 gb:AF237813.1 muscleblind (Drosophila)-like 3.23823 0.467215 1.39628 7.60E-03 /FL=gb:NM_021038.1 gb:AB007888.1 ESTs 4.49318 1.35004 1.91395 3.79E-02 muscleblind (Drosophila)-like 1.84877 -0.57315 0.732468 8.06E-03 /FL=gb:NM_021038.1 gb:AB007888.1 ESTs 6.068 3.42334 4.51189 1.89E-02 ESTs, Weakly similar to unnamed 3.24528 0.740266 1.98306 3.89E-04 protein product (H.sapiens) Human complement cytolysis inhibitor 6.50766 4.03647 5.33533 1.77E-02 (CLI) mRNA, complete cds. /FL=gb:J02908.1 gb:NM_001831.1 gb:M64722.1 gb:M25915.1 ESTs 5.36759 2.42249 3.24765 3.23E-03 ESTs 0.957239 -1.43055 -0.04796 5.55E-04 transporter similar to yeast MRS2 3.77395 1.18311 2.36844 1.83E-02 Homo sapiens, Similar to regulator for 5.09957 2.72179 4.14116 2.72E-02 276 ribosome resistance homolog (S. cerevisiae), clone MGC:2755, mRNA, complete cds. /PROD=Similar to regulator for ribosome resistancehomolog (S. cerevisiae) /FL=gb:BC001811.1 SWISNF related, matrix associated, 2.54229 -0.29226 0.695255 1.89E-02 actin dependent regulator of chromatin, subfamily a, member 2 /FL=gb:NM_003070.1 gb:D26155.1 Homo sapiens mRNA; cDNA 3.34446 0.795373 2.07147 1.03E-02 DKFZp586L2424 (from clone DKFZp586L2424) ESTs 4.63117 2.08252 3.36946 2.25E-03 Homo sapiens bicarbonate transporter- 3.17407 0.745852 2.17046 1.71 E-03 related protein BTR1 mRNA, complete cds. /PROD=bicarbonate transporter related protein BTR1 /FL=gb:AF336127.1 ESTs 1.08377 -1.27197 0.228305 4.76E-02 ESTs 2.94657 0.127188 1.20032 1.43E-02 Homo sapiens mRNA; cDNA 2.47798 -0.26439 0.894731 4.51 E-03 DKFZp434B2016 (from clone DKFZp434B2016). ESTs 2.39983 -1.04089 -0.57976 3.37E-02 Homo sapiens synaptotagmin interacting 2.11009 -0.57109 0.653181 1.78E-02 protein STIPI mRNA, partial cds. /PROD=synaptotagmin interacting protein STIP1 Homo sapiens connexin 26 (GJB2) 2.86049 -0.57377 -0.09328 4.27E-04 mRNA, complete cds. /PROD=connexin 26 /FL=gb:NM_004004.1 gb:M86849.2 Homo sapiens brain-derived 1.71599 -0.79412 0.616733 3.09E-02 neurotrophic factor (BDNF), mRNA. /PROD=brain-derived neurotrophic factor /FL=gb:NM_001709.1 ESTs, Weakly similar to unknown 2.33677 -0.04066 1.5217 1.87E-03 (H.sapiens) 277 ESTs 2.57265 0.177794 1.74876 2.74E-04 ESTs 2.6809 0.209095 1.70624 1.21E-02 Homo sapiens DKC1 gene, exons 1 to 4.18307 1.70283 3.20863 2.00E-02 11 Homo sapiens T cell receptor beta chain 4.45228 1.38318 2.30031 3.27E-03 (TCRBV1 3S1 -TCRBJ2S1) mRNA, complete cds. /PROD=T cell receptor beta chain /FL=gb:AF043179.1 Homo sapiens PR00066 mRNA, 0.466715 -1.87679 -0.22665 4.25E-03 complete cds. /PROD=PRO0066 /FL=gb:AFI 13007.1 axonal transport of synaptic vesicles 5.20385 2.74124 4.27648 3.33E-03 Homo sapiens, Similar to cyclin M2, 0.139313 -2.31405 -0.76333 1.46E-02 clone MGC:12933 IMAGE:4308662, mRNA, complete cds. /PROD=Similar to cyclin M2 /FL=gb:BC021222.1 Homo sapiens clone CDABPOO95 3.87201 2.7936 5.73958 9.63E-03 mRNA sequence H.sapiens mRNA for ribosomal protein 2.00401 0.354674 2.73013 4.70E-04 LI 8a homologue. /PROD=ribosomal protein L18a homologue ESTs, Weakly similar to ALU7_HUMAN 3.43639 0.843826 2.28468 3.37E-02 ALU SUBFAMILY SQ SEQUENCE CONTAMINATION WARNING ENTRY (H.sapiens) Homo sapiens, clone IMAGE:5242616, -0.525567 -2.07832 0.406964 2.23E-02 mRNA. Homo sapiens CIorf24 mRNA, complete 5.17968 2.58724 4.04213 1.98E-04 cds. /PROD=C1orf24 /FL=gb:AF288391.1 gb:AB050477.1 gb:NM_022083.1 Homo sapiens clone IMAGE:451939, 5.15776 2.22786 3.40438 2.60E-02 mRNA sequence Homo sapiens cDNA\ FLJ14942 fis, 0.682724 -2.08716 -0.74074 1.45E-02 clone PLACE1 011185, highly similar to INSERTION ELEMENT IS1 PROTEIN INSB. hypothetical protein FLJ20425 4.23689 1.90847 3.69988 1 .15E-02 278 /FL=gb:NM_017816.1 gb:AL136750.1 Homo sapiens matrix metalloproteinase 2.28308 -0.65903 0.521586 8.87E-03 10 (stromelysin 2) (MMPIO), mRNA. /PROD=matrix metalloproteinase 10 preproprotein /FL=gb:BC002591.1 gb:NM_002425.1 ESTs 3.67167 2.20619 4.86553 3.16E-03 Homo sapiens prominin (mouse)-like 1 5.46002 2.79737 4.29571 1.38E-03 (PROML1), mRNA. /PROD=prominin (mouse)-like 1 /FL=gb:NM_006017.1 gb:AF027208.1 Homo sapiens mRNA; cDNA 2.40278 -0.68409 0.399469 1.48E-02 DKFZp434M2415 (from clone DKFZp434M2415). Homo sapiens hypothetical protein 2.1471 0.312211 2.65409 2.28E-04 FLJ20701 (FLJ20701), mRNA. /PROD=hypothetical protein FLJ20701 /FL=gb:NM_017933.1 Homo sapiens cDNA FLJ35259 fis, 6.79033 3.86627 5.12737 1.23E-03 clone PROST2004251. Homo sapiens hypothetical protein 4.0369 1.34318 2.84336 7.69E-03 FLJ39553 (FLJ39553), mRNA. /FL=gb:NM_173549.1 Human microfibril-associated 3.89326 0.527618 1.35764 1.81E-03 glycoprotein-2 MAGP-2 mRNA, complete cds. /PROD=microfibril associated glycoprotein-2 MAGP-2 /FL=gb:NM_003480.1 gb:U37283.1 Homo sapiens proprotein convertase 3.76897 0.368734 1.17396 1.38E-02 subtilisinkexin type 5 (PCSK5), mRNA. /PROD=proprotein convertase subtilisinkexin type 5 /FL=gb:U56387.2 gb:NM_006200.1 Cluster Incl. A1735391:atlOeO9.xI Homo 2.59941 0.203564 2.03637 1.12E-04 sapiens cDNA, 3 end /clone=IMAGE 2354728 /cloneend=3 /gb=A1735391 /gi=5056915 /ug=Hs.20137 /len=567 ESTs 2.30031 -1.01596 -0.08964 1.46E-02 279 Kruppel-like factor 4 (gut) 3.50041 1.09954 2.95915 1.22E-02 Homo sapiens full length insert cDNA -1.40946 -3.04877 -0.39378 3.32E-02 Y125A03 ESTs 0.806666 -2.01081 -0.53076 1.91 E-02 Homo sapiens mRNA; cDNA 3.1892 0.012768 1.13562 1.35E-03 DKFZp761G02121 (from clone DKFZp761G02121); partial cds Homo sapiens TMEFF2 mRNA, 2.28638 -0.89508 0.225546 1.21 E-03 complete cds. /FL=gb:ABO17269.1 gb:NM_016192.2 gb:AF179274.2 gb:AF242222.1 Homo sapiens, clone MGC:3328, 3.54625 0.772486 2.30168 4.16E-02 mRNA, complete cds. /PROD=Unknown (protein for MGC:3328) /FL=gb:BC001745.1 gb:NM_014392.1 ESTs 2.18149 -0.58303 0.984522 2.68E-02 synaptojanin 2 4.166 1.83143 3.84199 0.OOE+00 KIAA0367 protein 1.5999 -1.50555 -0.26286 1.58E-02 ESTs, Moderately similar to 0.868185 -1.46804 0.573078 1.69E-02 ALU8_HUMAN ALU SUBFAMILY SX SEQUENCE CONTAMINATION WARNING ENTRY (H.sapiens) bromodor ain adjacent to zinc finger 1.60872 -1.12544 0.518361 2.11 E-02 domain, 1B Human complement cytolysis inhibitor 6.61592 3.91665 5.596 1.66E-02 (CLI) mRNA, complete cds. /FL=gb:J02908.1 gb:NM_001831.1 gb:M64722.1 gb:M25915.1 forkhead box 01A (rhabdomyosarcoma) 5.04975 2.59802 4.53545 1.60E-03 /FL=gb:NM_002015.2 gb:AF032885.1 gb:U02310.1 Homo sapiens cDNA: FLJ22727 fis, 4.88391 2.09093 3.68875 1.91 E-02 clone HS115054 cadherin 6, type 2, K-cadherin (fetal 3.27371 0.243335 1.61199 2.74E-04 kidney) /FL=gb:D31784.1 gb:NM_004932.1 ESTs 3.97749 0.786845 1.99803 1.73E-02 endonuclease G-like 1 1.11519 -2.09018 -0.88324 1.69E-02 280 /FL=gb:AB020523.1 gb:NM_005107.1 Homo sapiens cDNA FLJ13034 fis, 4.59641 0.64328 1.1121 1.66E-02 clone NT2RP3001232 Human DNA sequence from clone RP4- 2.91607 0.209555 1.92644 1.93E-02 61404 on chromosome 20q11.1-12 Contains the 3 part of the MMP24 (matrix metalloproteinase 24 (membrane-inserted)) gene, the ITGB4BP (integrin beta 4 binding protein) gene, the 3 end of a novel gene, the 3 end o... Homo sapiens, collapsin response 0.672753 -1.75265 0.250803 8.65E-03 mediator protein-5; CRMP3-associated molecule, clone MGC:1 1247, mRNA, complete cds. /PROD=collapsin response mediator protein-5;CRMP3 associated molecule /FL=gb:BC002874.1 ESTs, Moderately similar to 2.91576 0.289656 2.10334 2.57E-03 ALU7_HUMAN ALU SUBFAMILY SQ SEQUENCE CONTAMINATION WARNING ENTRY (H.sapiens) ESTs, Moderately similar to CAIC RAT 6.2681 1.94518 1.82747 4.12E-02 COLLAGEN ALPHA 1(XII) CHAIN (R.norvegicus) Homo sapiens alpha-aminoadipate 5.2604 2.72549 4.6685 4.33E-03 semialdehyde synthase mRNA, complete cds. /PROD=alpha aminoadipate semialdehyde synthase /FL=gb:AF229180.1 Homo sapiens Wnt inhibitory factor-1 1.03265 -1.51207 0.433159 8.62E-05 (WIF-1), mRNA. /PROD=Wnt inhibitory factor-1 /FL=gb:AF122922.1 gb:NM_007191.1 ribosomal protein S11 4.95358 2.25158 4.04683 2.98E-04 Homo sapiens tumor necrosis factor, 2.42729 -0.73843 0.613222 1.93E-02 alpha-induced protein 6 (TNFAIP6), mRNA. /PROD=tumor necrosis factor, 281 alpha-induced protein 6 /FL=gb:NM_007115.1 Homo sapiens hairyenhancer-of-split 2.3848 -0.44154 1.27956 3.16E-03 related with YRPW motif 2 (HEY2), mRNA. /PROD=hairyenhancer-of-split related with YRPW motif2 /FL=gb:NM_012259.1 gb:AF311884.1 gb:AB044755.1 gb:AF232238.1 gb:AF237949.1 gb:AF173901.1 Homo sapiens semenogelin I (SEMG1), 0.585816 -2.46893 -0.95223 3.05E-02 mRNA. /PROD=semenogelin I /FL=gb:J04440.1 gb:NM_003007.1 Homo sapiens, Similar to cadherin 6, 2.38648 -0.02212 2.14359 2.59E-03 type 2, K-cadherin (fetal kidney), clone MGC:1470, mRNA, complete cds. /PROD=Similar to cadherin 6, type 2, K cadherin (fetalkidney) /FL=gb:BC000019.1 Homo sapiens mRNA; cDNA 2.16899 -0.56794 1.27546 3.16E-03 DKFZp434H0350 (from clone DKFZp434HO350); partial cds. /PROD=hypothetical protein Homo sapiens growth factor receptor- 4.2346 1.17569 2.73613 4.80E-03 bound protein 14 (GRB14), mRNA. /PROD=growth factor receptor-bound protein 14 /FL=gb:L76687.1 gb:NM_004490.1 Homo sapiens, Similar to TAF5-like RNA 2.10954 -0.1313 2.24853 8.24E-04 polymerase 11, p300CBP-associated factor (PCAF)-associated factor, 65kDa, clone MGC:46101 IMAGE:5551246, mRNA, complete cds. /PROD=Similar to TAF5-like RNA polymerase ll,p300CBP associated factor (PCAF)-associat Homo sapiens mRNA; cDNA 1.42404 -1.99222 -0.77126 3.21 E-02 DKFZp761JI324 (from clone DKFZp761J1324) solute carrier family 30 (zinc 2.82535 0.288493 2.38889 0.OOE+00 282 transporter), member 1 antizyme inhibitor 3.65887 0.37346 1.74912 1.86E-02 Homo sapiens GROI oncogene 2.51473 0.107263 2.38874 7.16E-04 (melanoma growth stimulating activity, alpha) (GROI), mRNA. /PROD=GRO1 oncogene (melanoma growth stimulatingactivity, alpha) /FL=gb:NM_001511.1 Homo sapiens proprotein convertase 4.90999 0.871309 1.52441 1.71 E-02 subtilisinkexin type 5 (PCSK5), mRNA. /PROD=proprotein convertase subtilisinkexin type 5 /FL=gb:U56387.2 gb:NM_006200.1 ESTs 0.254736 -1.96122 0.51777 4.00E-02 G-protein gamma-12 subunit 3.93653 1.06178 2.88889 5.11E-04 /FL=gb:NM_018841.1 gb:AF119663.1 platelet-derived growth factor alpha 3.50343 0.651246 2.50207 3.99E-03 polypeptide clusterin (complement lysis inhibitor, SP- 2.88196 -0.42677 0.9712 8.48E-03 40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J) ESTs 2.82081 -1.69816 -1.89985 4.IOE-02 Homo sapiens insulinoma-associated 1 2.94347 0.120494 2.02248 1.43E-03 (INSM1), mRNA. /PROD=insulinoma associated I /FL=gb:NM_002196.1 gb:M93119.1 LBP protein 32 /FL=gb:NM_014552.1 2.68546 -0.16678 1.70626 1.87E-03 gb:AF198489.1 ESTs, Highly similar to T42654 2.84504 0.515703 2.95379 7.92E-04 hypothetical protein DKFZp434G1 115.1 (H.sapiens) Homo sapiens Friend leukemia virus 1.7744 -2.28064 -1.56765 3.14E-02 integration I (FL1I), mRNA. /PROD=Friend leukemia virus integration 1 /FL=gb:BC001670.1 gb:NM_002017.2 gb:M98833.3 ESTs 0.846429 -2.42046 -0.91891 1.57E-02 283 Homo sapiens oxidative 3 alpha 1.30153 -1.64227 0.196394 3.20E-03 hydroxysteroid dehydrogenase; retinol dehydrogenase; 3-hydroxysteroid epimerase (RODH), mRNA. /PROD=oxidative 3 alpha hydroxysteroid dehydrogenase;retinol dehydrogenase; 3-hydroxysteroid epimerase /FL=gb:AF016509.1 gb:A minor histocompatibility antigen HA-1 1.89498 -0.37136 2.15157 4.61E-02 UDP-glucose pyrophosphorylase 2 4.26327 0.968939 2.4776 6.20E-03 Homo sapiens regulator of G-protein 5.42952 3.05504 5.49711 1.21 E-03 signalling 2, 24kD (RGS2), mRNA. /PROD=regulator of G-protein signalling 2, 24kD /FL=gb:L13463.1 gb:NM_002923.1 ESTs 4.49987 1.01623 2.35659 1.86E-03 ESTs 0.623422 -1.94907 0.317138 8.95E-04 ESTs 0.326084 -1.69499 1.13586 1.10E-02 ESTs 3.82952 0.673296 2.37112 3.92E-02 Homo sapiens cDNA FLJ10160 fis, 2.80876 -0.24405 1.56853 1.39E-02 clone HEMBA1003545, highly similar to INSULIN GENE ENHANCER PROTEIN ISL-2. thyroid hormone receptor-associated 4.66717 2.01883 4.2391 4.63E-03 protein, 150 kDa subunit /FL=gb:NM_005119.1 gb:AFI 17756.1 ESTs 2.4548 -0.3811 1.65212 4.08E-03 Homo sapiens mRNA; cDNA 3.13835 0.605922 2.95511 1.53E-03 DKFZp667D095 (from clone DKFZp667D095) Homo sapiens synaptojanin 2 mRNA, 2.94452 0.23595 2.4148 3.63E-04 complete cds. /PROD=synaptojanin 2 /FL=gb:AF318616.1 Homo sapiens prucollagen C- 3.37999 0.343624 2.21149 1.46E-02 endopeptidase enhancer (PCOLCE), mRNA. /PROD=procollagen C endopeptidase enhancer /FL=gb:BC000574.1 gb:NM_002593.2 284 gb:AB008549.1 gb:L33799.1 ESTs 3.24495 0.925809 3.52818 1.70E-04 Homo sapiens mRNA for KIAA0930 3.65772 0.911608 3.09513 8.62E-05 protein, partial cds. /PROD=KIAA0930 protein Homo sapiens forkhead transcription 1.51993 -2.14186 -0.86243 3.75E-02 factor FOXL2 (BPES), mRNA. /PROD=forkhead transcription factor FOXL2 /FL=gb:AF301906.1 gb:NM_023067.1 ESTs 1.9867 -1.5948 -0.2171 2.81E-03 ESTs, Highly similar to AF174600 1 F- 3.06175 0.202953 2.35691 2.45E-02 box protein Fbx20 (H.sapiens) Homo sapiens ankyrin 3, node of 3.11644 0.101116 2.09865 2.90E-03 Ranvier (ankyrin G) (ANK3), transcript variant 2, mRNA. /PROD=ankyrin 3, isoform 2 /FL=gb:NM_001149.1 gb:U43965.1 Homo sapiens tumor necrosis factor 2.39086 -1.04254 0.558779 1.62E-02 receptor superfamily, member 6 (TNFRSF6), mRNA. /PROD=apoptosis (APO-1) antigen 1 /FL=gb:NM_000043.1 gb:M67454.1 Homo sapiens thyrotropin-releasing 1.30849 -1.50688 0.822517 4.91E-02 hormone degrading ectoenzyme (TRHDE), mRNA. /PROD=thyrotropin releasing hormone degradingectoenzyme /FL=gb:AF126372.1 gb:NM_013381.1 ESTs 4.65711 0.915563 2.32327 6.29E-03 Homo sapiens mRNA; cDNA 2.36072 -2.02594 -1.25286 1.50E-02 DKFZp564NI 116 (from clone DKFZp564N1 116) Homo sapiens placental protein 13-like 3.55894 0.434263 2.47085 3.48E-03 protein (LOC56891), mRNA. /PROD=placental protein 13-like protein /FL=gb:NM_020129.1 gb:AF267852.1 Homo sapiens, Similar to receptor 2.05578 0.178992 3.5007 4.46E-04 285 tyrosine kinase-like orphan receptor 1, clone MGC:12687, mRNA, complete cds. /PROD=Similar to receptor tyrosine kinase-like orphanreceptor I /FL=gb:BC006374.1 ESTs 0.159066 -2.96514 -0.84976 3.25E-02 Homo sapiens, Similar to v-ets avian 2.22285 -1.58562 -0.1074 2.63E-02 erythroblastosis virus E26 oncogene homolog 1, clone MGC:29755 IMAGE:3946751, mRNA, complete cds. /PROD=Similar to v-ets avian erythroblastosis virusE26 oncogene homolog 1 /FL=gb:BC017314.1 ESTs, Highly similar to dedicator of cyto- 0.83871 -2.29829 -0.12951 1.85E-02 kinesis 1 (H.sapiens) ESTs 1.1465 -1.7403 0.682768 3.99E-02 ESTs 1.7466 -1.67509 0.283174 2.97E-03 ESTs, Weakly similar to PMXBHUMAN 1.03192 -2.44485 -0.51457 1.87E-03 PAIRED MESODERM HOMEOBOX PROTEIN 2B (H.sapiens) ESTs 3.22222 -0.29339 1.59904 7.36E-03 Homo sapiens cDNA FLJ10561 fis, 2.295 -1.60823 -0.08369 3.93E-03 clone NT2RP2002672 Homo sapiens, Similar to KIAA0441 1.38545 -1.60426 0.86909 2.33E-03 gene product, clone MGC:45124 IMAGE:5578893, mRNA, complete cds. /PROD=Similar to KIAA0441 gene product /FL=gb:BC036731.1 Homo sapiens, clone IMAGE:4067166, 0.195869 -2.50507 0.276993 1.16E-03 mRNA ESTs 1.5857 -2.61787 -1.30022 1.12E-02 Homo sapiens methyl-CpG binding 0.490598 -3.45465 -1.70163 3.90E-03 protein MBD2 (MBD2) mRNA, complete cds. /PROD=methyl-CpG binding protein MBD2 /FL=gb:NM_003927.2 gb:AF072242.1 KIAA1 151 protein 0.642527 -2.04288 1.00885 4.09E-03 H.sapiens mRNA for B-HLH DNA 5.43034 1.56039 3.45122 1.12E-04 286 binding protein. /PROD=B-HLH DNA binding protein /FL=gb:NM_000474.1 Homo sapiens, Similar to hypothetical 0.520711 -1.99011 1.26899 2.63E-02 protein FLJ32001, clone MGC:39559 IMAGE:4828136, mRNA, complete cds. /PROD=Similar to hypothetical protein FLJ32001 /FL=gb:BC036200.1 Homo sapiens Wilms tumor 1 (WT1), 2.40462 -2.96375 -2.43546 1.41E-02 transcript variant D, mRNA. /PROD=Wilms tumor I isoform D /FL=gb:NM_024424.1 gb:NM_024426.1 ESTs 1.53104 -1.54553 1.37309 8.14E-03 Homo sapiens, Similar to cadherin 6, 2.54746 -0.69811 2.13419 1.45E-04 type 2, K-cadherin (fetal kidney), clone MGC:1470, mRNA, complete cds. /PROD=Similar to cadherin 6, type 2, K cadherin (fetalkidney) /FL=gb:BC000019.1 ESTs 0.133612 -3.77953 -1.56636 1.40E-02 paternally expressed 3 2.87581 -1.67669 -0.0118 2.17E-02 Homo sapiens Charot-Leyden crystal 3.30086 -0.41644 2.1096 2.08E-02 protein (CLC), mRNA. /PROD=Charot Leyden crystal protein /FL=gb:NM_001828.3 gb:LO1664.1 ESTs 3.26198 -0.72777 1.5682 3.16E-03 Homo sapiens tachykinin, precursor 1 2.77265 -1.02081 1.48319 4.07E-04 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin alpha, neuropeptide K,neuropeptide gamma) (TAC1), transcript variant beta, mRNA. /PROD=tachykinin 2 precursor, isoform beta /FL=gb:U3 Homo sapiens PNAS-123 mRNA, 1.59659 -1.46656 1.84663 3.90E03 complete cds Homo sapiens hypothetical protein -0.359245 -3.46654 -0.06528 2.55E-03 FLJ20075 (FLJ20075), mRNA. /PROD=hypothetical protein FLJ20075 287 /FL=gb:NM_017655.1 Human platelet-derived growth factor 2.44464 -0.5846 2.90484 3.63E-04 alpha-receptor (PDGFRA) mRNA, exons 13-16 Homo sapiens cDNA: FLJ22547 fis, 4.29365 -0.10882 2.09548 1.54E-02 clone HS100356 Homo sapiens HSPC156 protein 0.786188 -2.32161 1.29619 8.62E-05 (HSPC1 56), mRNA. /PROD=HSPC156 protein /FL=gb:NM_014178.1 gb:AF161505.1 Homo sapiens mRNA; cDNA 0.485642 -4.8524 -3.09356 2.02E-02 DKFZp586P1 124 (from clone DKFZp586P1 124) caldesmon 1 /FL=gb:M64110.1 7.09236 2.67863 5.63436 7.47E-03 gb:NM_004342.2 Homo sapiens, Similar to hypothetical 1.69808 -2.74939 0.215566 1.92E-02 protein FLJ10058, clone MGC:34305 IMAGE:5167647, mRNA, complete cds. /PROD=Similar to hypothetical protein FLJ10058 /FL=gb:BC034293.1 Homo sapiens, Similar to LIM homeobox -0.062884 -4.30121 -1.10961 1 .16E-02 protein 8, clone IMAGE:4839343, mRNA. Homo sapiens chorionic 0.812166 -2.21846 2.21843 3.60E-03 somatomammotropin hormone 2 (CSH2), transcript variant 4, mRNA. /PROD=chorionic somatomammotropin hormone 2, isoform4 /FL=gb:NM_022646.1 Homo sapiens HES-related repressor 2.80599 -1.19396 2.40562 2.44E-03 protein 1 HERPI mRNA, complete cds. /PROD=HES-related repressor protein 1 HERP1 /FL=gb:NM_012259.1 gb:AF311884.1 gb:AB044755.1 gb:AF232238.1 gb:AF237949.1 gb:AF173901.1 Homo sapiens cadherin 6, type 2, K- 0.824752 -3.83509 -0.87634 2.49E-02 cadherin (fetal kidney) (CDH6), mRNA. 288 /PROD=cadherin 6, type 2, K-cadherin (fetal kidney) /FL=gb:D31784.1 gb:NM_004932.1 paternally expressed 3 2.87398 -4.12925 -3.49232 2.19E-02 Homo sapiens cDNA FLJ 11398 fis, 2.5268 -1.71619 1.84868 4.46E-04 clone HEMBA1000637. Homo sapiens BCL2-interacting killer 4.30042 0.023414 3.56237 1.94E-03 (apoptosis-inducing) (BIK), mRNA. /PROD=BCL2-interacting killer /FL=gb:NM_001197.2 gb:BC001599.1 gb:U34584.1 gb:U49730.1 Homo sapiens testis expressed 3.51154 -2.84891 -1.3824 2.18E-02 sequence 14 (TEX14), mRNA. IPROD=testis expressed sequence 14 /FL=gb:NM_031272.1 Homo sapiens growth hormone 2 (GH2), 0.922569 -2.77587 1.4679 1.60E-03 transcript variant 2, mRNA. /PROD=growth hormone 2, isoform 2 precursor /FL=gb:J03756.1 gb:NM_022557.1 Homo sapiens, clone IMAGE:4828836, 0.972907 -4.24111 -1.48398 1.63E-02 mRNA. Homo sapiens galanin receptor 1 2.50745 -3.13141 -0.33802 3.38E-03 (GALR1), mRNA. /PROD=galanin receptor 1 /FL=gb:NM_001480.2 gb:U23854.1 gb:L34339.1 gb:U53511.1 Homo sapiens, serine (or cysteine) 1.96851 4.13943 -1.56568 3.06E-02 proteinase inhibitor, clade B (ovalbumin), member 3, clone MGC:12244, mRNA, complete cds. /PROD=serine (or cysteine) proteinase inhibitor, cladeB (ovalbumin), member 3 /FL=gb:NM_006919.1 gb:U19556.1 gb:BC005224.1 DKFZP566K1924 protein 2.88225 -2.59632 1.39062 0.OOE+00 ESTs, Moderately similar to 4.24074 -0.69782 3.87444 1.12E-04 ALU2_HUMAN ALU SUBFAMILY SB SEQUENCE CONTAMINATION 289 WARNING ENTRY (H.sapiens) Human mRNA upregulated during 0.494505 4.62912 -0.18915 4.38E-02 camptothecin-induced apoptosis of U937 cells. nuclear receptor subfamily 1, group I, 1.77902 -4.02806 -0.19682 4.34E-02 member 3 ESTs -1.3795 -6.08172 -0.94606 6.91E-04 Homo sapiens chorionic 1.12437 -3.12138 2.61605 1.12E-04 somatomammotropin hormone 2 (CSH2), transcript variant 1, mRNA. /PROD=chorionic somatomammotropin hormone 2, isoform 1 precursor /FL=gb:NM_020991.2 gb:BC002717.1 Homo sapiens mRNA for SCCA2b, 3.32911 -3.16288 0.568045 1.93E-02 complete cds. /PROD=SCCA2b /FL=gb:AB046400.1 Homo sapiens KIAA0469 gene product 4.03097 -1.94826 2.56518 2.49E-04 (KIAA0469), mRNA. /PROD=KIAA0469 gene product /FL=gb:AB007938.1 gb:NM_014851.1 ESTs 4.45389 -2.40636 5.33359 5.65E-04 290 TABLE VII: THE EFFECT OF WNT-3A TREAMENT ON CYTOKINE EXPRESSION IN POPULATIONS OF CELLS FROM THE HUMAN EMBRYONIC STEM CELL LINE H9. Cell lysate Cell conditioned media w/o wnt 1 w/o wnt 2 wl wnt 1 w/ wnt 2 wlowntl wlo wnt2 w/ wnt 1 wl wnt 2 POS 62,842.33 67,606.06 49,758.34 50,702.57 96,585.15 109,721.82 199,709.04 196,889.94 NEG 23.38 34.49 370.82 400.66 58.06 34.45 216.90 105.20 Anglogenin 38.50 132.91 619.40 750.85 13,726.35 11,749.55 57,442.48 84,969.04 BDNF 167.50 167.82 783.51 951.45 689.22 563.39 770.08 715.86 BLC 2.00 48.99 742.24 476.38 107.69 512.77 337.12 24,80 BMP-4 247.00 273.70 348.44 30448 583.40 541.83 1,158.54 771.19 BMP-6 8.50 141.92 571.23 641.05 354.91 355.28 985.70 670.60 CK beta 8-1 1.00 1.13 22.48 21.54 17.79 25.31 42.78 75.44 CNTF 1.00 55.19 1,382.51 1,060.82 282.81 211.86 787.19 541.51 EGF 32.50 82.22 742.24 984.39 1,681.85 1,406.12 23,231.57 22,768.53 Eotaxin 1.00 7.32 301.87 253.80 207.89 199.67 622.91 291.71 Eotadn-2 262.00 336.77 1,155.31 960.31 890.56 744.31 2,156.21 1,445.14 Eotaxin3 184.50 284.96 934.12 847,56 975.77 665.56 2,140.81 1,480.35 FGF-6 629.00 379.57 1,327.92 964.54 1,239.85 947.73 3,283.94 2,519.78 FGF-7 31.00 222.45 1,075.02 941.73 449.49 352.47 1,086.66 861.72 FIt-3 IUgand 48.00 180.21 857.45 795.19 315.58 277.47 511.67 792.98 Fractalkine 23.50 62.51 792.02 458.51 120.80 145.30 359.37 367.15 GCP-2 1.00 45.05 593.71 538.86 203.21 166.86 451.78 362.12 GDNF 84.00 292.84 436.75 444.68 176.99 194.98 443.22 509.66 GM-CSF 433.00 636.37 1,343.17 1,161.75 777.25 722.75 1,808.82 1,446.82 1-309 152.50 246.10 708.52 743.25 1,82887 179.05 318.30 288.36 IFN-gamma 349.00 441.52 1,202.67 1,037.60 283.74 559.64 1,238.97 1,435.08 IGFBP-1 1.50 3.38 59.41 85.73 33.71 24.37 227.60 155.91 IGFBP-2 3,785.50 5,554.45 2,671.90 2,414.72 27,656.85 28,473.95 42,215.53 43,934.33 IGFBP.4 5,583.00 6,043.27 4,459.85 4,173.19 10,091.09 6,029.45 18,988.34 13,380.14 IGF-I 1.00 225 558.38 208.19 88.96 148.11 254.98 187.77 IL-10 158.00 422.93 1,222.75 1,096.30 722.93 564.32 1,625.71 1,129.96 IL-13 428.50 555.84 1,486.89 1,407.96 1,114.36 786.49 2,52242 1,807.27 IL-15 599.50 808.13 1,677.16 1,601.79 1,140M.9 858.67 2,495.04 1,981.62 IL-16 2.00 137.97 651.11 668.50 259.39 214.67 436.38 405.71 IL-1alpha 1,236.00 1,218.99 1,612.93 1,421.89 10,155.70 5,842.90 3,999.26 3,545.79 IL-1beta 1.00 1.13 352.05 312.08 117.99 75.93 316.59 278.30 IL-ira 33.00 25.91 302.68 198.48 142.34 93.74 354.23 581.75 IL-2 210.50 681.99 966.23 1,133.88 188.22 363.72 758.10 581.84 IL3 3,146.50 1,976.13 2,119.94 1,497.48 4,598.86 5,260.77 11,345.78 12,174.73 IL-4 17.50 74.34 625.42 638.94 357.72 239.04 804.30 673.95 IL-5 400.50 65.84 1,245.23 1,167.24 1,056.31 791.18 2,120.27 1,713.38 IL-6 828.50 516.98 1,121.19 842.07 7,377.28 9,527.88 9,774.82 9,991.93 IL-7 190.00 313.12 1,212.31 531.68 456.98 430.27 681.09 1,017.63 Leptin 900.50 617.79 1,234.39 1,091.65 2,999.42 2,016.38 7,238.71 4,886.99 LIGHT 10.50 232.02 1,081.04 888.10 619.92 453.71 1,346.78 1,108.17 MCP-1 242.50 282.71 1,022.03 1,076.03 572.17 500.56 2,015.89 1,507.53 MCP-2 24.00 109.25 909.63 1,152.46 129.23 351.53 694.78 694.07 MCP-3 1.00 168.38 1,184.61 1,255.50 401.73 169.67 701.62 583.42 MCP-4 7.50 46.74 1,380.51 1,606.86 123.61 61.87 231.02 276.62 M-CSF 1.00 63.64 852.63 867.83 629.09 269.04 740.98 684.01 MDC 1.00 2.25 269.36 280.41 157.32 52.50 280.6 132.44 MIG 291.00 226.39 1,113.16 1,137.26 272.50 486.52 617.77 1,222.17 MIP-1-delta 1.50 1.13 491.75 322.22 144.21 66.56 474.02 291.71 MIP-3-alpha 1.00 5.63 1,602.09 1,399.93 55.25 0.00 208.78 184.41 NAP-2 1.00 6.19 4;5.66 177.37 97.39 110.61 371.35 343.68 NT3 1.00 1.13 316.73 275.76 97.39 171.55 571.57 427.51 PARC 1.00 2.25 352.85 353.04 170.43 81.56 474.02 363.80 PDGF-B 437.00 1,644.99 517.84 597.56 4,729.96 8,521.09 2,635.37 2,005.09 RANTES 1.00 89.54 724.98 637.25 393.31 347.78 682.80 855.01 SCF 74.50 148.67 1,152.50 1,021.13 691.09 487.46 1,394.69 2,155.98 SDF-1 23.50 51.25 940.14 1,294.78 382.07 123.74 326.85 616.95 TARC 1.50 5.07 372.93 343.33 206.95 71.24 277.23 1,642.97 TGF-beta 1 362.00 230.33 1,426.67 1,240.30 752.90 740.56 1,827.65 1,849.18 TGF-beta 3 3.00 25.91 377.74 1,130.93 111.44 115.30 294.34 343.68 TNF-alpha 431.00 579.49 2,851.74 1,285.91 1,205.20 929.91 2,609.70 2,167.71 TNF-beta 241.00 342.40 1,049.33 1,026.62 675.17 671.19 1,701.01 1,637.94 Internal Control 18,6..7 1,642.67 18,642.67 18,642.67 18,642.67 18,642.67 18,642,67 18,642,67 Pos 60,794.83 48,106.85 35,652.42 47,391.58 94,013.71 90,889.16 141,321.30 149,125.43 NEG 11.13 5.53 11.22 30.45 24.93 17.75 36.22 3327 Acrp30 1,036.00 744.50 601.61 690.66 1,797.52 1,319.88 2,795.71 2,302.99 AgRP 11.00 153.99 77.82 89.00 378.17 195.90 651.26 482.21 Anglopoletln-2 28.50 10.43 357.97 771.04 6.82 632.60 65,969.24 71,664.21 Amphlregulln 17.50 16.44 73.63 154.62 250,52 151.01 619.07 782.60 Axt 637.50 79583 88.59 139.03 401.31 324.05 610.40 748.34 bFGF 59,820.50 54,057.29 11,722.95 21,398.82 7,948.03 4,993.83 1,226.99 1,241.09 291 291 a [0309] This Application is a divisional application of the present Applicant's Australian Patent Application No. 2007244675, the disclosures of which are all included herein by reference. [0310] Throughout this specification and the claims which follow, unless the context requires otherwise, the word "comprise", and variations such as "comprises" and "comprising", will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integers or steps. [0311] The reference to any prior art in this specification is not and should not be taken as an acknowledgement or any form of suggestion that the prior art forms part of the common general knowledge. 09/01/14,va 21353 p291a speci,a

Claims (19)

1. 2. A method for differentiating pluripotent stem cells into pancreatic endocrine cells comprising the steps of: a. differentiating pluripotent stem cells into definitive endoderm cells; b. differentiating definitive endoderm cells into pancreatic endoderm cells by treating the definitive endoderm with at least one fibroblast growth factor or with retinoic acid and at least one fibroblast growth factor; and c. differentiating the pancreatic endoderm cells into pancreatic endocrine cells by the pancreatic endoderm with a gamma secretase inhibitor, wherein the step of differentiating pluripotent stem cells into definitive endoderm cells comprises: culturing the pluripotent stem cells in a chemically-defined medium supplemented medium comprising medium supplemented with B27 and activin A; or culturing the pluripotent stem cells with activin A, a Wnt ligand, and a GSK-3B inhibitor in a first culture medium, followed by culturing the pluripotent stem cells with activin A in a second culture medium wherein the second culture medium does not contain a Wnt ligand.
2. 3. The method of claim 1 or claim 2, wherein the method further comprises culturing the pluripotent stem cells prior to differentiation.
3. 4. The method of any one of claims 1 to 3, wherein the at least one fibroblast growth factor is selected from the group consisting of FGF-2, FGF-4 and FGF-10.
4. 5. The method of any one of claims 1 to 4, wherein the gamma secretase inhibitor is I SBenzyl-4R-[ 1 -(1 S-carbamoyl-2-phenethylcarbamoyl)-1 S-3-methylbutylcarbam-oyl]-5 2Rhydrozy-5 phenylpentyl]carbamic Acid tert-butyl Ester (L-685,458).
5. 6. The method of claim 5, wherein the method comprises from about 0.1 pM to about 100 pm of L-685,458,
6. 7. The method of any one of claims 1 to 6, wherein step a. comprises: 293 a. plating the pluripotent stem cells on a tissue culture substrate coated with an extracellular matrix, and lacking a feeder cell layer; b. culturing the pluripotent stem cells with activin A, a Wnt ligand, and a GSK-3B inhibitor in a first culture medium; and c. culturing the pluripotent stem cells with activin A in a second culture medium wherein the second culture medium does not contain a Wnt ligand.
7. 8. The method of any one of claims 1 to 6, wherein step a. comprises: a. plating the pluripotent stem cells on a tissue culture substrate coated with an extracellular matrix, and lacking a feeder cell layer; b. culturing the pluripotent stem cells with activin A and a Wnt ligand in a first culture medium supplemented with B27; and c. culturing the pluripotent stem cells with activin A in a second culture medium supplemented with B27.
8. 9. The method of any one of claims 1 to 6, wherein the method comprises culturing the pluripotent stem cells in a chemically-defined supplemented medium comprising medium supplemented with B27 and activin A.
9. 10. The method of claim 9, wherein further comprising plating the pluripotent stem cells on a fibroblast feeder layer.
10. 11. The method of claim 9, wherein the method comprises culturing the culturing the cells in a chemically-defined medium comprising DMEM-Fl 2 supplemented with B27 and activin A.
11. 12. The method of claim 9, wherein B27 is used at a concentration of about 0.5% to about 1%.
12. 13. The method of claim 9, wherein B27 is used at a concentration of about 1%.
13. 14. The method of claim 9, wherein the medium is further supplemented with a Wnt ligand.
14. 15. The method of claim 14, wherein the Wnt ligand is Wnt-3a. 294
15. 16. The method of any one of claims I to 6, wherein the method comprises culturing the pluripotent stem cells with activin A, a Wnt ligand, and a GSK-3B inhibitor in a first culture medium, followed by culturing the pluripotent stem cells with activin A in a second culture medium wherein the second culture medium does not contain a Wnt ligand.
16. 17. The method of claim 16, wherein the Wnt ligand is Wnt-3a.
17. 18. The method of claim 16, wherein the method comprises from about I nM to about 1000 mM of the GSK-3B inhibitor.
18. 19. Cells expressing marker characteristics of the pancreatic endocrine lineage produced by the method of claim 1.
19. 20. Pancreatic endocrine cells produced by the method of claim 2. 295