Patent Publication Number: US-10316085-B2

Title: Therapeutic and diagnostic methods relating to cancer stem cells

Description:
RELATED APPLICATION 
     This application claims priority under 35 U.S.C. § 119 from U.S. provisional application Ser. No. 61/114,490, filed Nov. 14, 2008, the contents of which are incorporated herein in their entirety. 
    
    
     FEDERALLY SPONSORED RESEARCH 
     This Application is a continuation which claims priority under 35 U.S.C. § 120 of U.S. application Ser. No. 13/128,915, entitled “THERAPEUTIC AND DIAGNOSTIC METHODS RELATING TO CANCER STEM CELLS” filed on Aug. 9, 2011, which is a National Stage Application of PCT International Application PCT/US20094/006089, entitled “THERAPEUTIC AND DIAGNOSTIC METHODS RELATING TO CANCER STEM CELLS”, with an international filing date of Nov. 13, 2009, which claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Application Ser. No. 61/114,490, entitled “THERAPEUTIC AND DIAGNOSTIC METHODS RELATING TO CANCER STEM CELLS” filed on Nov. 14, 2008, which are herein incorporated by reference in their entirety. 
    
    
     FIELD OF INVENTION 
     The present invention relates in part to methods for treating individuals having cancer. The methods involve modulating, e.g., inducing or inhibiting, the activity of genes that are deregulated in cancer stem cells. In some aspects, cell surface genes that are upregulated in cancer stem cells are targeted for selective isolation, detection, or killing of cancer stem cells in melanoma. Other aspects of the invention relate to reagents, arrays, compositions, and kits that are useful for diagnosing and treating cancer. 
     BACKGROUND OF INVENTION 
     Self-renewing cancer stem cells (CSCs) initiate tumours and drive malignant progression by generating and supporting replication of more differentiated non-stem cell progeny. (M. Al-Hajj, et al., Proc Natl Acad Sci USA 100 (7), 3983 (2003); D. Bonnet and J. E. Dick, Nat Med 3 (7), 730 (1997); C. A. O&#39;Brien, et al., Nature 445 (7123), 106 (2007); L. Ricci-Vitiani, et al., Nature 445 (7123), 111 (2007); S. K. Singh, et al., Nature 432 (7015), 396 (2004); T. Schatton and M. H. Frank, Pigment cell &amp; melanoma research 21 (1), 39 (2008)). The mechanisms by which CSCs cause tumour formation and growth and the potential role of CSC-specific differentiation plasticity in tumourigenicity are currently unknown. We recently identified a subpopulation of CSC based on expression of the chemoresistance mediator ABCB5 (ATP-binding cassette, sub-family B (MDR/TAP), member 5) (N. Y. Frank, A et al., Cancer Res 65 (10), 4320 (2005); Y. Huang, et al., Cancer Res 64 (12), 4294 (2004)) within human malignant melanoma (T. Schatton, et al., Nature 451 (7176), 345 (2008)), a highly aggressive and drug-resistant cancer. (T. Schatton and M. H. Frank, Pigment cell &amp; melanoma research 21 (1), 39 (2008); L. Chin, L. A. Garraway, and D. E. Fisher, Genes Dev 20 (16), 2149 (2006).) ABCB5 +  Malignant Melanoma Initiating Cells (MMIC) correlate with clinical disease progression and can be specifically targeted to abrogate tumour growth. (T. Schatton, et al., Nature 451 (7176), 345 (2008)). Consistent with these findings, the ABCB5 gene is also preferentially expressed by in vitro self-renewing melanoma minority populations (G. I. Keshet, et al., Biochem Biophys Res Commun 368 (4), 930 (2008)) and by melanoma cell lines of metastatic as opposed to primary, radial growth phase tumour origin (J. F. Sousa and E. M. Espreafico, BMC cancer 8, 19 (2008)). 
     SUMMARY OF INVENTION 
     The present invention relates in part to the discovery that a number of genes (referred to herein as CSC-associated genes) are deregulated in cancer stem cells. In some aspects, the invention relates to diagnostic arrays and methods for detecting cancer in an individual based on the expression of CSC-associated genes. In other aspects, the invention relates to methods useful for treating individuals having melanoma based on modulating the expression and/or activity of CSC-associated genes. Compositions and kits that are useful for the foregoing methods are also disclosed. 
     The invention, in some aspects, provides methods for diagnosing cancer in an individual. In some aspects, the methods involve determining an expression level of a cancer stem cell (CSC)-associated gene in Table 5 in a test sample from the individual and comparing the expression level of the CSC-associated gene to a reference value, wherein results of the comparison are diagnostic of cancer. In some embodiments, the cancer is melanoma, breast cancer, prostate cancer, colon cancer or renal cancer. In some embodiments, the test sample is a tissue biopsy. In some embodiments, the test sample is a skin biopsy. In some embodiments, the test sample is a sample of the cancer, such as a tumor biopsy. In some embodiments, the methods involve updating a patient record for the individual to indicate the diagnostic result of the comparison. In some embodiments, determining comprises detecting in the test sample a mRNA that is encoded by the CSC-associated gene. In some embodiments, determining comprises detecting in the test sample a polypeptide that is encoded by the CSC-associated gene. In certain embodiments, detecting comprises nucleic acid hybridization or nucleic acid amplification. In specific embodiments, the nucleic acid amplification is real-time RT-PCR or RT-PCR. In one embodiment, the nucleic acid hybridization is performed using a nucleic acid array. In certain other embodiments, detecting comprises immunodetection of the polypeptide. In one embodiment, the immunodetection comprises an Enzyme-Linked Immunosorbent Assay (ELISA). In one embodiment, the immunodetection comprises an antibody array. In one embodiment, the immunodetection comprises immunohistochemistry. 
     In some embodiments of the methods, the reference value is the expression level of the CSC-associated gene in a non-cancer reference sample, and if the expression level of the CSC-associated gene in the test sample is about equal to the expression level of the CSC-associated gene in the non-cancer reference sample, then the comparison does not indicate cancer. 
     In some embodiments of the methods, the reference value is the expression level of the CSC-associated gene in a cancer reference sample, and if the expression level of the CSC-associated gene is about equal to the expression level of the CSC-associated gene in the cancer reference sample, then the comparison indicates cancer. 
     In some embodiments of the methods, the CSC-associated gene is in Table 1 or 8 and the reference value is the expression level of the CSC-associated gene in a non-cancer reference sample, and if the expression level of the CSC-associated gene in the test sample is significantly higher than the expression level of the CSC-associated gene in the non-cancer reference sample, the comparison indicates cancer. 
     In some embodiments of the methods, the CSC-associated gene is in Table 1 or 8 and the reference value is the expression level of the CSC-associated gene in a cancer reference sample, and if the expression level of the CSC-associated gene in the test sample is significantly lower than the expression level of the CSC-associated gene in the cancer reference sample, the comparison does not indicate cancer. 
     In some embodiments of the methods, the CSC-associated gene is in Table 1 or 8 and the reference value is the expression level of the CSC-associated gene in a non-cancer reference sample, and if the expression level of the CSC-associated gene in the test sample is at least 10% higher than the expression level of the CSC-associated gene in the non-cancer reference sample, the comparison indicates cancer. 
     In some embodiments of the methods, the CSC-associated gene is in Table 2 or 7 and the reference value is the expression level of the CSC-associated gene in a non-cancer reference sample, and if the expression level of the CSC-associated gene in the test sample is significantly lower than the expression level of the CSC-associated gene in the non-cancer reference sample, the comparison indicates cancer. 
     In some embodiments of the methods, the CSC-associated gene is in Table 2 or 7 and the reference value is the expression level of the CSC-associated gene in a cancer reference sample, and if the expression level of the CSC-associated gene in the test sample is significantly higher than the expression level of the CSC-associated gene in the cancer reference sample, the comparison does not indicate cancer. 
     In some embodiments of the methods, the CSC-associated gene is in Table 2 or 7 and the reference value is the expression level of the CSC-associated gene in a non-cancer reference sample, and if the expression level of the CSC-associated gene in the test sample is at least 10% lower than the expression level of the CSC-associated gene in the non-cancer reference sample, the comparison indicates cancer. 
     The invention, in some aspects, provides methods for isolating a cancer stem cell. In some aspects, the methods involve contacting a sample with an agent that binds a polypeptide, which is encoded by a CSC-associated gene in Table 4 and expressed on the surface of the cancer stem cell, and isolating the agent from the sample. If the sample contains the cancer stem cell, the agent binds to the polypeptide on the surface of the cancer stem cell such that isolation of the agent from the sample results in isolation of the cancer stem cell. In some embodiments, the CSC-associated gene is selected from the group consisting of: ANK2, NCKAP1L, PTPRE, PTPRS, SBF1, SCN3A, SGCA, SGCB, SLC2A11, SLC2A8, SLC4A1, STX3, and TBC1D8. In some embodiments, the agent is an isolated peptide that specifically binds the polypeptide on the surface of the cancer stem cell. In certain embodiments, the isolated peptide is an antibody or antigen-binding fragment. In specific embodiments, the antibody or antigen-binding fragment is a monoclonal antibody, polyclonal antibody, human antibody, chimeric antibody, humanized antibody, single-chain antibody, F(ab′) 2 , Fab, Fd, Fv, or single-chain Fv fragment. In some embodiments, the isolated peptide is bound to a solid support. In some embodiments, the isolated peptide is conjugated to a detectable label. In some embodiments, the detectable label is a fluorophore which may be selected from: FITC, TRITC, Cy3, Cy5, Alexa Fluorescent Dyes, and Quantum Dots. In some embodiments, the isolating comprises performing fluorescent activated cell sorting to isolate a cancer stem cell bound to a detectable label. In some embodiments, the cancer stem cell is from a melanoma, breast cancer, prostate cancer, colon cancer or renal cancer. 
     The invention, in some aspects, provides methods for treating an individual having, or at risk of having, cancer. In some aspects, the methods involve administering a therapeutically effective amount of a composition that induces the expression of a CSC-associated gene selected from the group set forth in Table 2 or 7. In some embodiments, the cancer is melanoma, breast cancer, prostate cancer, colon cancer or renal cancer. 
     In some embodiments, the composition that induces the expression of a CSC-associated gene comprises an isolated plasmid that expresses the CSC-associated gene. In some embodiments, the isolated plasmid is in a virus capable of infecting the individual. In certain embodiments, the virus is selected from adenovirus, retrovirus, lentivirus, and adeno-associated virus. In some embodiments, the isolated plasmid comprises a cancer specific promoter operably linked to the CSC-associated gene. 
     The invention, in other aspects, provides methods for treating an individual having, or at risk of having, cancer that involve administering a therapeutically effective amount of a composition that targets a product of a CSC-associated gene selected from the group set forth in Table 1 or 8. In some embodiments, the cancer is melanoma, breast cancer, prostate cancer, colon cancer or renal cancer. In some embodiments, the CSC-associated gene is selected from the group set forth in Table 4. In certain embodiments, the CSC-associated gene is selected from the group consisting of: ANK2, NCKAP1L, PTPRE, PTPRS, SBF1, SCN3A, SGCA, SGCB, SLC2A11, SLC2A8, SLC4A1, STX3, and TBC1D8. 
     In some embodiments, the composition that targets a product of a CSC-associated gene comprises a small interfering nucleic acid that inhibits expression of the CSC-associated gene. In some embodiments, the composition comprises an isolated plasmid that expresses the small interfering nucleic acid. In certain embodiments, the plasmid is in a virus. In specific embodiments, the virus is selected from adenovirus, retrovirus, lentivirus, and adeno-associated virus. In certain embodiments, the isolated plasmid comprises a cancer-specific promoter operably linked to a gene encoding the small interfering nucleic acid. 
     In some embodiments, the composition that targets a product (e.g., protein or RNA) of a CSC-associated gene comprises an isolated molecule that selectively binds to a polypeptide encoded by the CSC-associated gene. In certain embodiments, the isolated molecule is conjugated to a therapeutic agent. In specific embodiments, the isolated molecule is an antibody or antigen-binding fragment. In particular embodiments, the antibody or antigen-binding fragment is a monoclonal antibody, polyclonal antibody, human antibody, chimeric antibody, humanized antibody, a single-chain antibody, F(ab′) 2 , Fab, Fd, Fv, or single-chain Fv fragment. In specific embodiments, the therapeutic agent is selected from: a toxin, a small-interfering nucleic acid, and a chemotherapeutic agent. In one embodiment, the toxin is a radioisotope. In particular embodiments, the radioisotope is selected from the group consisting of:  225 Ac,  211 At,  212 Bi,  213 Bi,  186 Rh,  188 Rh,  177 Lu,  90 Y,  131 I,  67 Cu,  125 I,  123 I,  77 Br,  153 Sm,  166 Bo,  64 Cu,  212 Pb,  224 Ra and  223 Ra. In some embodiments, the therapeutic agent is a small interfering nucleic acid that inhibits expression of a CSC-associated gene. In some embodiments, the isolated molecule binds to the polypeptide and enters an intracellular compartment of a cancer stem cell of the cancer. 
     In some embodiments, the treatment methods involve determining the expression level of the CSC-associated gene in the individual. In certain embodiments, the methods involve comparing the expression level of the CSC-associated gene to a reference value, wherein results of the comparison are diagnostic of cancer in the individual. In specific embodiments, if the comparison results in a diagnosis of cancer in the individual, the administering is performed. In one embodiment, the determining and the comparing are repeated at one or more intervals after the administering. In some embodiments, the administering is orally, intravenously, intrapleurally, intranasally, intramuscularly, subcutaneously, intraperitoneally, or as an aerosol. 
     The invention, in some aspects, provides methods of delivering a therapeutic agent to a cancer stem cell that involve contacting a cancer stem cell with an isolated molecule, which selectively binds to a polypeptide encoded by a CSC-associated gene selected from the group set forth in Table 4 and which is conjugated to a therapeutic agent, in an effective amount to deliver the therapeutic agent to the cancer stem cell. In some embodiments, the CSC-associated gene is selected from the group consisting of: ANK2, NCKAP1L, PTPRE, PTPRS, SBF1, SCN3A, SGCA, SGCB, SLC2A11, SLC2A8, SLC4A1, STX3, and TBC1D8. In some embodiments, the isolated molecule is an antibody or antigen-binding fragment that selectively binds the polypeptide. In some embodiments, the therapeutic agent is selected from: a toxin, a small-interfering nucleic acid, and a chemotherapeutic agent. In one embodiment, the toxin is a radioisotope. In particular embodiments, the radioisotope is selected from the group consisting of:  225 Ac,  211 At,  212 Bi,  213 Bi,  186 Rh,  188 Rh,  177 Lu,  90 Y,  131 I,  67 Cu,  125 I,  123 I,  77 Br,  153 Sm,  166 Bo,  64 Cu,  212 Pb,  224 Ra and  223 Ra. In some embodiments, the therapeutic agent is a small interfering nucleic acid that inhibits expression of a CSC-associated gene. In some embodiments, the cancer stem cell is in vitro. In other embodiments, the cancer stem cell is in vivo. 
     In some aspects, the invention provides nucleic acid arrays consisting essentially of at least 2, at least 5, at least 10, at least 20, at least 50, at least 100, at least 200, at least 300, or more CSC-associated genes set forth in Table 5. 
     In some aspects, the invention provides polypeptide arrays consisting essentially of at least 2, at least 5, at least 10, at least 20, at least 50, at least 100, or more polypeptides or immunogenic fragments thereof encoded by CSC-associated genes set forth in Table 1 or 8. 
     In some aspects, the invention provides antibody arrays consisting essentially of at least 2 or more different antibodies or antigen-binding fragments that selectively bind polypeptides encoded by CSC-associated genes set forth in Table 1 or 8. 
     In some aspects, the invention provides methods for stratifying a population comprising individuals having cancer. The methods involve determining expression levels of at least 2, at least 5, at least 10, at least 20, at least 50, at least 100, at least 200, at least 300, or more CSC-associated genes set forth in Table 5 and stratifying the population based on the expression levels. 
     In some aspects, the invention provides an isolated molecule that selectively binds to a polypeptide encoded by a CSC-associated gene set forth in Table 4, and that is conjugated to a therapeutic agent. In some embodiments, the CSC-associated gene is selected from the group consisting of: ANK2, NCKAP1L, PTPRE, PTPRS, SBF1, SCN3A, SGCA, SGCB, SLC2A11, SLC2A8, SLC4A1, STX3, and TBC1D8. In some embodiments, the therapeutic agent is selected from: a toxin, a small-interfering nucleic acid, and a chemotherapeutic agent. 
     In certain embodiments, the isolated molecule is an antibody or antigen-binding fragment. In certain embodiments, the antibody or antigen-binding fragment is a monoclonal antibody, polyclonal antibody, human antibody, chimeric antibody, humanized antibody, single-chain antibody, a F(ab′) 2 , Fab, Fd, or Fv fragment. In certain embodiments, the isolated molecule is an isolated receptor ligand of the polypeptide. 
     The invention, in some aspects, provides compositions comprising any of the foregoing isolated molecules. In some embodiments, the compositions include a pharmaceutically acceptable carrier. 
     The invention, in some aspects, provides pharmaceutical kits that include a container housing any of the foregoing compositions and instructions for administering the composition to an individual having cancer. 
     Use of a composition of the invention for treating cancer is also provided as an aspect of the invention. 
     A method for manufacturing a medicament of a composition of the invention for treating cancer is also provided. 
     Each of the limitations of the invention can encompass various embodiments of the invention. It is, therefore, anticipated that each of the limitations of the invention involving any one element or combinations of elements can be included in each aspect of the invention. This invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced or of being carried out in various ways. Also, the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. The use of “including,” “comprising,” or “having,” “containing,” “involving,” and variations thereof herein, is meant to encompass the items listed thereafter and equivalents thereof as well as additional items. 
    
    
     
       BRIEF DESCRIPTION OF DRAWINGS 
         FIGS. 1A-1I  depict an analysis of vasculogenic/angiogenic pathways in human melanoma.  FIG. 1 a   . is a graphical representation of pathway activation across ABCB5 +  MMIC. Genes represented by nodes (dark gray circles, TRIO, MET, FLT1, PSEN1, NRP2, RHOA, PTK2, PIP5K3, KIAAl267, MLL, GABPA, ETS1, and CHD8) are overexpressed in ABCB5 +  relative to ABCB5 −  human melanoma cells and those represented by black nodes are expressed at lower levels, respectively. Black lines between genes show known interactions. Known gene functions in vasculogenesis and angiogenesis, and genes known as relevant drug targets are annotated (dark gray lines). Gene relationships and figure layout are based on Ingenuity Pathway Analysis and references are provided elsewhere in the text.  FIG. 1 b   . shows detection of vasculogenic/angiogenic pathway members by RT-PCR in ABCB5 +  MMIC.  FIG. 1 c   . shows FLT1 (VEGFR-1) protein expression on ABCB5 +  MMIC (top) and ABCB5 −  melanoma cells (bottom) as determined by dual color flow cytometry using ABCB5 phenotype-specific cell gating, with mean percentages (mean±s.e.m., n=6 replicate experiments) shown on the right.  FIG. 1 d   . depicts representative immunofluorescence staining for CD144 expression (Texas red staining) by ABCB5 +  MMIC or ABCB5 −  melanoma cell subpopulations prior to (t=0 h) and upon 48 h of culture (t=48 h) in the presence of 100 ng/ml VEGF 11 , with nuclei counterstained with DAPI. Mean percentages (mean±s.e.m., n=3 replicate experiments) of cells staining positively for CD144 in each sample are shown on the right.  FIG. 1 e   . shows representative immunofluorescence staining for CD144 expression (Texas red staining) by melanoma cells cultured for 48 h (t=48 h) in the presence of 100 ng/ml VEGF as in above, but in the presence or absence of anti-FLT1 (VEGFR-1) blocking mAb or isotype control mAb. Nuclei are counterstained with DAPI. Mean percentages (mean±s.e.m., n=3 replicate experiments) of cells staining positively for CD144 in each sample are shown in the far right panel.  FIG. 1 f   . shows tube formation detected by phase contrast light microscopy of melanoma cells cultured for 24 h (t=24 h) in the presence of 100 ng/ml VEGF and the presence or absence of anti-FLT1 (VEGFR-1) blocking mAb or isotype control mAb. Number of tubes/microscopy field (mean±s.e.m., n=3 replicate experiments) and tube length (μm) (mean±s.e.m., n=3 replicate experiments) are illustrated for the different experimental conditions on the far right panels, respectively.  FIG. 1 g   . shows the adipogenic differentiation potential of ABCB5 +  and ABCB5 −  human melanoma cells (Oil Red O staining, nuclei are counterstained with hematoxylin).  FIG. 1 h   . shows the osteogenic differentiation potential of ABCB5 +  and ABCB5 −  human melanoma cells (Alizarin Red staining).  FIG. 1 i    shows the myogenic differentiation potential of ABCB5 +  and ABCB5 −  human melanoma cells. Absence of myogenin staining (FITC, green) is detected in ABCB5 +  or ABCB5 −  human melanoma cells (nuclei are counterstained with DAPI). 
         FIGS. 2A-2K  depict an analysis of MMIC-driven in vivo vasculogenesis.  FIG. 2 a   . shows conventionally-stained (H&amp;E) sections of human melanoma growing at melanoma cell injection site within human dermis of skin xenograft to NOD/SCID mouse.  FIG. 2 b   . shows immunohistochemistry for human CD31 indicating angiogenic response at perimeter of melanoma within human xenograft; broken line represents interface of tumour nodule with dermal connective tissue.  FIG. 2 c   . shows PAS (with diastase) immunochemical staining of CD31-negative interior regions of melanoma xenograft revealing numerous anastomosing channels (inset is laminin immunohistochemistry indicating identical pattern).  FIG. 2 d   . shows transmission electron micrographs of interior regions of melanoma xenograft; lumenal spaces containing blood products (erythrocytes) are lined by melanoma cells and associated basement membrane-like extracellular matrix.  FIG. 2 e   . shows the interior zone of melanoma xenograft derived from cells expressing GFP transgene and immunohistochemically stained for endothelial marker CD144 (FAST RED Chromogen (SIGNET) from Covance Research Products, Inc); CD144 expression is confined to cells forming lumen-like spaces lined by cells that co-express GFP and CD144 (indicated by dual staining).  FIGS. 2 f  and  g   . show low (f) and high (g) magnifications of immunohistochemistry for ABCB5 protein; reactivity is restricted to anastomosing channels identical to those seen in panel c. The inset in panel f depicts similar formation of ABCB5-reactive channels in a patient-derived melanoma biopsy.  FIG. 2 h   . depicts in situ hybridization for ABCB5 mRNA revealing a channel pattern corresponding to that of ABCB5 protein expression (compare with panel f; inset is sense control).  FIG. 2 i   . shows the detection of anti-ABCB5 mAb using anti-mouse Ig immunohistochemistry in melanoma xenografts after intravenous administration in vivo; note localization to channels (inset represents anti-mouse Ig staining after intravenous administration of irrelevant isotype-matched control mAb).  FIG. 2 j   . shows dual-labeling immunofluorescence microscopy for ABCB5 (left panel), CD144 (middle panel), and ABCB5 &amp; CD144 (right panel).  FIG. 2 k    shows dual-labeling immunofluorescence microscopy for ABCB5 (left panel), TIE-1 (middle panel), and ABCB5 &amp; TIE-1 (right panel). 
         FIGS. 3A-3F  depict the interdependency of MMIC-driven vasculogenesis and tumourigenesis.  FIG. 3 a   . shows representative flow cytometric ABCB5 expression or control staining (FITC, F11) plotted against forward scatter (FSC) for human A375, MUM-2B, and MUM-2C melanoma cell inocula.  FIG. 3 b   . shows representative histologic sections of melanomas that developed from three unsegregated and ABCB5-depleted melanoma cell lines injected intradermally into human skin xenografts.  FIG. 3 c   . shows histologically determined tumour formation rate (%) 3 weeks following intradermal transplantation of unsegregated vs. ABCB5 + -depleted human A375, MUM-2B or MUM-2C melanoma cells (2×10 6 /inoculum) into human skin/Rag2 −/−  chimeric mice (n=5, respectively).  FIG. 2 d   . shows histological tumour volumes (mean±s.e.m.) 3 weeks following intradermal transplantation of unsegregated vs. ABCB5 + -depleted human A375, MUM-2B or MUM-2C melanoma cells (2×10 6 /inoculum) into human skin/Rag2 −/−  chimeric mice.  FIG. 3 e    shows immunohistochemistry for laminin revealing extent of channel formation in melanomas that developed from unsegregated or ABCB5 + -depleted melanoma cell inocula derived from A375, MUM-2B or MUM-2C lines injected intradermally into human skin xenografts (arrows=necrosis).  FIG. 3 f    depicts image analysis of laminin immunoreactivity for melanomas derived from unsegregated and ABCB5 + -depleted cell inocula; y-axis is percent of pixelated area with reactivity (mean±s.e.m.); solid bar represents tumours derived from unsegregated melanoma cells, open bars represent tumours derived from ABCB5 + -depleted cells (A375, P&lt;0.0032; MUM-2B, P&lt;0.0005; MUM-2C, P&lt;0.0059). 
         FIGS. 4A and 4B  depict an analysis of the correlation of ABCB5 protein and mRNA expression across human melanoma cell lines.  FIG. 4 a   . shows western blots of ABCB5 and tubulin expression of a panel of human melanoma cell lines.  FIG. 4 b    shows relative ABCB5 mRNA expression (log 2 ) in a panel of human melanoma cell lines plotted against ABCB5 protein expression as determined by ratios of ABCB5 89 kD western blot band intensity and tubulin western blot band intensity for each human melanoma cell line. Data points in  FIG. 4 b    are: 1, SK-MEL-2; 2, SK-MEL-5; 3, SK-MEL-28; 4, MDA-MB-435; 5, UACC-62; 6, UACC-257; 7, M14; 8, MALME-3M. r, Spearman Rank Correlation r (corrected for ties). 
     
    
    
     DETAILED DESCRIPTION 
     The present invention relates in part to the discovery that numerous CSC-associated genes have altered expression or function in cancer stem cells, e.g., melanoma stem cells. In some aspects, the invention relates to diagnostic arrays and methods for detecting cancer, e.g., melanoma, in an individual based on the expression of CSC-associated genes. In other aspects, the invention relates to compositions, kits, and methods useful for treating individuals having cancer. In some embodiments, the treatment methods involve modulating e.g., inducing or inhibiting, the activity of CSC-associated genes. The CSC-associated genes can be modulated by any one of a number of ways known in the art and described herein e.g., overexpression, RNAi-based inhibition, etc. In some cases, the CSC-associated genes encode cell surface proteins which, when upregulated in cancer stem cells, may be selectively targeted for isolating, e.g., by flow cytometry, identifying, e.g., by immunolabeling, and killing of cancer stem cells, e.g., melanoma stem cells. 
     The mechanism by which CSCs cause tumor formation and growth and the potential role of CSC-specific differentiation plasticity in tumorigenicity are currently unknown. It has been demonstrated according to the invention that CSC play an important role in providing nutritional support to growing tumors. For instance we have shown herein (Examples) a selective capacity of ABCB5 +  malignant melanoma initiating cells (MMIC) 3  to undergo vasculogenic differentiation and to generate blood-perfused vessel-like channels in vivo. A repertoire of genes differentially expressed in MMIC compared to tumour bulk populations were identified by microarray analyses on purified ABCB5 +  and ABCB5 −  cell subsets derived from the established human melanoma cell lines and from three separate patient-derived melanoma specimens. Using this approach, 399 genes were identified that were differentially expressed between ABCB5 +  MMIC and ABCB5 −  melanoma bulk populations. The genes, which are outlined in Tables 1-8, are referred to herein as CSC-associated genes. Of the CSC-associated genes, 265 were upregulated (Table 1; Table 1 includes Table 1.1 and Table 1.2) and 150 were downregulated (Table 2). For certain CSC-associated genes, subcellular location, e.g., plasma membrane, nucleus, etc., gene type, e.g., enzyme, complex, transporter, etc., and drugs that affect, e.g., target, their activity are identified (Table 3). A summary of those annotations and networks is provide in Table 3. Genes that function share a common pathway have a common “network”) designation in Table 3. Some CSC-associated genes, e.g., those which have “plasma membrane” annotations, encode proteins that are associated with the cell surface. Such cell surface proteins are useful in a variety ways. For example, cell surface proteins that are upregulated in cancer stem cells, may be selectively targeted, e.g., using the methods disclosed herein, for isolating, identifying, and killing of cancer stem cells. A listing of exemplary cell surface proteins encoded by CSC-associated genes is provided in Table 4. 
     
       
         
           
               
             
               
                 TABLE 1.1 
               
             
            
               
                   
               
               
                 Upregulated CSC-associated genes (p &lt; 0.05) 
               
            
           
           
               
               
               
               
            
               
                   
                   
                   
                 Fold 
               
               
                   
                 GENESYMBOL 
                 ID 
                 Change 
               
               
                   
                   
               
            
           
           
               
               
               
               
            
               
                   
                 HECW1 
                 237295_at 
                 11.843 
               
               
                   
                 RP11-139H14.4 
                 1569124_at 
                 11.472 
               
               
                   
                 CDC16 
                 242359_at 
                 6.261 
               
               
                   
                 ANK2 
                 202921_s_at 
                 4.162 
               
               
                   
                 LOC146325 
                 1553826_a_at 
                 3.943 
               
               
                   
                 UGT1A6 
                 206094_x_at 
                 3.86 
               
               
                   
                 C12ORF51 
                 1557529_at 
                 3.632 
               
               
                   
                 SNRPA1 
                 242146_at 
                 3.54 
               
               
                   
                 PDE4B 
                 215671_at 
                 3.457 
               
               
                   
                 PAPD4 
                 222282_at 
                 3.39 
               
               
                   
                 ZNF536 
                 233890_at 
                 3.303 
               
               
                   
                 KSR2 
                 230551_at 
                 3.211 
               
               
                   
                 BUB1 
                 233445_at 
                 3.209 
               
               
                   
                 ZNF292 
                 236435_at 
                 3.201 
               
               
                   
                 CABIN1 
                 1557581_x_at 
                 3.052 
               
               
                   
                 SDAD1 
                 242190_at 
                 3.009 
               
               
                   
                 ASCC3L1 
                 214982_at 
                 3.009 
               
               
                   
                 ZNF224 
                 216983_s_at 
                 2.986 
               
               
                   
                 KIDINS220 
                 1557246_at 
                 2.97 
               
               
                   
                 WIPF2 
                 216006_at 
                 2.916 
               
               
                   
                 C12ORF51 
                 230216_at 
                 2.874 
               
               
                   
                 VPS37B 
                 236889_at 
                 2.85 
               
               
                   
                 NARG1 
                 1556381_at 
                 2.827 
               
               
                   
                 LOC145757 
                 1558649_at 
                 2.779 
               
               
                   
                 SDCCAG8 
                 243963_at 
                 2.67 
               
               
                   
                 ZNF154 
                 242170_at 
                 2.667 
               
               
                   
                 ZFR 
                 238970_at 
                 2.655 
               
               
                   
                 TRPV1 
                 1556229_at 
                 2.636 
               
               
                   
                 ANAPC5 
                 235926_at 
                 2.631 
               
               
                   
                 CUL4A 
                 232466_at 
                 2.607 
               
               
                   
                 TRIO 
                 240773_at 
                 2.607 
               
               
                   
                 LOC283888 
                 1559443_s_at 
                 2.56 
               
               
                   
                 RAB11FIP3 
                 228613_at 
                 2.546 
               
               
                   
                 PTK2 
                 234211_at 
                 2.539 
               
               
                   
                 MYO10 
                 243159_x_at 
                 2.528 
               
               
                   
                 NAT8B 
                 206964_at 
                 2.513 
               
               
                   
                 CDC14B 
                 234605_at 
                 2.512 
               
               
                   
                 TRIM33 
                 239716_at 
                 2.496 
               
               
                   
                 SF1 
                 210172_at 
                 2.452 
               
               
                   
                 SGCA 
                 1562729_at 
                 2.395 
               
               
                   
                 LOC285147 
                 236166_at 
                 2.377 
               
               
                   
                 N4BP2L2 
                 242576_x_at 
                 2.349 
               
               
                   
                 HNRPH1 
                 213472_at 
                 2.332 
               
               
                   
                 FLJ10357 
                 241627_x_at 
                 2.31 
               
               
                   
                 PHF20L1 
                 219606_at 
                 2.3 
               
               
                   
                 ANKRD28 
                 241063_at 
                 2.297 
               
               
                   
                 TRNT1 
                 243236_at 
                 2.295 
               
               
                   
                 GOLGA8A 
                 213650_at 
                 2.289 
               
               
                   
                 KIAA1618 
                 231956_at 
                 2.27 
               
               
                   
                 RBM5 
                 209936_at 
                 2.249 
               
               
                   
                 LOC645513 
                 239556_at 
                 2.24 
               
               
                   
                 LOC729397 
                 236899_at 
                 2.231 
               
               
                   
                 PABPN1 
                 213046_at 
                 2.228 
               
               
                   
                 SVIL 
                 215279_at 
                 2.228 
               
               
                   
                 PIP5K3 
                 1557719_at 
                 2.227 
               
               
                   
                 STRAP 
                 1558002_at 
                 2.189 
               
               
                   
                 KIAA2013 
                 1555933_at 
                 2.18 
               
               
                   
                 NUPL1 
                 241425_at 
                 2.179 
               
               
                   
                 IFNGR1 
                 242903_at 
                 2.171 
               
               
                   
                 AKAP9 
                 215483_at 
                 2.168 
               
               
                   
                 LOC254128 
                 1557059_at 
                 2.164 
               
               
                   
                 IRS2 
                 236338_at 
                 2.162 
               
               
                   
                 RHOA 
                 240337_at 
                 2.143 
               
               
                   
                 JARID2 
                 232835_at 
                 2.139 
               
               
                   
                 GPD2 
                 243598_at 
                 2.13 
               
               
                   
                 RADIL 
                 223693_s_at 
                 2.126 
               
               
                   
                 CROP 
                 242389_at 
                 2.121 
               
               
                   
                 EXT1 
                 242126_at 
                 2.116 
               
               
                   
                 XRCC5 
                 232633_at 
                 2.106 
               
               
                   
                 PDXDC1 
                 1560014_s_at 
                 2.105 
               
               
                   
                 MEF2C 
                 236395_at 
                 2.104 
               
               
                   
                 ZNF567 
                 242429_at 
                 2.103 
               
               
                   
                 ZNF337 
                 1565614_at 
                 2.096 
               
               
                   
                 TTLL4 
                 1557611_at 
                 2.092 
               
               
                   
                 FUBP1 
                 240307_at 
                 2.087 
               
               
                   
                 NPTN 
                 228723_at 
                 2.086 
               
               
                   
                 TPM4 
                 235094_at 
                 2.079 
               
               
                   
                 NCKAP1L 
                 209734_at 
                 2.071 
               
               
                   
                 KRTAP19-1 
                 1556410_a_at 
                 2.07 
               
               
                   
                 SLC30A9 
                 237051_at 
                 2.063 
               
               
                   
                 HDAC3 
                 240482_at 
                 2.062 
               
               
                   
                 C10ORF18 
                 244165_at 
                 2.046 
               
               
                   
                 SMA4 
                 238446_at 
                 2.035 
               
               
                   
                 GBF1 
                 233114_at 
                 2.03 
               
               
                   
                 GABPA 
                 243498_at 
                 2.03 
               
               
                   
                 SFRS15 
                 243759_at 
                 2.028 
               
               
                   
                 CREB3L2 
                 237952_at 
                 2.013 
               
               
                   
                 SLC2A8 
                 239426_at 
                 2.012 
               
               
                   
                 N4BP2L1 
                 213375_s_at 
                 2.01 
               
               
                   
                 IDS 
                 1559136_s_at 
                 2.001 
               
               
                   
                 COBRA1 
                 1556434_at 
                 1.985 
               
               
                   
                 TXNL1 
                 243664_at 
                 1.98 
               
               
                   
                 LOC388135 
                 230475_at 
                 1.979 
               
               
                   
                 MTUS1 
                 239576_at 
                 1.975 
               
               
                   
                 TAF15 
                 227891_s_at 
                 1.971 
               
               
                   
                 HNRPD 
                 241702_at 
                 1.962 
               
               
                   
                 TRIM46 
                 238147_at 
                 1.96 
               
               
                   
                 NBR1 
                 1568856_at 
                 1.957 
               
               
                   
                 WDR68 
                 233782_at 
                 1.924 
               
               
                   
                 HNRPD 
                 235999_at 
                 1.92 
               
               
                   
                 BLID 
                 239672_at 
                 1.91 
               
               
                   
                 LOC145786 
                 229178_at 
                 1.907 
               
               
                   
                 HOXD3 
                 206601_s_at 
                 1.897 
               
               
                   
                 AOC3 
                 204894_s_at 
                 1.894 
               
               
                   
                 PRPF38B 
                 230270_at 
                 1.888 
               
               
                   
                 SLC20A1 
                 230494_at 
                 1.884 
               
               
                   
                 SEC16B 
                 1552880_at 
                 1.877 
               
               
                   
                 FLT1 
                 232809_s_at 
                 1.861 
               
               
                   
                 HUWE1 
                 214673_s_at 
                 1.858 
               
               
                   
                 BUB1 
                 216277_at 
                 1.856 
               
               
                   
                 GPR135 
                 241085_at 
                 1.851 
               
               
                   
                 PSEN1 
                 242875_at 
                 1.851 
               
               
                   
                 KIAA0907 
                 230028_at 
                 1.83 
               
               
                   
                 POLR2J2 
                 1552622_s_at 
                 1.828 
               
               
                   
                 SFRS15 
                 222311_s_at 
                 1.818 
               
               
                   
                 CBS 
                 240517_at 
                 1.818 
               
               
                   
                 ETS1 
                 241435_at 
                 1.797 
               
               
                   
                 LRRFIP1 
                 239379_at 
                 1.796 
               
               
                   
                 OCIAD1 
                 235537_at 
                 1.794 
               
               
                   
                 LRCH3 
                 229387_at 
                 1.793 
               
               
                   
                 CCDC14 
                 240884_at 
                 1.771 
               
               
                   
                 HNRNPC 
                 235500_at 
                 1.769 
               
               
                   
                 DCUN1D2 
                 240478_at 
                 1.76 
               
               
                   
                 NPAS2 
                 1557690_x_at 
                 1.76 
               
               
                   
                 POFUT2 
                 207448_at 
                 1.759 
               
               
                   
                 CHD2 
                 244443_at 
                 1.757 
               
               
                   
                 TMEM165 
                 1560622_at 
                 1.756 
               
               
                   
                 FLJ31306 
                 239432_at 
                 1.753 
               
               
                   
                 HPS1 
                 239382_at 
                 1.749 
               
               
                   
                 WTAP 
                 1560274_at 
                 1.747 
               
               
                   
                 TNPO1 
                 1556116_s_at 
                 1.739 
               
               
                   
                 ZFHX3 
                 215828_at 
                 1.737 
               
               
                   
                 AKR1CL2 
                 1559982_s_at 
                 1.732 
               
               
                   
                 C20ORF4 
                 234654_at 
                 1.731 
               
               
                   
                 CCDC57 
                 214818_at 
                 1.703 
               
               
                   
                 MALAT1 
                 224568_x_at 
                 1.699 
               
               
                   
                 EWSR1 
                 229966_at 
                 1.686 
               
               
                   
                 MYO10 
                 244350_at 
                 1.677 
               
               
                   
                 MALAT1 
                 223940_x_at 
                 1.659 
               
               
                   
                 ATXN2L 
                 207798_s_at 
                 1.656 
               
               
                   
                 PDK1 
                 239798_at 
                 1.654 
               
               
                   
                 POLR2J2 
                 1552621_at 
                 1.652 
               
               
                   
                 CENPJ 
                 220885_s_at 
                 1.64 
               
               
                   
                 PDSS1 
                 236298_at 
                 1.64 
               
               
                   
                 UNK 
                 1562434_at 
                 1.637 
               
               
                   
                 BDP1 
                 224227_s_at 
                 1.632 
               
               
                   
                 N4BP2L2 
                 235547_at 
                 1.631 
               
               
                   
                 MDM4 
                 235589_s_at 
                 1.629 
               
               
                   
                 SNORA28 
                 241843_at 
                 1.628 
               
               
                   
                 ZFX 
                 207920_x_at 
                 1.625 
               
               
                   
                 NAPA 
                 239362_at 
                 1.624 
               
               
                   
                 PRO1073 
                 228582_x_at 
                 1.607 
               
               
                   
                 MLL 
                 212079_s_at 
                 1.599 
               
               
                   
                 SGOL2 
                 235425_at 
                 1.591 
               
               
                   
                 RBM25 
                 1557081_at 
                 1.57 
               
               
                   
                 BARD1 
                 205345_at 
                 1.559 
               
               
                   
                 LOC388969 
                 232145_at 
                 1.555 
               
               
                   
                 GGT1 
                 211417_x_at 
                 1.555 
               
               
                   
                 FAM62C 
                 239770_at 
                 1.551 
               
               
                   
                 TTC9C 
                 1569189_at 
                 1.55 
               
               
                   
                 TCAG7.907 
                 238678_at 
                 1.546 
               
               
                   
                 OSGEP 
                 242930_at 
                 1.541 
               
               
                   
                 RHOBTB2 
                 1556645_s_at 
                 1.538 
               
               
                   
                 C5ORF24 
                 229098_s_at 
                 1.531 
               
               
                   
                 RBM4 
                 213718_at 
                 1.53 
               
               
                   
                 SLC2A11 
                 232167_at 
                 1.529 
               
               
                   
                 DDX17 
                 213998_s_at 
                 1.528 
               
               
                   
                 C22ORF30 
                 216555_at 
                 1.521 
               
               
                   
                 C9ORF85 
                 244160_at 
                 1.52 
               
               
                   
                 DNM1L 
                 236032_at 
                 1.503 
               
               
                   
                 SQLE 
                 213577_at 
                 1.502 
               
               
                   
                 CRIPAK 
                 228318_s_at 
                 1.486 
               
               
                   
                 ZNF800 
                 227101_at 
                 1.484 
               
               
                   
                 RAD54L 
                 204558_at 
                 1.483 
               
               
                   
                 TAF1B 
                 239046_at 
                 1.468 
               
               
                   
                 THRAP3 
                 217847_s_at 
                 1.464 
               
               
                   
                 CNIH3 
                 232758_s_at 
                 1.451 
               
               
                   
                 UQCC 
                 229672_at 
                 1.451 
               
               
                   
                 HOXA2 
                 228642_at 
                 1.44 
               
               
                   
                 RBM26 
                 229433_at 
                 1.43 
               
               
                   
                 RFT1 
                 240281_at 
                 1.426 
               
               
                   
                 MTERFD3 
                 225341_at 
                 1.422 
               
               
                   
                 LOC641298 
                 208118_x_at 
                 1.419 
               
               
                   
                 ZNF326 
                 241720_at 
                 1.418 
               
               
                   
                 NBPF16 
                 201104_x_at 
                 1.411 
               
               
                   
                 ASPM 
                 232238_at 
                 1.411 
               
               
                   
                 RNF43 
                 228826_at 
                 1.401 
               
               
                   
                 IPW 
                 213447_at 
                 1.399 
               
               
                   
                 TTC3 
                 208664_s_at 
                 1.396 
               
               
                   
                 USP36 
                 224979_s_at 
                 1.393 
               
               
                   
                 KIAA0841 
                 36888_at 
                 1.389 
               
               
                   
                 NEK1 
                 213328_at 
                 1.381 
               
               
                   
                 AMZ2 
                 227567_at 
                 1.377 
               
               
                   
                 TBC1D8 
                 204526_s_at 
                 1.373 
               
               
                   
                 STK36 
                 231806_s_at 
                 1.362 
               
               
                   
                 SF3B1 
                 214305_s_at 
                 1.359 
               
               
                   
                 HELLS 
                 242890_at 
                 1.359 
               
               
                   
                 SYNE2 
                 202761_s_at 
                 1.356 
               
               
                   
                 KIAA1267 
                 224489_at 
                 1.355 
               
               
                   
                 C14ORF135 
                 1563259_at 
                 1.353 
               
               
                   
                 SF3B1 
                 201070_x_at 
                 1.35 
               
               
                   
                 CLN8 
                 229958_at 
                 1.344 
               
               
                   
                 STK36 
                 234005_x_at 
                 1.335 
               
               
                   
                 ZNF226 
                 219603_s_at 
                 1.332 
               
               
                   
                 COQ4 
                 218328_at 
                 1.328 
               
               
                   
                 DTX3 
                 49051_g_at 
                 1.32 
               
               
                   
                 WFS1 
                 1555270_a_at 
                 1.315 
               
               
                   
                 ZNF251 
                 226754_at 
                 1.313 
               
               
                   
                 ARS2 
                 201679_at 
                 1.307 
               
               
                   
                 ATAD2 
                 235266_at 
                 1.304 
               
               
                   
                 CCDC73 
                 239848_at 
                 1.294 
               
               
                   
                 BCL9L 
                 227616_at 
                 1.291 
               
               
                   
                 MET 
                 213816_s_at 
                 1.283 
               
               
                   
                 NFATC2IP 
                 217527_s_at 
                 1.272 
               
               
                   
                 CHD8 
                 212571_at 
                 1.27 
               
               
                   
                 TNRC6A 
                 234734_s_at 
                 1.268 
               
               
                   
                 OSBPL5 
                 233734_s_at 
                 1.261 
               
               
                   
                 COIL 
                 203653_s_at 
                 1.259 
               
               
                   
                 CPEB2 
                 226939_at 
                 1.251 
               
               
                   
                 TBC1D8 
                 221592_at 
                 1.246 
               
               
                   
                 RUNX3 
                 204198_s_at 
                 1.233 
               
               
                   
                 LBA1 
                 213261_at 
                 1.225 
               
               
                   
                 CENPJ 
                 234023_s_at 
                 1.22 
               
               
                   
                 MARCH6 
                 201737_s_at 
                 1.219 
               
               
                   
                 ANKRD44 
                 226641_at 
                 1.218 
               
               
                   
                 NAPE-PLD 
                 242635_s_at 
                 1.216 
               
               
                   
                 C12ORF48 
                 220060_s_at 
                 1.216 
               
               
                   
                 CCDC93 
                 219774_at 
                 1.208 
               
               
                   
                 ZUFSP 
                 228330_at 
                 1.205 
               
               
                   
                 SMC6 
                 218781_at 
                 1.203 
               
               
                   
                 TAOK3 
                 220761_s_at 
                 1.195 
               
               
                   
                 JARID1A 
                 226367_at 
                 1.192 
               
               
                   
                 DCLRE1C 
                 242927_at 
                 1.187 
               
               
                   
                 TTC26 
                 233999_s_at 
                 1.184 
               
               
                   
                 EIF4G3 
                 201935_s_at 
                 1.174 
               
               
                   
                 ORMDL1 
                 223187_s_at 
                 1.171 
               
               
                   
                 TCOF1 
                 202385_s_at 
                 1.169 
               
               
                   
                 CCDC52 
                 234995_at 
                 1.166 
               
               
                   
                 PMS2L3 
                 214473_x_at 
                 1.159 
               
               
                   
                 HERC5 
                 219863_at 
                 1.156 
               
               
                   
                 CASC5 
                 228323_at 
                 1.144 
               
               
                   
                 SON 
                 201085_s_at 
                 1.144 
               
               
                   
                 APBB2 
                 40148_at 
                 1.139 
               
               
                   
                 LOC338799 
                 226369_at 
                 1.137 
               
               
                   
                 PHC1 
                 218338_at 
                 1.123 
               
               
                   
                 DEPDC1 
                 232278_s_at 
                 1.119 
               
               
                   
                 NRP2 
                 210841_s_at 
                 1.106 
               
               
                   
                 ZMYND8 
                 209049_s_at 
                 1.102 
               
               
                   
                 CEP55 
                 218542_at 
                 1.096 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 1.2 
               
             
            
               
                   
               
               
                 Highly upregulated genes as detected by RT-PCR 
               
            
           
           
               
               
               
            
               
                   
                   
                 ABCB5+/ 
               
               
                   
                   
                 ABCB5− 
               
               
                 Description 
                 Gname 
                 Fold change 
               
               
                   
               
            
           
           
               
               
               
            
               
                 Angiopoietin-like 3 
                 ANGPT5 
                 3.0596 
               
               
                 Brain-specific angiogenesis inhibitor 
                 FLJ41988 
                 3.0596 
               
               
                 1 
               
               
                 Cadherin 5, type 2, VE-cadherin 
                 7B4/CD144 
                 3.0596 
               
               
                 (vascular epithelium) 
               
               
                 Epidermal growth factor (beta- 
                 HOMG4/URG 
                 187.8365 
               
               
                 urogastrone) 
               
               
                 C-fos induced growth factor 
                 VEGF-D/VEGFD 
                 3.5884 
               
               
                 (vascular endothelial growth factor 
               
               
                 D) 
               
               
                 Hepatocyte growth factor 
                 F-TCF/HGFB 
                 4.542 
               
               
                 (hepapoietin A; scatter factor) 
               
               
                 Heparanase 
                 HPA/HPR1 
                 286.6871 
               
               
                 Insulin-like growth factor 1 
                 IGFI 
                 4.7022 
               
               
                 (somatomedin C) 
               
               
                 Jagged 1 (Alagille syndrome) 
                 AGS/AHD 
                 1566.5046 
               
               
                 Laminin, alpha 5 
                 KIAA1907 
                 3.8727 
               
               
                 Platelet/endothelial cell adhesion 
                 CD31/PECAM-1 
                 11.9037 
               
               
                 molecule (CD31 antigen) 
               
               
                 Plexin domain containing 1 
                 DKFZp686F0937/ 
                 3.4184 
               
               
                   
                 TEM3 
               
               
                 Stabilin 1 
                 CLEVER-1/FEEL-1 
                 4.357 
               
               
                 Transforming growth factor, alpha 
                 TFGA 
                 3549.3357 
               
               
                 Tumor necrosis factor (TNF 
                 DIF/TNF-alpha 
                 4.0652 
               
               
                 superfamily, member 2) 
               
               
                 Vascular endothelial growth factor C 
                 Flt4-L/VRP 
                 446.7529 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Downregulated CSC-associated genes (p &lt; 0.05) 
               
            
           
           
               
               
               
               
            
               
                   
                 GENESYMBOL 
                 ID 
                 Fold Change 
               
               
                   
                   
               
            
           
           
               
               
               
               
            
               
                   
                 ECHDC1 
                 233124_s_at 
                 0.943 
               
               
                   
                 DARS 
                 201624_at 
                 0.928 
               
               
                   
                 GALNT1 
                 201722_s_at 
                 0.926 
               
               
                   
                 CGGBP1 
                 224600_at 
                 0.913 
               
               
                   
                 CSE1L 
                 201112_s_at 
                 0.911 
               
               
                   
                 GMFB 
                 202544_at 
                 0.904 
               
               
                   
                 RPL7L1 
                 225515_s_at 
                 0.899 
               
               
                   
                 SKP1 
                 200718_s_at 
                 0.898 
               
               
                   
                 IGHMBP2 
                 215980_s_at 
                 0.893 
               
               
                   
                 LOC137886 
                 212934_at 
                 0.886 
               
               
                   
                 CSE1L 
                 210766_s_at 
                 0.885 
               
               
                   
                 ERRFI1 
                 224657_at 
                 0.881 
               
               
                   
                 MAP2K4 
                 203266_s_at 
                 0.881 
               
               
                   
                 TNFAIP1 
                 201207_at 
                 0.88 
               
               
                   
                 TBXA2R 
                 207554_x_at 
                 0.877 
               
               
                   
                 SEPHS1 
                 208940_at 
                 0.875 
               
               
                   
                 IPO7 
                 200993_at 
                 0.875 
               
               
                   
                 C16ORF63 
                 225087_at 
                 0.872 
               
               
                   
                 INSIG2 
                 209566_at 
                 0.872 
               
               
                   
                 TFB1M 
                 228075_x_at 
                 0.87 
               
               
                   
                 PAK1 
                 226507_at 
                 0.869 
               
               
                   
                 C14ORF156 
                 221434_s_at 
                 0.867 
               
               
                   
                 SMYD2 
                 212922_s_at 
                 0.867 
               
               
                   
                 ENTPD5 
                 231676_s_at 
                 0.867 
               
               
                   
                 PPP3CA 
                 202457_s_at 
                 0.867 
               
               
                   
                 MBNL1 
                 201152_s_at 
                 0.867 
               
               
                   
                 MRPL42 
                 217919_s_at 
                 0.866 
               
               
                   
                 SUPT7L 
                 201838_s_at 
                 0.865 
               
               
                   
                 PMP22 
                 210139_s_at 
                 0.865 
               
               
                   
                 GABARAPL2 
                 209046_s_at 
                 0.863 
               
               
                   
                 PITPNA 
                 201190_s_at 
                 0.863 
               
               
                   
                 C2ORF30 
                 224630_at 
                 0.851 
               
               
                   
                 TXNDC12 
                 223017_at 
                 0.849 
               
               
                   
                 POP4 
                 202868_s_at 
                 0.847 
               
               
                   
                 MRPL51 
                 224334_s_at 
                 0.846 
               
               
                   
                 AK3 
                 224655_at 
                 0.845 
               
               
                   
                 GPR107 
                 211979_at 
                 0.843 
               
               
                   
                 TMEM126B 
                 221622_s_at 
                 0.843 
               
               
                   
                 PSMA2 
                 201316_at 
                 0.839 
               
               
                   
                 KIAA1737 
                 225623_at 
                 0.837 
               
               
                   
                 TRAPPC2L 
                 218354_at 
                 0.837 
               
               
                   
                 RLBP1L1 
                 224996_at 
                 0.835 
               
               
                   
                 CCDC127 
                 226515_at 
                 0.835 
               
               
                   
                 CPNE3 
                 202119_s_at 
                 0.833 
               
               
                   
                 HIAT1 
                 225222_at 
                 0.832 
               
               
                   
                 MECR 
                 218664_at 
                 0.832 
               
               
                   
                 ACBD6 
                 225317_at 
                 0.83 
               
               
                   
                 SLC16A1 
                 202235_at 
                 0.83 
               
               
                   
                 ANXA4 
                 201302_at 
                 0.83 
               
               
                   
                 DNAJC21 
                 230893_at 
                 0.829 
               
               
                   
                 C22ORF28 
                 200042_at 
                 0.829 
               
               
                   
                 SPOPL 
                 225659_at 
                 0.828 
               
               
                   
                 PDHB 
                 211023_at 
                 0.827 
               
               
                   
                 EIF2S1 
                 201144_s_at 
                 0.824 
               
               
                   
                 LOC645166 
                 228158_at 
                 0.823 
               
               
                   
                 CAMK2D 
                 225019_at 
                 0.823 
               
               
                   
                 LIMS1 
                 212687_at 
                 0.822 
               
               
                   
                 VTI1B 
                 209452_s_at 
                 0.821 
               
               
                   
                 YY1 
                 224711_at 
                 0.821 
               
               
                   
                 TRAPPC2 
                 219351_at 
                 0.821 
               
               
                   
                 LOC126917 
                 225615_at 
                 0.819 
               
               
                   
                 STX8 
                 204690_at 
                 0.819 
               
               
                   
                 NANP 
                 228073_at 
                 0.817 
               
               
                   
                 NDFIP1 
                 217800_s_at 
                 0.815 
               
               
                   
                 UBE3C 
                 1560739_a_at 
                 0.815 
               
               
                   
                 KPNA6 
                 226976_at 
                 0.814 
               
               
                   
                 C19ORF42 
                 219097_x_at 
                 0.813 
               
               
                   
                 DHX40 
                 218277_s_at 
                 0.812 
               
               
                   
                 NUCB2 
                 203675_at 
                 0.812 
               
               
                   
                 RAB1A 
                 213440_at 
                 0.81 
               
               
                   
                 USP8 
                 229501_s_at 
                 0.808 
               
               
                   
                 MAP1LC3B 
                 208785_s_at 
                 0.808 
               
               
                   
                 PDHB 
                 208911_s_at 
                 0.807 
               
               
                   
                 SH2B3 
                 203320_at 
                 0.806 
               
               
                   
                 PPP1R3D 
                 204554_at 
                 0.805 
               
               
                   
                 DEGS1 
                 209250_at 
                 0.804 
               
               
                   
                 HSDL2 
                 209513_s_at 
                 0.803 
               
               
                   
                 LOC203547 
                 225556_at 
                 0.802 
               
               
                   
                 CANX 
                 238034_at 
                 0.8 
               
               
                   
                 PSMA3 
                 201532_at 
                 0.798 
               
               
                   
                 PIGY 
                 224660_at 
                 0.793 
               
               
                   
                 CYB5R3 
                 1554574_a_at 
                 0.793 
               
               
                   
                 BRI3 
                 223376_s_at 
                 0.792 
               
               
                   
                 CREB1 
                 204313_s_at 
                 0.791 
               
               
                   
                 LOC389203 
                 225014_at 
                 0.79 
               
               
                   
                 WDR41 
                 218055_s_at 
                 0.789 
               
               
                   
                 C9ORF78 
                 218116_at 
                 0.789 
               
               
                   
                 GNPDA1 
                 202382_s_at 
                 0.787 
               
               
                   
                 RPE 
                 225039_at 
                 0.787 
               
               
                   
                 HSPA4L 
                 205543_at 
                 0.786 
               
               
                   
                 SEPT11 
                 201307_at 
                 0.784 
               
               
                   
                 HEATR2 
                 241352_at 
                 0.784 
               
               
                   
                 ENAH 
                 222433_at 
                 0.783 
               
               
                   
                 MED19 
                 226300_at 
                 0.782 
               
               
                   
                 TBC1D5 
                 201814_at 
                 0.782 
               
               
                   
                 EMP2 
                 225079_at 
                 0.781 
               
               
                   
                 STX11 
                 235670_at 
                 0.778 
               
               
                   
                 ANKH 
                 229176_at 
                 0.776 
               
               
                   
                 ENDOD1 
                 212573_at 
                 0.775 
               
               
                   
                 IL13RA1 
                 201887_at 
                 0.775 
               
               
                   
                 RAB14 
                 200927_s_at 
                 0.772 
               
               
                   
                 TMEM30A 
                 232591_s_at 
                 0.771 
               
               
                   
                 DDX52 
                 212834_at 
                 0.771 
               
               
                   
                 PTPMT1 
                 229535_at 
                 0.769 
               
               
                   
                 SRPRB 
                 218140_x_at 
                 0.767 
               
               
                   
                 FAM98A 
                 212333_at 
                 0.767 
               
               
                   
                 SRP72 
                 208803_s_at 
                 0.766 
               
               
                   
                 RPE 
                 221770_at 
                 0.766 
               
               
                   
                 HOXB9 
                 216417_x_at 
                 0.766 
               
               
                   
                 MAEA 
                 207922_s_at 
                 0.765 
               
               
                   
                 GHITM 
                 1554510_s_at 
                 0.764 
               
               
                   
                 CAPZB 
                 201949_x_at 
                 0.764 
               
               
                   
                 ANKRD52 
                 228257_at 
                 0.762 
               
               
                   
                 MOBKL1B 
                 214812_s_at 
                 0.762 
               
               
                   
                 MIA3 
                 1569057_s_at 
                 0.759 
               
               
                   
                 UBE2E3 
                 210024_s_at 
                 0.758 
               
               
                   
                 CAMK2D 
                 228555_at 
                 0.758 
               
               
                   
                 UBXD7 
                 212840_at 
                 0.754 
               
               
                   
                 C18ORF10 
                 213617_s_at 
                 0.754 
               
               
                   
                 HSD17B1 
                 228595_at 
                 0.753 
               
               
                   
                 PDLIM5 
                 212412_at 
                 0.752 
               
               
                   
                 SRP72 
                 208801_at 
                 0.751 
               
               
                   
                 ZNF618 
                 226590_at 
                 0.75 
               
               
                   
                 TSPAN31 
                 203227_s_at 
                 0.744 
               
               
                   
                 MAP3K15 
                 200979_at 
                 0.741 
               
               
                   
                 C18ORF10 
                 212055_at 
                 0.737 
               
               
                   
                 ATP5I 
                 207335_x_at 
                 0.737 
               
               
                   
                 TOX4 
                 201685_s_at 
                 0.73 
               
               
                   
                 TBXA2R 
                 336_at 
                 0.73 
               
               
                   
                 COL4A2 
                 211966_at 
                 0.729 
               
               
                   
                 TIMM23 
                 218119_at 
                 0.723 
               
               
                   
                 NDUFAF2 
                 228355_s_at 
                 0.722 
               
               
                   
                 FOXN3 
                 218031_s_at 
                 0.721 
               
               
                   
                 EIF2S1 
                 201142_at 
                 0.717 
               
               
                   
                 NDUFB6 
                 203613_s_at 
                 0.712 
               
               
                   
                 TM6SF1 
                 1558102_at 
                 0.704 
               
               
                   
                 ELOVL2 
                 213712_at 
                 0.699 
               
               
                   
                 PPP1R7 
                 201213_at 
                 0.698 
               
               
                   
                 BAT3 
                 230513_at 
                 0.697 
               
               
                   
                 ZNF668 
                 219047_s_at 
                 0.691 
               
               
                   
                 ERBB3 
                 1563253_s_at 
                 0.691 
               
               
                   
                 C12ORF45 
                 226349_at 
                 0.688 
               
               
                   
                 PGRMC2 
                 213227_at 
                 0.686 
               
               
                   
                 NUDT4 
                 212183_at 
                 0.685 
               
               
                   
                 AABHD7 
                 239579_at 
                 0.661 
               
               
                   
                 CEP27 
                 228744_at 
                 0.651 
               
               
                   
                 RAB11FIP3 
                 216043_x_at 
                 0.551 
               
               
                   
                 FHL3 
                 218818_at 
                 0.546 
               
               
                   
                 NAALAD2 
                 1554506_x_at 
                 0.464 
               
               
                   
                 LOC219731 
                 1557208_at 
                 0.419 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 CSC-genes annotations 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                 Entrez 
                   
                   
                   
                   
                   
                   
               
               
                   
                 Gene ID 
               
               
                   
                 for 
                   
                 Fold 
               
               
                 Name 
                 Human 
                 Affymetrix 
                 Change 
                 Networks 
                 Location 
                 Type 
                 Drugs 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Actin 
                   
                 — 
                   
                 1 
                 Unknown 
                 group 
                   
               
               
                 ADA 
                 100 
                 — 
                   
                 8 
                 Cytoplasm 
                 enzyme 
                 pentostatin, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 vidarabine 
               
               
                 Adaptor protein 2 
                   
                 — 
                   
                 8 
                 Unknown 
                 complex 
               
               
                 AFP 
                 174 
                 — 
                   
                 5 
                 Extracellular 
                 transporter 
               
               
                   
                   
                   
                   
                   
                 Space 
               
               
                 AGT 
                 183 
                 — 
                   
                 8 
                 Extracellular 
                 other 
               
               
                   
                   
                   
                   
                   
                 Space 
               
               
                 AHR 
                 196 
                 — 
                   
                 7 
                 Nucleus 
                 ligand- 
               
               
                   
                   
                   
                   
                   
                   
                 dependent 
               
               
                   
                   
                   
                   
                   
                   
                 nuclear 
               
               
                   
                   
                   
                   
                   
                   
                 receptor 
               
               
                 AKAP9 
                 10142 
                 215483_at 
                 2.168 
                 1 
                 Cytoplasm 
                 other 
               
               
                 Akt 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 amino acids 
                   
                 — 
                   
                 6 
                 Unknown 
                 chemical - 
               
               
                   
                   
                   
                   
                   
                   
                 endogenous 
               
               
                   
                   
                   
                   
                   
                   
                 mammalian 
               
               
                 AMPH 
                 273 
                 — 
                   
                 8 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 AMZ2 
                 51321 
                 227567_at 
                 1.377 
                 8 
                 Unknown 
                 other 
               
               
                 ANAPC1 
                 64682 
                 — 
                   
                 4 
                 Nucleus 
                 other 
               
               
                 ANAPC10 
                 10393 
                 — 
                   
                 4 
                 Nucleus 
                 enzyme 
               
               
                 ANAPC11 
                 51529 
                 — 
                   
                 4 
                 Unknown 
                 enzyme 
               
               
                 ANAPC13 
                 25847 
                 — 
                   
                 4 
                 Unknown 
                 other 
               
               
                 ANAPC2 
                 29882 
                 — 
                   
                 4 
                 Nucleus 
                 enzyme 
               
               
                 ANAPC4 
                 29945 
                 — 
                   
                 4 
                 Unknown 
                 enzyme 
               
               
                 ANAPC5 
                 51433 
                 235926_at 
                 2.631 
                 4 
                 Nucleus 
                 enzyme 
               
               
                 ANAPC7 
                 51434 
                 — 
                   
                 4 
                 Unknown 
                 other 
               
               
                 ANK2 
                 287 
                 202921_s_at 
                 4.162 
                 4 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 ANKRD28 
                 23243 
                 241063_at 
                 2.297 
                 13 
                 Unknown 
                 other 
               
               
                 AOC3 
                 8639 
                 204894_s_at 
                 1.894 
                 2 
                 Plasma 
                 enzyme 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 AP2A2 
                 161 
                 — 
                   
                 8 
                 Cytoplasm 
                 transporter 
               
               
                 APBB2 
                 323 
                 40148_at 
                 1.139 
                 9 
                 Cytoplasm 
                 other 
               
               
                 APP 
                 351 
                 — 
                   
                 9 
                 Plasma 
                 other 
                 AAB-001 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 ARD1A 
                 8260 
                 — 
                   
                 8 
                 Nucleus 
                 enzyme 
               
               
                 Arf 
                   
                 — 
                   
                 8 
                 Unknown 
                 group 
               
               
                 ARF5 
                 381 
                 — 
                   
                 8 
                 Cytoplasm 
                 transporter 
               
               
                 ARHGDIB 
                 397 
                 — 
                   
                 7 
                 Cytoplasm 
                 other 
               
               
                 ASCC3L1 
                 23020 
                 214982_at 
                 3.009 
                 9 
                 Nucleus 
                 enzyme 
               
               
                 (includes 
               
               
                 EG: 23020) 
               
               
                 ASCL1 
                 429 
                 — 
                   
                 9 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 ASPM 
                 259266 
                 232238_at 
                 1.411 
                 3 
                 Nucleus 
                 other 
               
               
                 ATAD2 
                 29028 
                 235266_at 
                 1.304 
                 7 
                 Unknown 
                 other 
               
               
                 ATP 
                   
                 — 
                   
                 9 
                 Unknown 
                 chemical - 
               
               
                   
                   
                   
                   
                   
                   
                 endogenous 
               
               
                   
                   
                   
                   
                   
                   
                 mammalian 
               
               
                 ATXN2L 
                 11273 
                 207798_s_at 
                 1.656 
                 9 
                 Unknown 
                 other 
               
               
                 BARD1 
                 580 
                 205345_at 
                 1.559 
                 1 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 BCL2 
                 596 
                 — 
                   
                 6 
                 Cytoplasm 
                 other 
                 oblimersen, (−)- 
               
               
                   
                   
                   
                   
                   
                   
                   
                 gossypol 
               
               
                 BCL9L 
                 283149 
                 227616_at 
                 1.291 
                 6 
                 Cytoplasm 
                 other 
               
               
                 BDP1 
                 55814 
                 224227_s_at 
                 1.632 
                 9 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 beta-estradiol 
                   
                 — 
                   
                 3 
                 Unknown 
                 chemical - 
               
               
                   
                   
                   
                   
                   
                   
                 endogenous 
               
               
                   
                   
                   
                   
                   
                   
                 mammalian 
               
               
                 BRF1 
                 2972 
                 — 
                   
                 9 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 BUB1 (includes 
                 699 
                 233445_at 
                 3.209 
                 5 
                 Nucleus 
                 kinase 
               
               
                 EG: 699) 
               
               
                 BUB1B 
                 701 
                 — 
                   
                 4 
                 Nucleus 
                 kinase 
               
               
                 C12ORF48 
                 55010 
                 220060_s_at 
                 1.216 
                   
                 Unknown 
                 other 
               
               
                 C12ORF51 
                 283450 
                 1557529_at 
                 3.632 
                 4 
                 Unknown 
                 other 
               
               
                 CABIN1 
                 23523 
                 1557581_x_at 
                 3.052 
                 1 
                 Nucleus 
                 other 
               
               
                 Calmodulin 
                   
                 — 
                   
                 1 
                 Unknown 
                 group 
               
               
                 CASC5 
                 57082 
                 228323_at 
                 1.144 
                 3 
                 Nucleus 
                 other 
               
               
                 CASP3 
                 836 
                 — 
                   
                 4 
                 Cytoplasm 
                 peptidase 
                 IDN-6556 
               
               
                 CASP6 
                 839 
                 — 
                   
                 9 
                 Cytoplasm 
                 peptidase 
               
               
                 CBS 
                 875 
                 240517_at 
                 1.818 
                 1 
                 Cytoplasm 
                 enzyme 
               
               
                 CD151 
                 977 
                 — 
                   
                 7 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 CDC14B 
                 8555 
                 234605_at 
                 2.512 
                 5 
                 Nucleus 
                 phosphatase 
               
               
                 CDC16 
                 8881 
                 242359_at 
                 6.261 
                 4 
                 Nucleus 
                 other 
               
               
                 CDC20 
                 991 
                 — 
                   
                 3 
                 Nucleus 
                 other 
               
               
                 CDC23 (includes 
                 8697 
                 — 
                   
                 4 
                 Nucleus 
                 enzyme 
               
               
                 EG: 8697) 
               
               
                 CDC26 
                 246184 
                 — 
                   
                 4 
                 Nucleus 
                 other 
               
               
                 CDC27 
                 996 
                 — 
                   
                 4 
                 Nucleus 
                 other 
               
               
                 CDC5L 
                 988 
                 222179_at 
                 1.292 
                 9 
                 Nucleus 
                 other 
               
               
                 CDK2 
                 1017 
                 — 
                   
                 7 
                 Nucleus 
                 kinase 
                 BMS-387032, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 flavopiridol 
               
               
                 CDKN1A 
                 1026 
                 — 
                   
                 7 
                 Nucleus 
                 kinase 
               
               
                 CDT1 
                 81620 
                 — 
                   
                 7 
                 Nucleus 
                 other 
               
               
                 CDX1 
                 1044 
                 — 
                   
                 9 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 CENPJ 
                 55835 
                 220885_s_at 
                 1.64 
                 4 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 CEP55 
                 55165 
                 218542_at 
                 1.096 
                 5 
                 Unknown 
                 other 
               
               
                 CHD8 
                 57680 
                 212571_at 
                 1.27 
                 1 
                 Nucleus 
                 enzyme 
               
               
                 CHEK2 
                 11200 
                 — 
                   
                 5 
                 Nucleus 
                 kinase 
               
               
                 CHRM3 
                 1131 
                 — 
                   
                 8 
                 Plasma 
                 G-protein 
                 fesoterodine, ABT- 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                 coupled 
                 089, 
               
               
                   
                   
                   
                   
                   
                   
                 receptor 
                 atropine/edrophonium, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 cyclopentolate/phenylephrine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 ipratropium/albuterol, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 trihexyphenidyl, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 carbamylcholine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 darifenacin, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 methacholine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 diphenhydramine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 quinidine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 procyclidine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 trospium, atropine 
               
               
                   
                   
                   
                   
                   
                   
                   
                 sulfate/benzoic 
               
               
                   
                   
                   
                   
                   
                   
                   
                 acid/hyoscyamine/methenamine/ 
               
               
                   
                   
                   
                   
                   
                   
                   
                 methylene 
               
               
                   
                   
                   
                   
                   
                   
                   
                 blue/phenyl 
               
               
                   
                   
                   
                   
                   
                   
                   
                 salicylate, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 homatropine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 dicyclomine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 methantheline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 orphenadrine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 fluoxetine/olanzapine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 doxacurium, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 aspirin/caffeine/orphenadrine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 propantheline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 tridihexethyl, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 biperiden, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 anisotropine 
               
               
                   
                   
                   
                   
                   
                   
                   
                 methylbromide, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 glycopyrrolate, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 diphenhydramine/8- 
               
               
                   
                   
                   
                   
                   
                   
                   
                 chlorotheophylline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 atropine/hyoscyamine/ 
               
               
                   
                   
                   
                   
                   
                   
                   
                 phenobarbital/scopolamine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 atropine 
               
               
                   
                   
                   
                   
                   
                   
                   
                 sulfate/diphenoxylate 
               
               
                   
                   
                   
                   
                   
                   
                   
                 hydrochloride, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 pipecuronium, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 flavoxate, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 chlorpheniramine/methscopolamine/ 
               
               
                   
                   
                   
                   
                   
                   
                   
                 phenylephrine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 mepenzolic 
               
               
                   
                   
                   
                   
                   
                   
                   
                 acid, atropine 
               
               
                   
                   
                   
                   
                   
                   
                   
                 sulfate/difenoxin 
               
               
                   
                   
                   
                   
                   
                   
                   
                 hydrochloride, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 homatropine 
               
               
                   
                   
                   
                   
                   
                   
                   
                 methylbromide, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 hydroxyamphetamine/ 
               
               
                   
                   
                   
                   
                   
                   
                   
                 tropicamide, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 cisatracurium, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 hyoscyamine/phenobarbital, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 bethanechol, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 olanzapine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 oxybutynin, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 tropicamide, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 solifenacin, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 cyclopentolate, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 tolterodine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 cevimeline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 acetylcholine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 ipratropium, atropine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 pilocarpine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 benztropine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 hyoscyamine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 arecoline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 scopolamine, N- 
               
               
                   
                   
                   
                   
                   
                   
                   
                 methylscopolamine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 tiotropium, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 carbinoxamine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 buclizine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 diphenhydramine/phenylephrine, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 brompheniramine 
               
               
                 CIB1 
                 10519 
                 — 
                   
                 7 
                 Nucleus 
                 other 
               
               
                 Ck2 
                   
                 — 
                   
                 1 
                 Unknown 
                 complex 
               
               
                 CKM 
                 1158 
                 — 
                   
                 5 
                 Cytoplasm 
                 kinase 
               
               
                 CLIC1 
                 1192 
                 — 
                   
                 9 
                 Nucleus 
                 ion channel 
               
               
                 CLIC4 
                 25932 
                 — 
                   
                 6 
                 Cytoplasm 
                 ion channel 
               
               
                 CLIC5 
                 53405 
                 — 
                   
                 1 
                 Cytoplasm 
                 ion channel 
               
               
                 CLN8 
                 2055 
                 229958_at 
                 1.344 
                   
                 Cytoplasm 
                 other 
               
               
                 COIL 
                 8161 
                 203653_s_at 
                 1.259 
                 6 
                 Nucleus 
                 other 
               
               
                 COL4A1 
                 1282 
                 — 
                   
                 5 
                 Extracellular 
                 other 
                 collagenase 
               
               
                   
                   
                   
                   
                   
                 Space 
               
               
                 COPB1 
                 1315 
                 — 
                   
                 8 
                 Cytoplasm 
                 transporter 
               
               
                 Creb 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 CREB3L2 
                 64764 
                 237952_at 
                 2.013 
                 3 
                 Unknown 
                 other 
               
               
                 CRIPAK 
                 285464 
                 228318_s_at 
                 1.486 
                   
                 Cytoplasm 
                 other 
               
               
                 CROP 
                 51747 
                 242389_at 
                 2.121 
                 7 
                 Nucleus 
                 other 
               
               
                 CRY1 
                 1407 
                 — 
                   
                 7 
                 Nucleus 
                 enzyme 
               
               
                 CTNNA1 
                 1495 
                 — 
                   
                 6 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 CTNNAL1 
                 8727 
                 — 
                   
                 6 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 CTNNB1 
                 1499 
                 — 
                   
                 6 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 CUL4A 
                 8451 
                 232466_at 
                 2.607 
                 1 
                 Nucleus 
                 other 
               
               
                 DAPK1 
                 1612 
                 — 
                   
                 6 
                 Cytoplasm 
                 kinase 
               
               
                 DCLRE1C 
                 64421 
                 242927_at 
                 1.187 
                   
                 Nucleus 
                 enzyme 
               
               
                 DDX17 
                 10521 
                 213998_s_at 
                 1.528 
                 6 
                 Nucleus 
                 enzyme 
               
               
                 DENND4A 
                 10260 
                 230607_at 
                 2.368 
                 1 
                 Nucleus 
                 other 
               
               
                 DMD 
                 1756 
                 — 
                   
                 8 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 DNM1L 
                 10059 
                 236032_at 
                 1.503 
                 2 
                 Cytoplasm 
                 enzyme 
               
               
                 DSN1 
                 79980 
                 — 
                   
                 3 
                 Nucleus 
                 other 
               
               
                 DTX 
                   
                 — 
                   
                 3 
                 Unknown 
                 group 
               
               
                 DTX1 
                 1840 
                 — 
                   
                 3 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 DTX2 
                 113878 
                 — 
                   
                 3 
                 Nucleus 
                 other 
               
               
                 DTX3 
                 196403 
                 49051_g_at 
                 1.32 
                 3 
                 Cytoplasm 
                 other 
               
               
                 DUB 
                   
                 — 
                   
                 18 
                 Unknown 
                 group 
               
               
                 DVL1 
                 1855 
                 — 
                   
                 6 
                 Cytoplasm 
                 other 
               
               
                 DVL2 
                 1856 
                 — 
                   
                 6 
                 Cytoplasm 
                 other 
               
               
                 Dynamin 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 EGFR 
                 1956 
                 — 
                   
                 7 
                 Plasma 
                 kinase 
                 cetuximab, AEE 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                   
                 788, panitumumab, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 BMS-599626, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 ARRY-334543, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 XL647, canertinib, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 gefitinib, HKI-272, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 PD 153035, lapatinib, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 vandetanib, erlotinib 
               
               
                 EIF4G3 
                 8672 
                 201935_s_at 
                 1.174 
                 4 
                 Cytoplasm 
                 translation 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 EPOR 
                 2057 
                 — 
                   
                 9 
                 Plasma 
                 transmembrane 
                 erythropoietin, 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                 receptor 
                 darbepoetin alfa, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 continuous 
               
               
                   
                   
                   
                   
                   
                   
                   
                 erythropoietin 
               
               
                   
                   
                   
                   
                   
                   
                   
                 receptor activator 
               
               
                 ERBB2 
                 2064 
                 — 
                   
                 3 
                 Plasma 
                 kinase 
                 trastuzumab, BMS- 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                   
                 599626, ARRY- 
               
               
                   
                   
                   
                   
                   
                   
                   
                 334543, XL647, CP- 
               
               
                   
                   
                   
                   
                   
                   
                   
                 724,714, HKI-272, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 lapatinib, erlotinib 
               
               
                 ETS1 
                 2113 
                 241435_at 
                 1.797 
                 2 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 EWSR1 
                 2130 
                 229966_at 
                 1.686 
                 1 
                 Nucleus 
                 other 
               
               
                 EXT1 
                 2131 
                 242126_at 
                 2.116 
                 4 
                 Cytoplasm 
                 enzyme 
               
               
                 FLOT1 
                 10211 
                 — 
                   
                 3 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 FLT1 
                 2321 
                 232809_s_at 
                 1.861 
                 2 
                 Plasma 
                 kinase 
                 sunitinib, axitinib, 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                   
                 CEP 7055 
               
               
                 FMR1 
                 2332 
                 — 
                   
                 7 
                 Nucleus 
                 other 
               
               
                 FRK 
                 2444 
                 — 
                   
                 9 
                 Nucleus 
                 kinase 
               
               
                 FUBP1 
                 8880 
                 240307_at 
                 2.087 
                 1 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 FZR1 
                 51343 
                 — 
                   
                 4 
                 Nucleus 
                 other 
               
               
                 GABPA 
                 2551 
                 243498_at 
                 2.03 
                 2 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 GBF1 
                 8729 
                 233114_at 
                 2.03 
                 8 
                 Cytoplasm 
                 other 
               
               
                 GGT1 
                 2678 
                 211417_x_at 
                 1.555 
                 6 
                 Cytoplasm 
                 enzyme 
               
               
                 GPD2 
                 2820 
                 243598_at 
                 2.13 
                 3 
                 Cytoplasm 
                 enzyme 
               
               
                 HDAC3 
                 8841 
                 240482_at 
                 2.062 
                 1 
                 Nucleus 
                 transcription 
                 tributyrin, PXD101, 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
                 pyroxamide, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 MGCD0103, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 vorinostat, FR901228 
               
               
                 HECW1 
                 23072 
                 237295_at 
                 11.843 
                 6 
                 Cytoplasm 
                 enzyme 
               
               
                 HELLS 
                 3070 
                 242890_at 
                 1.359 
                 3 
                 Nucleus 
                 enzyme 
               
               
                 HERC5 
                 51191 
                 219863_at 
                 1.156 
                 6 
                 Cytoplasm 
                 enzyme 
               
               
                 Histone h3 
                   
                 — 
                   
                 1 
                 Unknown 
                 group 
               
               
                 HNRNPC 
                 3183 
                 235500_at 
                 1.769 
                 1 
                 Nucleus 
                 other 
               
               
                 HNRPD 
                 3184 
                 241702_at 
                 1.962 
                 4 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 HNRPH1 
                 3187 
                 213472_at 
                 2.332 
                 8 
                 Nucleus 
                 other 
               
               
                 HOXA2 
                 3199 
                 228642_at 
                 1.44 
                 8 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 HOXD3 
                 3232 
                 206601_s_at 
                 1.897 
                 7 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 HPS1 
                 3257 
                 239382_at 
                 1.749 
                 14 
                 Cytoplasm 
                 other 
               
               
                 HPS4 
                 89781 
                 — 
                   
                 14 
                 Cytoplasm 
                 other 
               
               
                 HSPA5 
                 3309 
                 — 
                   
                 3 
                 Cytoplasm 
                 other 
               
               
                 HUWE1 
                 10075 
                 214673_s_at 
                 1.858 
                 6 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 IFNG 
                 3458 
                 — 
                   
                 9 
                 Extracellular 
                 cytokine 
               
               
                   
                   
                   
                   
                   
                 Space 
               
               
                 IFNGR1 
                 3459 
                 242903_at 
                 2.171 
                 4 
                 Plasma 
                 transmembrane 
                 interferon gamma-1b 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                 receptor 
               
               
                 IL1B 
                 3553 
                 — 
                   
                 4 
                 Extracellular 
                 cytokine 
                 IL-1 trap 
               
               
                   
                   
                   
                   
                   
                 Space 
               
               
                 Insulin 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 IRS2 
                 8660 
                 236338_at 
                 2.162 
                 2 
                 Cytoplasm 
                 other 
               
               
                 ITGB3 
                 3690 
                 — 
                   
                 7 
                 Plasma 
                 transmembrane 
                 TP 9201, 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                 receptor 
                 EMD121974, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 tirofiban 
               
               
                 ITPR1 
                 3708 
                 — 
                   
                 4 
                 Cytoplasm 
                 ion channel 
               
               
                 JARID1A 
                 5927 
                 226367_at 
                 1.192 
                 9 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 JARID2 
                 3720 
                 232835_at 
                 2.139 
                 4 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 Jnk 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 KIAA1267 
                 284058 
                 224489_at 
                 1.355 
                 1 
                 Nucleus 
                 other 
               
               
                 KIDINS220 
                 57498 
                 1557246_at 
                 2.97 
                 6 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 KIR2DL3 
                 3804 
                 — 
                   
                 9 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 KITLG (includes 
                 4254 
                 — 
                   
                 9 
                 Extracellular 
                 growth factor 
               
               
                 EG: 4254) 
                   
                   
                   
                   
                 Space 
               
               
                 KLF6 
                 1316 
                 — 
                   
                 5, 9 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 LCN2 
                 3934 
                 — 
                   
                 9 
                 Extracellular 
                 transporter 
               
               
                   
                   
                   
                   
                   
                 Space 
               
               
                 LMO2 
                 4005 
                 — 
                   
                 9 
                 Nucleus 
                 other 
               
               
                 LOC388135 
                 388135 
                 230475_at 
                 1.979 
                 5 
                 Unknown 
                 other 
               
               
                 LRRFIP1 
                 9208 
                 239379_at 
                 1.796 
                 3 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 MALAT1 
                 378938 
                 224568_x_at 
                 1.699 
                   
                 Unknown 
                 other 
               
               
                 Mapk 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 MEF2C 
                 4208 
                 236395_at 
                 2.104 
                 2 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 MET 
                 4233 
                 213816_s_at 
                 1.283 
                 2 
                 Plasma 
                 kinase 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 mGluR 
                   
                 — 
                   
                 8 
                 Unknown 
                 group 
               
               
                 MIS12 
                 79003 
                 — 
                   
                 3 
                 Nucleus 
                 other 
               
               
                 MLL 
                 4297 
                 212079_s_at 
                 1.599 
                 1 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 MPL 
                 4352 
                 — 
                   
                 9 
                 Plasma 
                 transmembrane 
                 SB-497115 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                 receptor 
               
               
                 MTUS1 
                 57509 
                 239576_at 
                 1.975 
                 1 
                 Unknown 
                 other 
               
               
                 MYC 
                 4609 
                 — 
                   
                 6 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 MYF6 
                 4618 
                 — 
                   
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 MYO10 
                 4651 
                 243159_x_at 
                 2.528 
                 3 
                 Cytoplasm 
                 other 
               
               
                 MYOD1 
                 4654 
                 — 
                   
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 N4BP2L1 
                 90634 
                 213375_s_at 
                 2.01 
                   
                 Unknown 
                 other 
               
               
                 Nap125 
                   
                 — 
                   
                 16 
                 Unknown 
                 group 
               
               
                 NAPA 
                 8775 
                 239362_at 
                 1.624 
                 2 
                 Cytoplasm 
                 transporter 
               
               
                 NAPE-PLD 
                 222236 
                 242635_s_at 
                 1.216 
                 8 
                 Cytoplasm 
                 enzyme 
               
               
                 NARG1 
                 80155 
                 1556381_at 
                 2.827 
                 8 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 NAT13 
                 80218 
                 — 
                   
                 8 
                 Cytoplasm 
                 enzyme 
               
               
                 NBPF15 
                 284565 
                 201104_x_at 
                 1.411 
                 1 
                 Unknown 
                 other 
               
               
                 NBR1 
                 4077 
                 1568856_at 
                 1.957 
                 5 
                 Unknown 
                 other 
               
               
                 NCKAP1L 
                 3071 
                 209734_at 
                 2.071 
                 16 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 NCOA3 
                 8202 
                 — 
                   
                 7 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 NEK1 
                 4750 
                 213328_at 
                 1.381 
                 6 
                 Nucleus 
                 kinase 
               
               
                 NES 
                 10763 
                 — 
                   
                 5 
                 Cytoplasm 
                 other 
               
               
                 NFATC2IP 
                 84901 
                 217527_s_at 
                 1.272 
                 1 
                 Nucleus 
                 other 
               
               
                 NFkB 
                   
                 — 
                   
                 2 
                 Unknown 
                 complex 
               
               
                 NFKBIE (includes 
                 4794 
                 — 
                   
                 13 
                 Nucleus 
                 transcription 
               
               
                 EG: 4794) 
                   
                   
                   
                   
                   
                 regulator 
               
               
                 NMB 
                 4828 
                 — 
                   
                 8 
                 Extracellular 
                 other 
               
               
                   
                   
                   
                   
                   
                 Space 
               
               
                 NPAS2 
                 4862 
                 1557690_x_at 
                 1.76 
                 7 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 NPTN 
                 27020 
                 228723_at 
                 2.086 
                 1 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 NRP2 
                 8828 
                 210841_s_at 
                 1.106 
                 2, 3 
                 Plasma 
                 kinase 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 NUPL1 
                 9818 
                 241425_at 
                 2.179 
                 17 
                 Nucleus 
                 transporter 
               
               
                 OGG1 
                 4968 
                 — 
                   
                 9 
                 Nucleus 
                 enzyme 
               
               
                 OSBPL5 
                 114879 
                 233734_s_at 
                 1.261 
                 3 
                 Cytoplasm 
                 other 
               
               
                 OSGEP 
                 55644 
                 242930_at 
                 1.541 
                 3 
                 Unknown 
                 peptidase 
               
               
                 P38 MAPK 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 PABPN1 
                 8106 
                 213046_at 
                 2.228 
                 5 
                 Nucleus 
                 other 
               
               
                 PAX3 
                 5077 
                 — 
                   
                 7 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 PCBP1 (includes 
                 5093 
                 — 
                   
                 6 
                 Nucleus 
                 translation 
               
               
                 EG: 5093) 
                   
                   
                   
                   
                   
                 regulator 
               
               
                 PDE4B 
                 5142 
                 215671_at 
                 3.457 
                 2 
                 Cytoplasm 
                 enzyme 
                 dyphylline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 nitroglycerin, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 arofylline, tetomilast, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 L 869298, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 aminophylline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 anagrelide, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 cilomilast, milrinone, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 rolipram, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 dipyridamole, L- 
               
               
                   
                   
                   
                   
                   
                   
                   
                 826,141, roflumilast, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 tolbutamide, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 theophylline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 pentoxifylline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 caffeine 
               
               
                 PDE5A 
                 8654 
                 239556_at 
                 2.24 
                 4 
                 Cytoplasm 
                 enzyme 
                 dyphylline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 nitroglycerin, DA- 
               
               
                   
                   
                   
                   
                   
                   
                   
                 8159, aminophylline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 sildenafil, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 dipyridamole, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 aspirin/dipyridamole, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 vardenafil, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 tolbutamide, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 tadalafil, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 theophylline, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 pentoxifylline 
               
               
                 PDGF BB 
                   
                 — 
                   
                 2 
                 Unknown 
                 complex 
               
               
                 PDK1 
                 5163 
                 239798_at 
                 1.654 
                 1 
                 Cytoplasm 
                 kinase 
               
               
                 PDSS1 
                 23590 
                 236298_at 
                 1.64 
                 15 
                 Unknown 
                 enzyme 
               
               
                 PDXDC1 
                 23042 
                 1560014_s_at 
                 2.105 
                 8 
                 Unknown 
                 other 
               
               
                 PHC1 
                 1911 
                 218338_at 
                 1.123 
                 5 
                 Nucleus 
                 other 
               
               
                 PI3K 
                   
                 — 
                   
                 2 
                 Unknown 
                 complex 
               
               
                 PIP5K1C 
                 23396 
                 — 
                   
                 7 
                 Plasma 
                 kinase 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 PIP5K3 
                 200576 
                 1557719_at 
                 2.227 
                 2 
                 Cytoplasm 
                 kinase 
               
               
                 Pka 
                   
                 — 
                   
                 1 
                 Unknown 
                 complex 
               
               
                 Pkc(s) 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 PLAA 
                 9373 
                 — 
                   
                 4 
                 Cytoplasm 
                 other 
               
               
                 PLC gamma 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 Pld 
                   
                 — 
                   
                 8 
                 Unknown 
                 group 
               
               
                 PLK1 
                 5347 
                 — 
                   
                 7 
                 Nucleus 
                 kinase 
                 BI 2536 
               
               
                 PMS2L3 
                 5387 
                 214473_x_at 
                 1.159 
                 3 
                 Unknown 
                 other 
               
               
                 POLR2J2 
                 246721 
                 1552622_s_at 
                 1.828 
                 1 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 POU4F2 
                 5458 
                 — 
                   
                 6 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 PP2A 
                   
                 — 
                   
                 6 
                 Unknown 
                 complex 
               
               
                 PRDM5 
                 11107 
                 — 
                   
                 5 
                 Nucleus 
                 other 
               
               
                 PRKCB1 
                 5579 
                 — 
                   
                 7 
                 Cytoplasm 
                 kinase 
                 enzastaurin, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 ruboxistaurin 
               
               
                 progesterone 
                   
                 — 
                   
                 8 
                 Unknown 
                 chemical- 
               
               
                   
                   
                   
                   
                   
                   
                 endogenous 
               
               
                   
                   
                   
                   
                   
                   
                 mammalian 
               
               
                 PSEN1 
                 5663 
                 242875_at 
                 1.851 
                 2 
                 Plasma 
                 peptidase 
                 (R)-flurbiprofen 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 PTEN 
                 5728 
                 — 
                   
                 3 
                 Cytoplasm 
                 phosphatase 
               
               
                 PTK2 
                 5747 
                 234211_at 
                 2.539 
                 2 
                 Cytoplasm 
                 kinase 
               
               
                 PTPN12 
                 5782 
                 — 
                   
                 7 
                 Cytoplasm 
                 phosphatase 
               
               
                 PTPN14 
                 5784 
                 — 
                   
                 6 
                 Cytoplasm 
                 phosphatase 
               
               
                 PTPRA 
                 5786 
                 — 
                   
                 7 
                 Plasma 
                 phosphatase 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 PTPRD 
                 5789 
                 — 
                   
                 6 
                 Plasma 
                 phosphatase 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 PTPRE 
                 5791 
                 — 
                   
                 7 
                 Plasma 
                 phosphatase 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 PTPRS (includes 
                 5802 
                 1556116_s_at 
                 1.739 
                 7 
                 Plasma 
                 phosphatase 
               
               
                 EG: 5802) 
                   
                   
                   
                   
                 Membrane 
               
               
                 RAB11FIP3 
                 9727 
                 228613_at 
                 2.546 
                 8 
                 Cytoplasm 
                 other 
               
               
                 RAB11FIP4 
                 84440 
                 — 
                   
                 8 
                 Cytoplasm 
                 other 
               
               
                 Rac 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 RAD50 
                 10111 
                 — 
                   
                 5 
                 Nucleus 
                 enzyme 
               
               
                 RAD54L 
                 8438 
                 204558_at 
                 1.483 
                 5 
                 Nucleus 
                 enzyme 
               
               
                 RB1 
                 5925 
                 — 
                   
                 9 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 RBM25 
                 58517 
                 1557081_at 
                 1.57 
                 7 
                 Nucleus 
                 other 
               
               
                 RBM4 
                 5936 
                 213718_at 
                 1.53 
                 7 
                 Nucleus 
                 other 
               
               
                 RBM5 
                 10181 
                 209936_at 
                 2.249 
                 6 
                 Nucleus 
                 other 
               
               
                 RDBP 
                 7936 
                 — 
                   
                 3 
                 Nucleus 
                 other 
               
               
                 RHOA 
                 387 
                 240337_at 
                 2.143 
                 2 
                 Cytoplasm 
                 enzyme 
               
               
                 RHOBTB2 
                 23221 
                 1556645_s_at 
                 1.538 
                   
                 Unknown 
                 enzyme 
               
               
                 RNA polymerase II 
                   
                 — 
                   
                 1 
                 Unknown 
                 complex 
               
               
                 RNU1A 
                 6060 
                 — 
                   
                 1 
                 Unknown 
                 other 
               
               
                 RP13-122B23.3 
                 25920 
                 1556434_at 
                 1.985 
                 3 
                 Nucleus 
                 other 
               
               
                 RPL10 
                 6134 
                 — 
                   
                 6 
                 Cytoplasm 
                 other 
               
               
                 RUNX3 
                 864 
                 204198_s_at 
                 1.233 
                 7 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 SBF1 
                 6305 
                 — 
                   
                 3 
                 Plasma 
                 phosphatase 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SCMH1 
                 22955 
                 — 
                   
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 SCN3A 
                 6328 
                 — 
                   
                 4 
                 Plasma 
                 ion channel 
                 riluzole 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SEC16A 
                 9919 
                 — 
                   
                 10 
                 Cytoplasm 
                 phosphatase 
               
               
                 SEC16B 
                 89866 
                 1552880_at 
                 1.877 
                 10 
                 Nucleus 
                 other 
               
               
                 Secretase gamma 
                   
                 — 
                   
                 9 
                 Unknown 
                 complex 
               
               
                 SF1 
                 7536 
                 210172_at 
                 2.452 
                 1, 4 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 SF3B1 
                 23451 
                 214305_s_at 
                 1.359 
                 1 
                 Nucleus 
                 other 
               
               
                 SFRS15 
                 57466 
                 243759_at 
                 2.028 
                   
                 Nucleus 
                 other 
               
               
                 SGCA 
                 6442 
                 1562729_at 
                 2.395 
                 8 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SGCB 
                 6443 
                 — 
                   
                 8 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SGCD 
                 6444 
                 — 
                   
                 8 
                 Cytoplasm 
                 other 
               
               
                 SGCG 
                 6445 
                 — 
                   
                 8 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SH2D1A (includes 
                 4068 
                 — 
                   
                 5 
                 Cytoplasm 
                 other 
               
               
                 EG: 4068) 
               
               
                 SKIL 
                 6498 
                 — 
                   
                 4 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 SLC29A1 
                 2030 
                 — 
                   
                 9 
                 Plasma 
                 transporter 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SLC2A11 
                 66035 
                 232167_at 
                 1.529 
                 9 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SLC2A8 
                 29988 
                 239426_at 
                 2.012 
                   
                 Plasma 
                 transporter 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SLC30A9 
                 10463 
                 237051_at 
                 2.063 
                 7 
                 Nucleus 
                 transporter 
               
               
                 SLC4A1 
                 6521 
                 — 
                   
                 9 
                 Plasma 
                 transporter 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SMAD4 
                 4089 
                 — 
                   
                 6 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 SMARCA5 
                 8467 
                 — 
                   
                 9 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 SMC5 
                 23137 
                 — 
                   
                 12 
                 Nucleus 
                 other 
               
               
                 SMC6 
                 79677 
                 218781_at 
                 1.203 
                 12 
                 Nucleus 
                 other 
               
               
                 SMN1 
                 6606 
                 — 
                   
                 6 
                 Nucleus 
                 other 
               
               
                 SNRPA1 
                 6627 
                 242146_at 
                 3.54 
                 8 
                 Nucleus 
                 other 
               
               
                 SNW1 
                 22938 
                 — 
                   
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 SON 
                 6651 
                 201085_s_at 
                 1.144 
                 5 
                 Nucleus 
                 other 
               
               
                 SP4 
                 6671 
                 — 
                   
                 3 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 sphingomyelin 
                   
                 — 
                   
                 9 
                 Unknown 
                 chemical- 
               
               
                   
                   
                   
                   
                   
                   
                 endogenous 
               
               
                   
                   
                   
                   
                   
                   
                 mammalian 
               
               
                 SPN 
                 6693 
                 — 
                   
                 3 
                 Plasma 
                 transmembrane 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                 receptor 
               
               
                 SPTBN1 
                 6711 
                 — 
                   
                 4, 6, 8 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SQLE 
                 6713 
                 213577_at 
                 1.502 
                 3 
                 Cytoplasm 
                 enzyme 
               
               
                 SQSTM1 
                 8878 
                 — 
                   
                 5 
                 Cytoplasm 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 SRC 
                 6714 
                 — 
                   
                 6 
                 Cytoplasm 
                 kinase 
                 dasatinib, AZM- 
               
               
                   
                   
                   
                   
                   
                   
                   
                 475271 
               
               
                 STK36 
                 27148 
                 231806_s_at 
                 1.362 
                 6 
                 Unknown 
                 kinase 
               
               
                 STRAP 
                 11171 
                 1558002_at 
                 2.189 
                 2 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 STX3 
                 6809 
                 — 
                   
                 7 
                 Plasma 
                 transporter 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SUMO1 
                 7341 
                 — 
                   
                 8 
                 Nucleus 
                 enzyme 
               
               
                 SUMO2 
                 6613 
                 — 
                   
                 9 
                 Nucleus 
                 other 
               
               
                 SVIL 
                 6840 
                 215279_at 
                 2.228 
                 4 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 SYNE2 
                 23224 
                 202761_s_at 
                 1.356 
                 1 
                 Nucleus 
                 other 
               
               
                 TAF15 
                 8148 
                 227891_s_at 
                 1.971 
                 1 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TAF1A 
                 9015 
                 — 
                   
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TAF1B 
                 9014 
                 239046_at 
                 1.468 
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TAF1C 
                 9013 
                 — 
                   
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TAOK3 
                 51347 
                 220761_s_at 
                 1.195 
                 2 
                 Cytoplasm 
                 kinase 
               
               
                 Tap 
                   
                 — 
                   
                 17 
                 Unknown 
                 complex 
               
               
                 TBC1D8 
                 11138 
                 204526_s_at 
                 1.373 
                 3 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 TCERG1 
                 10915 
                 — 
                   
                 8 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TCF7L2 
                 6934 
                 — 
                   
                 6 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TCOF1 (includes 
                 6949 
                 202385_s_at 
                 1.169 
                 1 
                 Nucleus 
                 transporter 
               
               
                 EG: 6949) 
               
               
                 TCR 
                   
                 — 
                   
                 2 
                 Unknown 
                 complex 
               
               
                 TERF2 
                 7014 
                 — 
                   
                 5 
                 Nucleus 
                 other 
               
               
                 TH1L 
                 51497 
                 — 
                   
                 3 
                 Nucleus 
                 other 
               
               
                 THAP7 
                 80764 
                 — 
                   
                 1 
                 Nucleus 
                 other 
               
               
                 THRAP3 
                 9967 
                 217847_s_at 
                 1.464 
                 1 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TIMP1 
                 7076 
                 — 
                   
                 9 
                 Extracellular 
                 other 
               
               
                   
                   
                   
                   
                   
                 Space 
               
               
                 TNF 
                 7124 
                 — 
                   
                 4 
                 Extracellular 
                 cytokine 
                 adalimumab, 
               
               
                   
                   
                   
                   
                   
                 Space 
                   
                 etanercept, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 infliximab, CDP870, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 golimumab, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 thalidomide 
               
               
                 TNRC6A 
                 27327 
                 234734_s_at 
                 1.268 
                 9 
                 Nucleus 
                 other 
               
               
                 TP53 
                 7157 
                 — 
                   
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TP53BP1 
                 7158 
                 — 
                   
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TPM4 
                 7171 
                 235094_at 
                 2.079 
                 8 
                 Cytoplasm 
                 other 
               
               
                 Trans- 
                   
                 — 
                   
                 15 
                 Unknown 
                 group 
               
               
                 hexaprenyltranstransferase 
               
               
                 TRIM33 
                 51592 
                 239716_at 
                 2.496 
                 6 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TRIO 
                 7204 
                 240773_at 
                 2.607 
                 2 
                 Plasma 
                 kinase 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 tRNA 
                   
                 — 
                   
                 19 
                 Unknown 
                 group 
               
               
                 adenylyltransferase 
               
               
                 tRNA 
                   
                 — 
                   
                 19 
                 Unknown 
                 group 
               
               
                 cytidylyltransferase 
               
               
                 TRNT1 
                 51095 
                 243236_at 
                 2.295 
                 19 
                 Cytoplasm 
                 enzyme 
               
               
                 TRPV1 
                 7442 
                 1556229_at 
                 2.636 
                 2 
                 Plasma 
                 ion channel 
                 SB-705498, 
               
               
                   
                   
                   
                   
                   
                 Membrane 
                   
                 capsaicin 
               
               
                 TSG101 
                 7251 
                 — 
                   
                 5, 7 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 TSPAN7 
                 7102 
                 — 
                   
                 7 
                 Plasma 
                 other 
               
               
                   
                   
                   
                   
                   
                 Membrane 
               
               
                 TTC3 
                 7267 
                 208664_s_at 
                 1.396 
                 7 
                 Cytoplasm 
                 other 
               
               
                 TXNL1 
                 9352 
                 243664_at 
                 1.98 
                 9 
                 Cytoplasm 
                 enzyme 
               
               
                 Ubiquitin 
                   
                 — 
                   
                 1 
                 Unknown 
                 group 
               
               
                 UGT 
                   
                 — 
                   
                 7 
                 Unknown 
                 group 
               
               
                 UGT1A6 
                 54578 
                 206094_x_at 
                 3.86 
                 7 
                 Cytoplasm 
                 enzyme 
               
               
                 USP36 
                 57602 
                 224979_s_at 
                 1.393 
                 18 
                 Nucleus 
                 peptidase 
               
               
                 Vegf 
                   
                 — 
                   
                 2 
                 Unknown 
                 group 
               
               
                 VEGFA 
                 7422 
                 — 
                   
                 3 
                 Extracellular 
                 growth factor 
                 bevacizumab, 
               
               
                   
                   
                   
                   
                   
                 Space 
                   
                 ranibizumab, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 pegaptanib 
               
               
                 VEGFB (includes 
                 7423 
                 — 
                   
                 3 
                 Extracellular 
                 growth factor 
               
               
                 EG: 7423) 
                   
                   
                   
                   
                 Space 
               
               
                 VPS28 
                 51160 
                 — 
                   
                 5 
                 Cytoplasm 
                 transporter 
               
               
                 VPS37B 
                 79720 
                 236889_at 
                 2.85 
                 5 
                 Nucleus 
                 other 
               
               
                 WAS 
                 7454 
                 — 
                   
                 11 
                 Cytoplasm 
                 other 
               
               
                 WDR68 
                 10238 
                 233782_at 
                 1.924 
                 4 
                 Cytoplasm 
                 other 
               
               
                 WFS1 
                 7466 
                 1555270_a_at 
                 1.315 
                 3 
                 Cytoplasm 
                 enzyme 
               
               
                 WIPF2 
                 147179 
                 216006_at 
                 2.916 
                 11 
                 Unknown 
                 other 
               
               
                 WT1 
                 7490 
                 — 
                   
                 6 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 WTAP 
                 9589 
                 1560274_at 
                 1.747 
                 2 
                 Nucleus 
                 other 
               
               
                 XRCC5 
                 7520 
                 232633_at 
                 2.106 
                 5 
                 Nucleus 
                 enzyme 
               
               
                 YWHAG 
                 7532 
                 — 
                   
                 4 
                 Cytoplasm 
                 other 
               
               
                 ZEB1 
                 6935 
                 — 
                   
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 ZFHX3 
                 463 
                 215828_at 
                 1.737 
                 5 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 ZFR 
                 51663 
                 238970_at 
                 2.655 
                   
                 Nucleus 
                 other 
               
               
                 ZFX 
                 7543 
                 207920_x_at 
                 1.625 
                 9 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 ZMYND8 
                 23613 
                 209049_s_at 
                 1.102 
                 7 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 ZNF224 
                 7767 
                 216983_s_at 
                 2.986 
                 6 
                 Nucleus 
                 other 
               
               
                 ZNF226 
                 7769 
                 219603_s_at 
                 1.332 
                 8 
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 ZNF326 
                 284695 
                 241720_at 
                 1.418 
                   
                 Nucleus 
                 transcription 
               
               
                   
                   
                   
                   
                   
                   
                 regulator 
               
               
                 ZNF536 
                 9745 
                 233890_at 
                 3.303 
                   
                 Unknown 
                 other 
               
               
                 ZWINT (includes 
                 11130 
                 — 
                   
                 3 
                 Nucleus 
                 other 
               
               
                 EG: 11130) 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Cell Surface Genes 
               
            
           
           
               
               
               
            
               
                 Entrez Gene ID 
                   
                   
               
               
                 for Human 
                 Name 
                 Location 
               
               
                   
               
            
           
           
               
               
               
            
               
                 7204 
                 TRIO 
                 Plasma Membrane 
               
               
                 1956 
                 EGFR 
                 Plasma Membrane 
               
               
                 7102 
                 TSPAN7 
                 Plasma Membrane 
               
               
                 977 
                 CD151 
                 Plasma Membrane 
               
               
                 2064 
                 ERBB2 
                 Plasma Membrane 
               
               
                 2321 
                 FLT1 
                 Plasma Membrane 
               
               
                 2030 
                 SLC29A1 
                 Plasma Membrane 
               
               
                 11171 
                 STRAP 
                 Plasma Membrane 
               
               
                 8828 
                 NRP2 
                 Plasma Membrane 
               
               
                 4233 
                 MET 
                 Plasma Membrane 
               
               
                 273 
                 AMPH 
                 Plasma Membrane 
               
               
                 351 
                 APP 
                 Plasma Membrane 
               
               
                 1756 
                 DMD 
                 Plasma Membrane 
               
               
                 1495 
                 CTNNA1 
                 Plasma Membrane 
               
               
                 8727 
                 CTNNAL1 
                 Plasma Membrane 
               
               
                 10211 
                 FLOT1 
                 Plasma Membrane 
               
               
                 3459 
                 IFNGR1 
                 Plasma Membrane 
               
               
                 23396 
                 PIP5K1C 
                 Plasma Membrane 
               
               
                 5663 
                 PSEN1 
                 Plasma Membrane 
               
               
                 6445 
                 SGCG 
                 Plasma Membrane 
               
               
                 6693 
                 SPN 
                 Plasma Membrane 
               
               
                 6711 
                 SPTBN1 
                 Plasma Membrane 
               
               
                 6840 
                 SVIL 
                 Plasma Membrane 
               
               
                 2057 
                 EPOR 
                 Plasma Membrane 
               
               
                 5789 
                 PTPRD 
                 Plasma Membrane 
               
               
                 4352 
                 MPL 
                 Plasma Membrane 
               
               
                 5786 
                 PTPRA 
                 Plasma Membrane 
               
               
                 27020 
                 NPTN 
                 Plasma Membrane 
               
               
                 3690 
                 ITGB3 
                 Plasma Membrane 
               
               
                 7442 
                 TRPV1 
                 Plasma Membrane 
               
               
                 8639 
                 AOC3 
                 Plasma Membrane 
               
               
                 1131 
                 CHRM3 
                 Plasma Membrane 
               
               
                 3804 
                 KIR2DL3 
                 Plasma Membrane 
               
               
                 287 
                 ANK2 
                 Plasma Membrane 
               
               
                 3071 
                 NCKAP1L 
                 Plasma Membrane 
               
               
                 5791 
                 PTPRE 
                 Plasma Membrane 
               
               
                 5802 
                 PTPRS 
                 Plasma Membrane 
               
               
                 6305 
                 SBF1 
                 Plasma Membrane 
               
               
                 6328 
                 SCN3A 
                 Plasma Membrane 
               
               
                 6442 
                 SGCA 
                 Plasma Membrane 
               
               
                 6443 
                 SGCB 
                 Plasma Membrane 
               
               
                 66035 
                 SLC2A11 
                 Plasma Membrane 
               
               
                 29988 
                 SLC2A8 
                 Plasma Membrane 
               
               
                 6521 
                 SLC4A1 
                 Plasma Membrane 
               
               
                 6809 
                 STX3 
                 Plasma Membrane 
               
               
                 11138 
                 TBC1D8 
                 Plasma Membrane 
               
               
                   
               
            
           
         
       
     
     A used herein “CSC-associated gene” refers to a gene whose expression or function is altered in cancer stem cells. CSC-associated genes include genes whose expression is signficantly altered, e.g., significantly upregulated or significantly downregulated, in cancer stem cells compared with non-cancer stem cells, e.g., cancer cells that are not stem cells, normal cells, etc. In some embodiments, genes that have significantly altered expression levels in cancer stem cells are identified by using an appropriate statistical test for establishing the significance of differences between expression levels in a cancer stem cell and a non-cancer stem cell. Tests for statistical significance are well known in the art and are exemplified in  Applied Statistics for Engineers and Scientists  by Petruccelli, Chen and Nandram 1999 Reprint Ed. The magnitude of up-, or down-, regulated expression of a CSC-associated gene in a cancer stem cell compared with a non-cancer stem cell may vary. In some embodiments, the expression level of a CSC-associated gene is at least 10%, at least 25%, at least 50%, at least 100%, at least 250%, at least 500%, or at least 1000% higher, or lower, than its expression level in a non-cancer stem cell. In other embodiments, the expression level of a CSC-associated gene is at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 20-fold, at least 30-fold, at least 40-fold, at least 50-fold, at least 100-fold, or more higher, or lower, than its expression level a non-cancer stem cell. 
     CSC-associated genes are not limited to genes which are upregulated or downregulated in cancer stem cells. In some embodiments, a CSC-associated gene is a gene that may or may not have altered expression in a cancer stem cell, but that nevertheless functions in a pathway that is deregulated in cancer stem cells. Typically, deregulated pathways in cancer stem cells involve the product(s) of one or more genes whose expression is upregulated or downregulated and/or the product(s) of one or more genes with altered functionality, e.g., due to a mutation, thereby resulting in altered function of the pathway, e.g., overactivity or underactivity of the pathway. 
     In some embodiments, CSC-associated genes are identified in cancer stem cells of a breast cancer, prostate cancer, colon cancer, lung cancer, renal cancer or melanoma. In some instances, CSC-associated genes are identified in cancer stem cells of a melanoma, which are also referred to as malignant melanoma initiating cells (MMIC). Other cancer stem cells (e.g., non-ABCB5 +  CSCs) are known in the art. 
     Exemplary CSC-associated genes are disclosed in Tables 1-8. In some embodiments, a CSC-associated gene is selected from the group consisting of: ANK2, NCKAP1L, PTPRE, PTPRS, SBF1, SCN3A, SGCA, SGCB, SLC2A11, SLC2A8, SLC4A1, STX3, and TBC1D8. In some embodiments, the CSC-associated gene is one that is not a gene of the group consisting of EGFR, CD151, ERBB2, FLT1, SLC29A1, NRP2, MET, AMPH, APP, DMD, and ITGB3. In some embodiments, the CSC-associated gene is one that is not a gene of the group consisting of: TRIO, TSPAN7, STRAP, CTNNA1, CTNNAL1, FLOT1, IFNGR1, PIP5K1C, PSEN1, SGCG, SPN, SPTBN1, SVIL, EPOR, PTPRD, MPL, PTPRA, NPTN, TRPV1, AOC3, CHRM3, and KIR2DL3. In some embodiments, the CSC-associated gene is one that is not a gene that has previously been indicated as a tumor suppressor or oncogene. In some embodiments, the CSC-associated gene is one that is not a gene of the group consisting of: EWSR1, TP53, EGFR, ITPR1, NBR1, MLL, PTK2, PTPN14, RB1, JARID1A, SKIL, TNF, TP53BP1, TRIO, SF1, TAF15, NCOA3, RAD54L, CUL4A, SMARCA5, RAD50, AKAP9, DENND4A, DDX17, HECW1, ZMYND8, ANAPC13, ANAPC5, TH1L, TRIM33, and CHD8. In some embodiments, the CSC-associated gene is one that is not a gene of the group consisting of: BARD1, BCL2, CBS, CTNNB1, ERBB2, EWSR1, HPS1, IFNG, IL1B, PTEN, TP53, VEGFA, CHEK2, and HPS4. 
     In part, the disclosure relates to CSC-associated genes as well as the RNAs and polypeptides (CSC-associated RNA and polypeptides) that they encode and antibodies and antigen-binding fragments that specifically bind them. The CSC-associated genes, RNAs and polypeptides, encompass variants, homologues, and fragments. Variants may result from alternative splicing or allelic variation of certain genes provided in Tables 5. In general, homologues and alleles typically will share at least 90% nucleotide identity and/or at least 95% amino acid identity to the sequences of the cancer antigen nucleic acids and polypeptides, respectively, in some instances will share at least 95% nucleotide identity and/or at least 97% amino acid identity, in other instances will share at least 97% nucleotide identity and/or at least 98% amino acid identity, in other instances will share at least 99% nucleotide identity and/or at least 99% amino acid identity, and in other instances will share at least 99.5% nucleotide identity and/or at least 99.5% amino acid identity. Homology can be calculated using various, publicly available software tools known in the art, such as those developed by NCBI (Bethesda, Md.) that are available through the internet. Exemplary tools include the BLAST system (e.g., using the default nucleic acid (Blastn) or protein (Blastp) search parameters) available from the website of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. 
     The CSC-associated genes are, among other things, useful for diagnosing cancer, such as breast cancer, prostate cancer, colon cancer, lung cancer, renal cancer or melanoma. Because CSC-associated gene expression is altered in cancer (e.g., upregulated or downregulated), the expression level of CSC-associated gene(s), e.g., a gene listed in Table 5 or 7, in an individual is diagnostic of cancer in that individual. Accordingly, the diagnostic methods disclosed herein can involve determining the CSC-associated RNA or protein (polypeptide) levels. 
     The term “individual” as used herein means any mammalian individual or subject, including, e.g., humans and non-human mammals, such as primates, rodents, and dogs. Individuals specifically intended for diagnosis and treatment using the methods described herein are preferably humans. 
     The expression level of CSC-associated gene(s) may be determined by using any of a number of methods known in the art. In some embodiments, the expression levels are determined from a biological sample (e.g., a test sample) obtained from a individual (e.g., a human). Exemplary, biological samples include an isolated cell, an isolated tissue, saliva, gingival secretions, cerebrospinal fluid (spinal fluid), gastrointestinal fluid, mucus, urogenital secretions, synovial fluid, blood, serum, plasma, urine, cystic fluid, lymph fluid, ascites, pleural effusion, interstitial fluid, intracellular fluid, ocular fluids, seminal fluid, mammary secretions, vitreal fluid, and nasal secretions. However, biological samples are not so limited and other exemplary biological specimens will be readily apparent to one of ordinary skill in the art. For the purposes of diagnosing melanoma, for example, the biological sample is preferably a skin tissue sample, e.g., a skin biopsy containing a suspicious lesion. 
     Expression levels of CSC-associated genes may be determined for diagnostic purposes using nucleic acid hybridization or nucleic acid amplification to detect the mRNAs that they encode. Methods for nucleic acid hybridization or amplification are well known in the art. In some embodiments, the nucleic acid amplification is real-time RT-PCR or RT-PCR. Other methods known to one of ordinary skill in the art could be employed to analyze mRNA levels, for example nucleic acid arrays, cDNA analysis, Northern analysis, and RNase Protection Assays. Nucleic acid arrays may be used to assay (e.g., for diagnostic purposes) the expression levels of multiple CSC-associated genes in parallel. Other suitable nucleic acid detection methods will be apparent to the skilled artisan. 
     Expression levels of CSC-associated genes may be determined for diagnostic purposes by detecting the polypeptides that they encode. Methods for detecting polypeptides are well known in the art. Exemplary polypeptide detection methods include, but are not limited to, Enzyme Linked Immunosorbent Assays (ELISA), radioimmunoassays (RIA), sandwich immunometric assays, flow cytometry, western blot assays, immunoprecipitation assays, immunohistochemistry, immunomicroscopy, lateral flow immuno-chromatographic assays, BIACORE technology, and proteomics methods, such as mass spectroscopy. Antibody arrays may be used to assay (e.g., for diagnostic purposes) the expression levels of multiple CSC-associated genes in parallel. Other suitable polypeptide detection methods will be apparent to the skilled artisan. 
     In some embodiments, e.g., where polypeptide, antibody or nucleic acid arrays are used, expression levels of up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, or more CSC-associated genes may be tested in parallel. 
     The diagnostic methods of the invention involve a comparison between expression levels of CSC-associated genes in a test sample and a reference value. The results of the comparison are diagnostic of cancer, e.g., melanoma. In some embodiments, the reference value is the expression level of the gene in a reference sample. A reference value may be a predetermined value and may also be determined from reference samples (e.g., control biological samples) tested in parallel with the test samples. A reference value may be a positive or negative control level. A reference value can be a single cut-off value, such as a median or mean or a range of values, such as a confidence interval. Reference values can be established for various subgroups of individuals, such as individuals predisposed to cancer, individuals having early or late stage cancer, male and/or female individuals, or individuals undergoing cancer therapy. The level of the reference value will depend upon the particular population or subgroup selected. For example, an apparently healthy population will have a different “normal” value than will a population which has cancer, or a population that has a predisposition for cancer. Appropriate ranges and categories for reference values can be selected with no more than routine experimentation by those of ordinary skill in the art. 
     The reference sample can be any of a variety of biological samples against which a diagnostic assessment may be made. Examples of reference samples include biological samples from control populations or control samples. Reference samples may be generated through manufacture to be supplied for testing in parallel with the test samples, e.g., reference sample may be supplied in diagnostic kits. When the reference sample is from a cancer, e.g., tumor tissue, the expression level of the reference sample (the reference value) is the expression level of the CSC-associated gene in the cancer. Similarly, when the reference sample is a normal sample, e.g., non-tumor tissue, the expression level of the reference sample (the reference value) is the expression level of the CSC-associated gene in the non-tumor tissue. Similarly, when the reference sample is a cancer stem cell sample, the expression level of the reference sample (the reference value) is the expression level of the CSC-associated gene in the cancer stem cell sample. In some embodiments, the reference sample is of a melanoma and the expression level of the reference sample is the expression level of the CSC-associated gene in melanoma. In some embodiments, the reference sample is of a non-melanoma tissue and the expression level of the reference sample is the expression level of the CSC-associated gene in non-melanoma tissue. Other appropriate reference samples will be apparent to the skilled artisan. 
     The diagnostic methods are based in part on a comparison of expression levels of CSC-associated genes between test samples and reference sample. In some embodiments, if the expression level of the CSC-associated gene in the test sample is about equal to the expression level of the CSC-associated gene in the reference sample, then the test sample and reference sample are likely of a similar origin, category or class. For example, if expression levels in a test sample and reference sample are about the same (e.g., not statistically significantly different), and the reference sample is from a normal tissue, then the test sample is likely a normal tissue sample, and a normal diagnosis could be indicated. Alternatively, if expression levels in a test sample and reference sample are about the same, and the reference sample is from a cancer tissue, then the test sample is likely a cancer sample, and a diagnosis of cancer could be indicated. In certain embodiments, if the expression level in a test sample and reference sample are about the same, and the reference sample is from a melanoma, then the test sample is likely a melanoma sample, and a diagnosis of melanoma could be indicated. 
     In some cases, depending on factors such as the particular CSC-associated gene(s) being evaluated, the condition being diagnosed, and the type of reference sample, an expression level of a CSC-associated gene in a test sample that is statistically significantly higher or statistically significantly lower than its expression level in a reference sample indicates a diagnosis. For example, when the CSC-associated gene is among those listed in Table 1 or 8 and the reference value is the expression level of the CSC-associated gene in a normal (e.g., non-cancerous) reference sample, if the expression level of the CSC-associated gene in the test sample is significantly higher than the expression level of the CSC-associated gene in the normal reference sample, the comparison indicates cancer, e.g., melanoma. Similarly, when the CSC-associated gene is among those listed in Table 1 or 8 and the reference value is the expression level of the CSC-associated gene in a cancer, e.g., melanoma, reference sample, if the expression level of the CSC-associated gene in the test sample is significantly lower than the expression level of the CSC-associated gene in the cancer reference sample, the comparison does not indicate cancer. Alternatively, when the CSC-associated gene is among those listed in Table 2 or 7 and the reference value is the expression level of the CSC-associated gene in a normal reference sample, if the expression level of the CSC-associated gene in the test sample is significantly lower than the expression level of the CSC-associated gene in the normal reference sample, the comparison indicates cancer. Similarly, when the CSC-associated gene is in Table 2 or 7 and the reference value is the expression level of the CSC-associated gene in a cancer, e.g., melanoma, reference sample, if the expression level of the CSC-associated gene in the test sample is significantly higher than the expression level of the CSC-associated gene in the cancer reference sample, the comparison does not indicate melanoma. Appropriate combinations of particular CSC-associated gene(s), conditions to be diagnosed, and types of reference samples, can be selected with no more than routine experimentation by those of ordinary skill in the art for use in the diagnostic methods disclosed herein. 
     The magnitude of the difference between the test sample and reference sample that is sufficient to indicate a diagnosis will depend on a variety of factors such as the particular CSC-associated gene(s) being evaluated, the condition being diagnosed, heterogeneity in healthy or disease populations from which samples are drawn, the type of reference sample, the magnitude of expression level of a CSC-associated gene, the assay being used, etc. It is well within the purview of the skilled artisan to determine the appropriate magnitude of difference between the test sample and reference sample that is sufficient to indicate a diagnosis. In some embodiments, the expression level of the CSC-associated gene in the test sample is at least 10%, at least 20%, at least 50%, at least 100%, at least 200%, at least 500%, at least 1000% or more higher than the expression level of the gene in the reference sample. In other embodiments, the expression level of the CSC-associated gene in the test sample is at least 10%, at least 20%, at least 50%, at least 100%, at least 200%, at least 500%, at least 1000% or more lower than the expression level of the gene in the reference sample. 
     Some CSC-associated genes that are normally produced in very low quantities but whose production is dramatically increased in tumor cells, e.g., a CSC-associated gene in Table 1 or 8, can trigger an immune response. Thus, in some instances, specific immunoreactivity against a CSC-associated polypeptide, e.g., a polypeptide encoded by a gene listed in Table 1 or 8, in a individual may be diagnostic of cancer in the individual. Immunoreactivity against CSC-associated polypeptides may be humoral or cellular, and is associated with a specific immune response to a CSC-associated polypeptide that is upregulated in a cancer stem cell in an individual. In the case of a humoral response the diagnostic methods may involve detecting the presence of one or more antibodies in an individual that specifically bind CSC-associated polypeptides. Methods for detecting antibodies are disclosed herein (e.g., ELISA, peptide arrays, etc.) and are well known in the art. In some cases, the presence of CSC-polypeptide specific effector cells is diagnostic of an immune response specific to that CSC-polypeptide. 
     T Lymphocytes recognize complexes of peptide ligands (e.g., CSC-associated polypeptides) and Major Histocompatibility Complex (MHC) molecules presented at the surface of Antigen Presenting Cells (APC). Class I tetramers bind to a distinct set of T cell receptors (TCRs) on a subset of CD8+ T cells, and Class II tetramers bind to a distinct population of CD4+ T cells. Methods for detecting antigen-specific T cells using MHC tetramers are well known in the art (e.g., New Microarray Detects Antigen-Specific T Cells and Immune Responses. PLoS Biol 1(3): e76 2003) and can be used to detect CSC-polypeptide specific T cells which may be diagnostic of cancer in an individual. ITAG reagents, for example, from Beckman Coulter provide a convenient way to measure the cellular response directed toward a single CSC-associated peptide using MHC tetramers. 
     The methods for evaluating expression of CSC-associated genes, e.g., diagnostic methods, disclosed herein may be combined with methods for treating an individual having or suspected of having cancer. The treatment may comprise a step of determining the expression level of the CSC-associated gene in the individual. The treatment may also comprise a step of comparing the expression level of the CSC-associated gene to a reference value, such that the results of the comparison are diagnostic of cancer in the individual. In certain cases, if the comparison results in a diagnosis of cancer in the individual, the administering step is performed. In some cases, after a diagnosis is made using the methods disclosed herein, a treatment plan is selected. For example, if a diagnostic assay reveals that the expression of a particular CSC-associated gene is altered, e.g., increased or decreased, compared to a normal reference sample, then a treatment directed at that particular CSC-associated gene may be implemented. The diagnostic methods can also be used to evaluate the response to a treatment. For example, the determining and the comparing may be repeated at one or more intervals after the administering step to evaluate the response to the treatment. 
     CSC-associated polypeptide arrays and arrays of antibodies that bind CSC-associated polypeptides may be constructed by immobilizing large numbers of isolated CSC associated polypeptides or antibodies, or antigen binding fragments, to a solid support. Methods for producing polypeptide and antibody arrays are well known in the art. The methods typically involve production of proteins (CSC-associated polypeptides or antibodies) from an expression library, cloned into  E. coli , yeast, or mammalian cells, or similar system, e.g., hybridomas etc., from which the expressed proteins are then purified, for example via His, GST tag, or Protein A/G affinity purification. Cell free protein transcription/translation is an alternative for synthesis of proteins which do not express well in bacterial or other in vivo systems. The purified isolated CSC associated polypeptides or antibodies are immobilized on the array surface (solid support surface) using art known methods. For example, proteins can be immobilized by adsorption, covalent (e.g., aldehydes) and non-covalent (e.g., biotin-streptavidin) interactions. Other methods of conjugation will be readily apparent to one of ordinary skill in the art. In some embodiments, the polypeptide arrays of the invention consist essentially of at least 2, at least 5, at least 10, at least 20, at least 50, at least 100, or more polypeptides or immunogenic fragments thereof encoded by a CSC-associated gene set forth in Table 1, 5, 7, or 8. In some embodiments, the antibody arrays of the invention consist essentially of at least 2, at least 5, at least 10, at least 20, at least 50, at least 100, or more different antibodies or antigen-binding fragments that specifically bind polypeptides (CSC-associated polypeptides) encoded by a CSC-associated gene set forth in Table 1, 5, 7, or 8. 
     Methods for producing nucleic acid arrays are well known in the art. Nucleic acid arrays may be constructed by, e.g., immobilizing to a solid support large numbers oligonucleotides, polynucleotides, or cDNAs having sequences complementary to CSC-associated mRNAs. The skilled artisan is also referred to Chapter 22 “Nucleic Acid Arrays” of Current Protocols In Molecular Biology (Eds. Ausubel et al. John Wiley and #38; Sons NY, 2000), International Publication WO00/58516, U.S. Pat. Nos. 5,677,195 and 5,445,934 which provide exemplary methods relating to nucleic acid array construction and use in detection of nucleic acids of interest. In some embodiments, the nucleic acid arrays consist essentially of at least 2, at least 5, at least 10, at least 20, at least 50, at least 100, at least 200, at least 300, or more of the CSC-associated genes set forth in Table 1, 5, 7, or 8. 
     In some embodiments, the expression levels of multiple CSC-associated genes may be combined to produce an expression profile. As used herein, “expression profile” refers to a set of expression levels of a plurality (e.g., 2 or more) of CSC-associated genes. Expression profiles have a variety of uses. For example, expression profiles may be used to classify (or sub-classify) a sample, preferably a clinical sample. In some embodiments, reference samples, for which a classification, e.g., a disease category, e.g., breast cancer, prostate cancer, melanoma, etc., has already been ascertained, are used to produce known expression profiles. In some embodiments, the similarity of an expression profile of a test sample and a known expression profile, is assessed by comparing the level of the same CSC-associated gene in the test and known expression profiles (i.e., expression level pairs). In some cases, a test expression profile is compared with one or more members of a plurality of known expression profiles, and a known expression profile that most closely resembles (i.e., is most similar to) the test profile is identified. In certain cases, the classification of a known expression profile that is identified as similar to a test expression profile is assigned to the test expression profile, thereby classifying the clinical sample associated with the test expression profile. The methods are useful for classifying samples across a range of phenotypes, e.g., disease status, risk status, etc., based on expression profiles. In some embodiments, a classification model (e.g., discriminant function, naïve bayes, support vector machine, logistic regression, and others known in the art) may be built based on the reference expression profiles from various samples from individuals known to have different disorders (e.g., cancers) and/or from healthy individuals, and used to classify subsequently obtained samples (e.g., clinical samples). 
     The invention also provides methods for stratifying a population comprising individuals having cancer. In some embodiments, methods involve determining expression levels of at least 2, at least 5, at least 10, at least 20, at least 50, at least 100, at least 200, at least 300, or more of the CSC-associated genes set forth in Table 5, 7, or 8, for example, by using the arrays of the invention, and stratifying the population based on the expression levels. The stratification methods are useful in epidemiological studies, for example, to identify subpopulations of individuals at risk of cancer. The methods are also useful in clinical studies to identify patient subpopulations that respond better or worse to a particular treatment. 
     In some aspects, CSC-associated genes provide a basis for identifying, isolating, cloning, propagating, and expanding CSC populations in vitro. The present invention contemplates any suitable method of employing agents, e.g., isolated peptides, e.g., antibodies, that bind to CSC-associated polypeptides to separate CSCs from other cells. Accordingly, included in the present invention is a method of producing a population of isolated CSCs. The methods involve contacting a sample, e.g., a cell suspension, with one or a combination of agents, e.g., antibodies or antigen binding fragments or ligands, which recognize and bind to an epitope, e.g., a cell surface protein, including CSC-associated polypeptides (e.g., polypeptides encoded by the genes listed in Table 4), on the CSC and separating and recovering from the sample the cells bound by the agents. The CSC-associated polypeptide may be encoded by a CSC-associated gene that is selected from the group consisting of: ANK2, NCKAP1L, PTPRE, PTPRS, SBF1, SCN3A, SGCA, SGCB, SLC2A11, SLC2A8, SLC4A1, STX3, and TBC1D8. 
     In some instances, commerically available antibodies or antibody fragments that bind CSC-associated polypeptides may be used in the methods disclosed herein. For example, antibodies against ANK2 include, e.g., rabbit anti-human Ankyrin brain polyclonal antibody from Abcam; mouse anti-human ANK2 monoclonal antibody clone 2.2 from Genway Biotech, Inc.; and mouse anti-human Ankyrin, brain variant 2 (ANK2) monoclonal, clone 2.20 and rabbit anti-human ankyrin, brain variant 2 (ank2) polyclonal from Lifespan Biosciences. Antibodies against NCKAP1L include, e.g., rabbit anti-human HEM1 polyclonal antibody from Proteintech Group, Inc. and are described in Weiner O D, et al., (2006) Hem-1 Complexes Are Essential for Rac Activation, Actin Polymerization, and Myosin Regulation during Neutrophil Chemotaxis. PLoS Biol 4(2): e38. Antibodies against PTPRE include, e.g., rabbit anti-PTPepsilon C-term RB0551-0552 polyclonal antibody from Abgent, mouse anti-human PTPRE polyclonal antibody from Abnova Corporation; mouse anti-PTPRE monoclonal antibody Clone 2D10 from Abnova Corporation; chicken anti-human PTPRE polyclonal antibody from Thermo Scientific; and Rabbit Anti-Protein Tyrosine phosphatase epsilon (PTPRE) antibody from Acris Antibodies GmbH. Antibodies against PTPRS include, e.g., mouse anti-PTPRS monoclonal antibody from Abcam; mouse anti-human PTPRS monoclonal antibody Clone 1H6 from Abnova Corporation; chicken anti-human PTPRS polyclonal antibody from ABR-Affinity Bioreagents, now sold as Thermo Scientific; chicken anti-human PTPRS polyclonal antibody from GeneTex; and mouse anti-human PTPRS monoclonal antibody, Clone 1H6 from GeneTex. Antibodies against SCN3A include, e.g., rabbit anti-SCN3A polyclonal antibody from Abcam; mouse anti-human SCN3A monoclonal antibody Clone 3F3 from Abnova Corporation; and mouse Anti-human SCN3A monoclonal antibody Clone 3F3 from GeneTex. Antibodies against SCNB include, e.g., mouse anti-beta Sarcoglycan Monoclonal Antibody from Abcam; mouse anti-human SGCB monoclonal antibody Clone 1C10 from Abnova Corporation; mouse anti-human SGCB monoclonal antibody Clone 1C10 from GeneTex; and rabbit anti-human Beta-sarcoglycan (SGCB) Polyclonal from Lifespan Biosciences. Antibodies against SLC2A8 include, e.g., rabbit anti-human Glucose Transporter 8 Polyclonal Antibody from Abcam; goat anti-GLUT8/SLC2A8 polyclonal antibody from Everest Biotech; rabbit anti-GLUCOSE TRANSPORTER 8 Polyclonal Antibody from GenWay Biotech, Inc.; rabbit Anti-Human GLUCOSE TRANSPORTER 5, C Terminus Polyclonal Antibody from GenWay Biotech, Inc.; goat anti-SLC2A8 polyclonal antibody from IMGENEX; and rabbit anti-Human Solute Carrier Family 2 (Facilitated Glucose Transporter) Member 8 (S1c2a8) polyclonal from Lifespan Biosciences. Antibodies against SBF1 include, e.g., rabbit Anti-MTMRS C-term RB0717 polyclonal antibody from Abgent. Antibodies against SGCA include, e.g., mouse Anti-SGCA monoclonal antibody Clone 3C4 from Abnova Corporation; rabbit Anti-Human SGCA polyclonal antibody from Atlas Antibodies; mouse Anti-SGCA monoclonal antibody clone 3C4 from Novus Biologicals; rabbit Anti-Human SGCA PRESTIGE ANTIBODIES from Sigma-Aldrich. Antibodies against SLC2A11 include, e.g., rabbit anti-human Solute Carrier Family 2 (Facilitated Glucose Transporter), Member 11 (S1c2a11) polyclonal from Lifespan Biosciences. Antibodies against SLC4A1 include, e.g., rabbit anti-human Band 3, N Terminus polyclonal antibody from Abcam; mouse anti-human SLC4A1 MaxPab® polyclonal antibody from Abnova Corporation; rabbit anti-human SLC4A1 polyclonal antibody from Aviva Systems Biology; mouse anti-Band 3 Monoclonal Antibody Clone BIII 136 from GenWay Biotech, Inc.; and mouse anti-human Solute Carrier Family 4, Anion Exchanger, Member 1 (SLC4A1) monoclonal Clone 3h3 from Lifespan Biosciences. Antibodies against STX3 include, e.g., rabbit anti-human STX3 Polyclonal Antibody from Atlas Antibodies and rabbit anti-human STX3 from Sigma-Aldrich. Antibodies against TBC1D8 include, e.g., mouse anti-human TBC1D8 monoclonal antibody Clone 1A12 from Abnova Corporation; mouse anti-human TBC1D8 monoclonal antibody Clone 1A12 from GeneTex; mouse anti-human TBC1D8 monoclonal antibody Clone SS-18 from Santa Cruz Biotechnology, Inc.; and rabbit anti-human TBC1D8, aa 132-231 polyclonal antibody from Strategic Diagnostics, Inc. 
     Agents may be linked to a solid-phase and utilized to capture CSCs from a sample. The bound cells may then be separated from the solid phase by known methods depending on the nature of the agent, e.g., antibody, and solid phase. Alternatively, the agents may be conjugated to a detectable label, e.g., a fluorophore, that can be utilized to separate cells in a liquid phase, such as by fluorescent activated cell sorting. Exemplary fluorophores are well known in the art (e.g., Invitrogen&#39;s MOLECULAR PROBES technologies) and include FITC, TRITC, Cy3, Cy5, Alexa Fluorescent Dyes, and Quantum Dots. 
     Systems appropriate for preparing the desired cell population include magnetic bead/paramagnetic particle column utilizing isolated peptides that bind CSC-associated polypeptides for either positive or negative selection; separation based on biotin or streptavidin affinity; and high speed flow cytometric sorting of immunofluorescent-stained CSCs mixed in a suspension of other cells. Thus, the methods of the present invention include the isolation of a population of CSCs. 
     Isolated CSCs may be prepared as substantially pure preparations. The term “substantially pure” means that a preparation is substantially free of other cells. For example, an isolated CSC should constitute at least 70 percent of the total cells present with greater percentages, e.g., at least 85, 90, 95 or 99 percent, being preferred. The cells may be packaged in a finished container such as a cryovial along with any other components that may be desired, e.g., agents for preserving cells, or reducing bacterial growth. The CSCs are useful for a variety of purposes. The isolated cells may be used in basic research setting and in screening assays to identify compounds or compositions that affect growth of CSCs. 
     Isolated CSCs, prepared according to the methods disclosed herein, may be useful in a drug discovery context for lead compound identification and optimization in cell-based screens. For example, the effect of a compound on the growth and/or survival of a CSC may be determined in a cell-based screen that uses an assay selected from: a cell counting assay, a replication labeling assay, a cell membrane integrity assay, a cellular ATP-based viability assay, a mitochondrial reductase activity assay, a caspase activity assay, an Annexin V staining assay, a DNA content assay, a DNA degradation assay, and a nuclear fragmentation assay. Other exemplary assays include BrdU, EdU, or H3-Thymidine incorporation assays; DNA content assays using a nucleic acid dye, such as Hoechst Dye, DAPI, Actinomycin D, 7-aminoactinomycin D or Propidium Iodide; Cellular metabolism assays such as AlamarBlue, MTT, XTT, and CellTitre Glo; Nuclear Fragmentation Assays; Cytoplasmic Histone Associated DNA Fragmentation Assay; PARP Cleavage Assay; TUNEL staining; and Annexin staining. 
     In some aspects, the agents for isolating CSCs are antibody or antigen-binding fragments. The antibodies and antigen binding fragments of the invention include monoclonal antibodies, polyclonal antibodies, human antibodies, chimeric antibodies, humanized antibodies, single-chain antibodies, F(ab′) 2 , Fab, Fd, Fv, or single-chain Fv fragments. 
     Other aspects of the invention relate to treatment methods. In some embodiments, the methods involve modulating, e.g., inducing or inhibiting, the activity of CSC-associated genes (RNA or protein) and, thereby, inhibiting the growth and survival of cancer stem cells. In some embodiments, the treatment methods involve selective delivery, e.g., by antibodies or antigen-binding fragments, of therapeutic agents to cancer stem cells. The methods are useful for inhibiting the proliferation and/or survival of cancer stem cells and, therefore, are useful for treating cancer, e.g., melanoma. The level of modulation, e.g., inducing or inhibiting, of the activity of a CSC-associated gene that is sufficient to affect the growth and/or survival of a cancer stem cell compared with a control level depends on a variety of factors, including the particular CSC-associated gene being modulated, the cancer stem cell within which the modulation occurs, and the level of expression in the control sample. It is well within the purview of the skilled artisan to determine the appropriate level of modulation that is sufficient to sufficient to inhibit the growth and/or survival of a cancer stem cell. 
     The term “inhibiting” refers to any decrease in expression level or activity. As used herein, “inhibit”, “suppress”, or “reduce” may, or may not, be complete. For example, cell proliferation, may, or may not, be decreased to a state of complete arrest for an effect to be considered one of suppression, inhibition or reduction of cell proliferation. Moreover, “suppress”, “inhibit”, or “reduce” may comprise the maintenance of an existing state and the process of effecting a change in state. For example, inhibition of cell proliferation may refer to the prevention of proliferation of a non-proliferating cell (maintenance of a non-proliferating state) and the process of inhibiting the proliferation of a proliferating cell (process of affecting a proliferation state change). Similarly, inhibition of cell survival may refer to killing of a cell, or cells, such as by necrosis or apoptosis, and the process of rendering a cell susceptible to death, such as by inhibiting the expression or activity of an anti-apoptotic regulatory factor. The suppression, inhibition, or reduction may be at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% of control level (e.g., an untreated state). In some cases, the level of modulation (e.g., suppression, inhibition, or reduction) compared with a control level is statistically significant. “Statistically signficant” is a term well known in the art and, for example, may refer to a p-value of less than 0.05, e.g., a p-value of less than 0.025 or a p-value of less than 0.01, using an appropriate statistical test (e.g., ANOVA, MANOVA, t-test, multiple comparison test, etc.). 
     The methods involve treating an individual having, or at risk of having, cancer. As used herein an “individual at risk of having cancer” is an individual, e.g., a human, with an increased likelihood of having cancer compared with a control population, e.g., a general population. Any one of a number of risk factors known in the art may be evaluated to determine whether or not an individual is at risk of having cancer. For example, factors that render an individual at risk of having melanoma include, for example, UV exposure, family history of melanoma, personal history of melanoma, fair skin, freckles, high numbers of nevi (moles), light hair, age, gender, and Xeroderma pigmento sum. 
     The treatment methods disclosed herein may involve administering a therapeutically effective amount of a composition that induces the expression of a CSC-associated gene which is downregulated in cancer (e.g., a gene in Table 2 or 7). In some instances, the composition that induces expression of a CSC-associated gene comprises a vector, such as an isolated plasmid, that expresses the CSC-associated gene. 
     As used herein, a “vector” may be any of a number of nucleic acid molecules into which a desired sequence may be inserted by restriction and ligation for transport between different genetic environments or for expression in a host cell. Vectors are typically composed of DNA although RNA vectors are also available. Vectors include, but are not limited to, plasmids, phagemids and virus genomes or portions thereof. 
     An expression vector is one into which a desired sequence may be inserted, e.g., by restriction and ligation such that it is operably joined to regulatory sequences and may be expressed as an RNA transcript. Vectors may further contain one or more marker sequences suitable for use in the identification of cells that have or have not been transformed or transfected with the vector. Markers include, for example, genes encoding proteins that increase or decrease either resistance or sensitivity to antibiotics or other compounds, genes that encode enzymes whose activities are detectable by standard assays known in the art (e.g., β-galactosidase or alkaline phosphatase), and genes that visibly affect the phenotype of transformed or transfected cells, hosts, colonies or plaques (e.g., green fluorescent protein). 
     Methods for identifying and obtaining coding sequences for use in the methods disclosed herein are routine in the art. For example, the skilled artisan may search Entrez Gene database using a GeneID or GeneAlias of a CSC-associated gene, e.g., a GeneID listed in Table 5, 7 or 8, to identify transcripts associated with CSC-associated genes. In most cases, links to commercial suppliers (e.g., Open Biosystems) of cDNA&#39;s containing the transcripts are provided in the Entrez Gene webinterface, which can be utilized to procure a copy cDNA clone. In other cases, commerical sources (e.g., Sigma Aldrich) can be contacted directly. 
     As used herein, a coding sequence and regulatory sequences are said to be “operably” joined when they are covalently linked in such a way as to place the expression or transcription of the coding sequence under the influence or control of the regulatory sequences. If it is desired that the coding sequences be translated into a functional protein, two DNA sequences are said to be operably joined if induction of a promoter in the 5′ regulatory sequences results in the transcription of the coding sequence and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region to direct the transcription of the coding sequences, or (3) interfere with the ability of the corresponding RNA transcript to be translated into a protein. Thus, a promoter region would be operably joined to a coding sequence if the promoter region were capable of effecting transcription of that DNA sequence such that the resulting transcript might be translated into the desired protein or polypeptide. It will be appreciated that a coding sequence need not encode a protein but may instead, for example, encode a functional RNA such as an shRNA. 
     The precise nature of the regulatory sequences needed for gene expression may vary between species or cell types, but shall in general include, as necessary, 5′ non-transcribed and 5′ non-translated sequences involved with the initiation of transcription and translation respectively, such as a TATA box, capping sequence, CAAT sequence, and the like. Such 5′ non-transcribed regulatory sequences will include a promoter region that includes a promoter sequence for transcriptional control of the operably joined gene. Regulatory sequences may also include enhancer sequences or upstream activator sequences as desired. The vectors of the invention may optionally include 5′ leader or signal sequences. The choice and design of an appropriate vector is within the ability and discretion of one of ordinary skill in the art. One of skill in the art will be aware of appropriate regulatory sequences for expression of interfering RNA, e.g., shRNA, miRNA, etc. 
     In some embodiments, a virus vector for delivering a nucleic acid molecule, an isolated plasmid, is selected from the group consisting of adenoviruses, adeno-associated viruses, poxviruses including vaccinia viruses and attenuated poxviruses, Semliki Forest virus, Venezuelan equine encephalitis virus, retroviruses, Sindbis virus, and Ty virus-like particle. Examples of viruses and virus-like particles which have been used to deliver exogenous nucleic acids include: replication-defective adenoviruses (e.g., Xiang et al.,  Virology  219:220-227, 1996; Eloit et al.,  J. Virol.  7:5375-5381, 1997; Chengalvala et al.,  Vaccine  15:335-339, 1997), a modified retrovirus (Townsend et al.,  J. Virol.  71:3365-3374, 1997), a nonreplicating retrovirus (Irwin et al.,  J. Virol.  68:5036-5044, 1994), a replication defective Semliki Forest virus (Zhao et al.,  Proc. Natl. Acad. Sci. USA  92:3009-3013, 1995), canarypox virus and highly attenuated vaccinia virus derivative (Paoletti,  Proc. Natl. Acad. Sci. USA  93:11349-11353, 1996), non-replicative vaccinia virus (Moss,  Proc. Natl. Acad. Sci. USA  93:11341-11348, 1996), replicative vaccinia virus (Moss, Dev.  Biol. Stand.  82:55-63, 1994), Venzuelan equine encephalitis virus (Davis et al.,  J. Virol.  70:3781-3787, 1996), Sindbis virus (Pugachev et al.,  Virology  212:587-594, 1995), lentiviral vectors (Naldini L, et al.,  Proc Natl Acad Sci USA.  1996 Oct. 15; 93(21):11382-8) and Ty virus-like particle (Allsopp et al.,  Eur. J. Immunol  26:1951-1959, 1996). 
     Another virus useful for certain applications is the adeno-associated virus, a double-stranded DNA virus. The adeno-associated virus is capable of infecting a wide range of cell types and species and can be engineered to be replication-deficient. It further has advantages, such as heat and lipid solvent stability, high transduction frequencies in cells of diverse lineages, including hematopoietic cells, and lack of superinfection inhibition thus allowing multiple series of transductions. The adeno-associated virus can integrate into human cellular DNA in a site-specific manner, thereby minimizing the possibility of insertional mutagenesis and variability of inserted gene expression. In addition, wild-type adeno-associated virus infections have been followed in tissue culture for greater than 100 passages in the absence of selective pressure, implying that the adeno-associated virus genomic integration is a relatively stable event. The adeno-associated virus can also function in an extrachromosomal fashion. 
     Other useful viral vectors are based on non-cytopathic eukaryotic viruses in which non-essential genes have been replaced with the gene of interest. Non-cytopathic viruses include certain retroviruses, the life cycle of which involves reverse transcription of genomic viral RNA into DNA with subsequent proviral integration into host cellular DNA. In general, the retroviruses are replication-deficient (i.e., capable of directing synthesis of the desired transcripts, but incapable of manufacturing an infectious particle). Such genetically altered retroviral expression vectors have general utility for the high-efficiency transduction of genes in vivo. Standard protocols for producing replication-deficient retroviruses (including the steps of incorporation of exogenous genetic material into a plasmid, transfection of a packaging cell lined with plasmid, production of recombinant retroviruses by the packaging cell line, collection of viral particles from tissue culture media, and infection of the target cells with viral particles) are provided in Kriegler, M., “Gene Transfer and Expression, A Laboratory Manual,” W.H. Freeman Co., New York (1990) and Murry, E. J. Ed. “Methods in Molecular Biology,” vol. 7, Humana Press, Inc., Clifton, N.J. (1991). 
     In some embodiments, isolated plasmid vectors comprises a tumor-specific, e.g., melanoma-specific, e.g., a tyrosinase promoter, operably linked to the CSC-associated gene (See, e.g., Lillehammer, T. et al., Cancer Gene Therapy (2005) 12, 864-872). Other exemplary tumor-specific promoters are known in the art and will be apparent to the skilled artisan. 
     The treatment methods may involve administering a therapeutically effective amount of a composition that targets a product of a CSC-associated gene (i.e., Table 1), which are CSC-associated genes that upregulated in cancer stem cells. The composition may target a product of a CSC-associated gene selected from the group set forth in Table 4, which are upregulated in cancer stem cells and are associated with the cell surface. 
     The product, e.g., mRNA or protein, of a CSC-associated gene can be targeted by any one of a number of methods known in the art. For example, the composition may comprise a gene knockdown reagent, e.g., siRNA, that is complementary to a CSC-associated mRNA and inhibits its expression. In other embodiments, the composition may comprise an isolated molecule, e.g., antibody or antigen binding fragment, that is conjugated to a siRNA and that specifically binds to a CSC-associated polypeptide. Such antibody conjugated siRNAs (or similar gene suppression agents) may target a CSC-associated mRNA such as any of those encoded by the genes set forth in Table 1. 
     The CSC-associated gene may be selected from the following group ANK2, NCKAP1L, PTPRE, PTPRS, SBF1, SCN3A, SGCA, SGCB, SLC2A11, SLC2A8, SLC4A1, STX3, and TBC1D8 which are upregulated in cancer stem cells and associated with the cell surface. The siRNA may target another gene in the cell that is useful for inhibiting the growth and/or survival of the cell, for example an oncogene. For example, oncogenes that may be targeted include FOS, JUN, MYB, RAS, and ABL. Other exemplary oncogenes are well known in the art and several such examples are described in, for example, The Genetic Basis of Human Cancer (Vogelstein, B. and Kinzler, K. W. eds. McGraw-Hill, New York, N.Y., 1998). Other upregulated genes include Epidermal growth factor (beta-urogastrone, HOMG4/URG); Heparanase (HPA/HPR1); Jagged 1 (Alagille syndrome, AGS/AHD); Platelet/endothelial cell adhesion molecule (CD31 antigen, CD31/PECAM-1); Transforming growth factor, alpha (TFGA); and Vascular endothelial growth factor C (Flt4-L/VRP). Homologues of such genes can also be used. 
     Various strategies for gene knockdown known in the art can be used to inhibit gene expression (e.g., expression of CSC-associated genes). For example, gene knockdown strategies may be used that make use of RNA interference (RNAi) and/or microRNA (miRNA) pathways including small interfering RNA (siRNA), short hairpin RNA (shRNA), double-stranded RNA (dsRNA), miRNAs, and other small interfering nucleic acid-based molecules known in the art. In one embodiment, vector-based RNAi modalities (e.g., shRNA or shRNA-mir expression constructs) are used to reduce expression of a gene (e.g., a CSC-associated) in a cell. In some embodiments, therapeutic compositions of the invention comprise an isolated plasmid vector (e.g., any isolated plasmid vector known in the art or disclosed herein) that expresses a small interfering nucleic acid such as an shRNA. The isolated plasmid may comprise a tumor-specific, e.g., melanoma-specific, promoter operably linked to a gene encoding the small interfering nucleic acid, e.g., an shRNA. In some cases, the isolated plasmid vector is packaged in a virus capable of infecting the individual. Exemplary viruses include adenovirus, retrovirus, lentivirus, adeno-associated virus, and others that are known in the art and disclosed herein. 
     A broad range of RNAi-based modalities could be employed to inhibit expression of a gene in a cell, such as siRNA-based oligonucleotides and/or altered siRNA-based oligonucleotides. Altered siRNA based oligonucleotides are those modified to alter potency, target affinity, safety profile and/or stability, for example, to render them resistant or partially resistant to intracellular degradation. Modifications, such as phosphorothioates, for example, can be made to oligonucleotides to increase resistance to nuclease degradation, binding affinity and/or uptake. In addition, hydrophobization and bioconjugation enhances siRNA delivery and targeting (De Paula et al., RNA. 13(4):431-56, 2007) and siRNAs with ribo-difluorotoluyl nucleotides maintain gene silencing activity (Xia et al., ASC Chem. Biol. 1(3):176-83, (2006)). siRNAs with amide-linked oligoribonucleosides have been generated that are more resistant to S1 nuclease degradation than unmodified siRNAs (Iwase R et al. 2006 Nucleic Acids Symp Ser 50: 175-176). In addition, modification of siRNAs at the 2′-sugar position and phosphodiester linkage confers improved serum stability without loss of efficacy (Choung et al., Biochem. Biophys. Res. Commun. 342(3):919-26, 2006). Other molecules that can be used to inhibit expression of a gene (e.g., a CSC-associated gene) include sense and antisense nucleic acids (single or double stranded), ribozymes, peptides, DNAzymes, peptide nucleic acids (PNAs), triple helix forming oligonucleotides, antibodies, and aptamers and modified form(s) thereof directed to sequences in gene(s), RNA transcripts, or proteins. Antisense and ribozyme suppression strategies have led to the reversal of a tumor phenotype by reducing expression of a gene product or by cleaving a mutant transcript at the site of the mutation (Carter and Lemoine Br. J. Cancer. 67(5):869-76, 1993; Lange et al., Leukemia. 6(11):1786-94, 1993; Valera et al., J. Biol. Chem. 269(46):28543-6, 1994; Dosaka-Akita et al., Am. J. Clin. Pathol. 102(5):660-4, 1994; Feng et al., Cancer Res. 55(10):2024-8, 1995; Quattrone et al., Cancer Res. 55(1):90-5, 1995; Lewin et al., Nat Med. 4(8):967-71, 1998). Ribozymes have also been proposed as a means of both inhibiting gene expression of a mutant gene and of correcting the mutant by targeted trans-splicing (Sullenger and Cech Nature 371(6498):619-22, 1994; Jones et al., Nat. Med. 2(6):643-8, 1996). Ribozyme activity may be augmented by the use of, for example, non-specific nucleic acid binding proteins or facilitator oligonucleotides (Herschlag et al., Embo J. 13(12):2913-24, 1994; Jankowsky and Schwenzer Nucleic Acids Res. 24(3):423-9, 1996). Multitarget ribozymes (connected or shotgun) have been suggested as a means of improving efficiency of ribozymes for gene suppression (Ohkawa et al., Nucleic Acids Symp Ser. (29):121-2, 1993). 
     Triple helix approaches have also been investigated for sequence-specific gene suppression. Triple helix forming oligonucleotides have been found in some cases to bind in a sequence-specific manner (Postel et al., Proc. Natl. Acad. Sci. U.S.A. 88(18):8227-31, 1991; Duval-Valentin et al., Proc. Natl. Acad. Sci. U.S.A. 89(2):504-8, 1992; Hardenbol and Van Dyke Proc. Natl. Acad. Sci. U.S.A. 93(7):2811-6, 1996; Porumb et al., Cancer Res. 56(3):515-22, 1996). Similarly, peptide nucleic acids have been shown to inhibit gene expression (Hanvey et al., Antisense Res. Dev. 1(4):307-17, 1991; Knudsen and Nielson Nucleic Acids Res. 24(3):494-500, 1996; Taylor et al., Arch. Surg. 132(11):1177-83, 1997). Minor-groove binding polyamides can bind in a sequence-specific manner to DNA targets and hence may represent useful small molecules for suppression at the DNA level (Trauger et al., Chem. Biol. 3(5):369-77, 1996). In addition, suppression has been obtained by interference at the protein level using dominant negative mutant peptides and antibodies (Herskowitz Nature 329(6136):219-22, 1987; Rimsky et al., Nature 341(6241):453-6, 1989; Wright et al., Proc. Natl. Acad. Sci. U.S.A. 86(9):3199-203, 1989). In some cases suppression strategies have led to a reduction in RNA levels without a concomitant reduction in proteins, whereas in others, reductions in RNA have been mirrored by reductions in protein. The diverse array of suppression strategies that can be employed includes the use of DNA and/or RNA aptamers that can be selected to target a protein of interest (e.g, a CSC-associated polypeptide). 
     Methods of delivering a therapeutic agent to a cancer stem cell are also provided. The methods involve a step of contacting a cancer stem cell with an isolated molecule that selectively binds to a cell surface polypeptide encoded by a CSC-associated gene, such as those selected from the group set forth in Table 4. The CSC-associated gene may be selected from the group consisting of: ANK2, NCKAP1L, PTPRE, PTPRS, SBF1, SCN3A, SGCA, SGCB, SLC2A11, SLC2A8, SLC4A1, STX3, and TBC1D8. The cancer stem cell may be in vivo or in vitro. Isolated molecules that bind to CSC-associated polypeptides on the surface of a cancer stem cell may be taken up into an intracellular compartment of the cancer stem cell. 
     Cancer stem cells include stem cells of a colon carcinoma, a pancreatic cancer, a breast cancer, an ovarian cancer, a prostate cancer, a squamous cell carcinoma, a cervical cancer, a lung carcinoma, a small cell lung carcinoma, a bladder carcinoma, a squamous cell carcinoma, a basal cell carcinoma, an adenocarcinoma, a sweat gland carcinoma, a sebaceous gland carcinoma, a papillary carcinoma, a papillary adenocarcinoma, a cystadenocarcinoma, a medullary carcinoma, a bronchogenic carcinoma, a renal cancer, e.g., renal cell carcinoma, a hepatocellular carcinoma, a bile duct carcinoma, a choriocarcinoma, a seminoma, a embryonal carcinoma, a Wilms&#39; tumor, or a testicular tumor. In specific embodiments, the cancer stem cells are stem cells of melanoma. Cancer stem cells include ABCB5 +  cells and ABCB5 −  cells. Stem cells of other cancers will be known to one of ordinary skill in the art. 
     The treatment methods of the invention involve administering compositions that comprise isolated molecules, or combinations of different isolated molecules, that specifically bind to CSC-associated polypeptides (polypeptides encoded by the CSC-associated gene) to treat cancer, e.g., melanoma, in an individual. When the CSC-associated polypeptide is associated with the extracellular surface of a cell, e.g., a cancer stem cell, e.g., a melanoma stem cell, the isolated molecule can bind the CSC-associated polypeptide and, for example, serve as an vehicle for specifically targeting therapeutic agents (therapeutic molecules) to the cell. In some embodiments, isolated molecules that binds to a CSC-associated polypeptide on the surface of a cell are taken up into an intracellular compartment of the cell bind to a secreted molecule, such as a growth factor that may assist the tumor (such as those listed in Table 1.2). The isolated molecules that interact with unregulated proteins may be used alone as therapeutics or in combination with other therapeutics. 
     As used herein treatment of or treating cancer includes preventing the development of a cancer, reducing the symptoms of a cancer and/or inhibiting, slowing the growth of or preventing further growth of an existing cancer. Treatment may include amelioration, cure, and/or maintenance of a cure (i.e., prevention or delay of relapse) of a disorder, e.g., cancer. Treatment after a disorder has started aims to reduce, ameliorate or altogether eliminate the disorder, and/or its associated symptoms, to prevent it from becoming worse, to slow the rate of progression, or to prevent the disorder from re-occurring once it has been initially eliminated (i.e., to prevent a relapse). 
     Cancers include for instance a colon carcinoma, a pancreatic cancer, a breast cancer, an ovarian cancer, a prostate cancer, a squamous cell carcinoma, a cervical cancer, a lung carcinoma, a small cell lung carcinoma, a bladder carcinoma, a squamous cell carcinoma, a basal cell carcinoma, an adenocarcinoma, a sweat gland carcinoma, a sebaceous gland carcinoma, a papillary carcinoma, a papillary adenocarcinoma, a cystadenocarcinoma, a medullary carcinoma, a bronchogenic carcinoma, a renal cell carcinoma, a hepatocellular carcinoma, a bile duct carcinoma, a choriocarcinoma, a seminoma, an embryonal carcinoma, a Wilms&#39; tumor, or a testicular tumor. In certain embodiments, the cancer is melanoma. 
     The invention, in some aspects, relates to an isolated molecule that selectively binds to a polypeptide encoded by a CSC-associated gene set forth in Table 4 and that is conjugated to a therapeutic agent. In some instances, the CSC-associated gene is selected from the group consisting of: ANK2, NCKAP1L, PTPRE, PTPRS, SBF1, SCN3A, SGCA, SGCB, SLC2A11, SLC2A8, SLC4A1, STX3, and TBC1D8. Compositions comprising the foregoing isolated molecules are also disclosed. 
     As used herein an “isolated molecule” is a molecule such as a polypeptide, nucleic acid, polysaccharide, drug, nucleoprotein, lipoprotein, glycoprotein, steroid, and lipid that is isolated from its natural environment or produced synthetically. In some embodiments, the isolated molecule is a ligand of a CSC-associated polypeptide. In other embodiments, the isolated molecule is an antibody or antigen-binding fragment. As disclosed herein, antibody or antigen-binding fragments include monoclonal antibodies, polyclonal antibodies, human antibodies, chimeric antibodies, humanized antibodies, single-chain antibodies, F(ab′) 2 , Fab, Fd, Fv, or single-chain Fv fragments. In some embodiments, an isolated molecule may have therapeutic utility alone and need not be conjugated to a therapeutic agent. For example, an isolated molecule may bind to a cell surface receptor that is a CSC-associated polypeptide and function as an antagonist or competitive inhibitor of the receptor (e.g., to inhibit a signaling pathway). 
     In some embodiments, isolated molecules are conjugated to therapeutic agents. As used herein, a “therapeutic agent” is a molecule such as a polypeptide, nucleic acid, polysaccharide, drug, nucleoprotein, lipoprotein, glycoprotein, steroid, and lipid that is capable of altering the state of a cell (e.g., killing a cell, inhibiting growth of a cell) for therapeutic purposes. A therapeutic agent may be, for instance, a toxin, a small-interfering nucleic acid, or a chemotherapeutic agent. Alternatively the therapeutic may be administered in conjunction with the molecule. In conjunction refers to delivery to the same subject. The actual administration may be at the same or a different time or in the same or a different delivery vehicle. 
     Toxins include for example, radioisotopes such as  225 Ac,  211 At,  212 Bi,  213 Bi,  186 Rh,  188 Rh,  177 Lu,  90 Y,  131 I,  67 Cu,  125 I,  123 I,  77 Br,  153 Sm,  166 Bo,  64 Cu,  212 Pb,  224 Ra,  223 Ra, and others known in the art. Suitable chemical toxins include members of the enediyne family of molecules, such as calicheamicin and esperamicin as well as poisonous lectins, plant toxins such as ricin, abrin, modeccin, botulina and diphtheria toxins. Of course, combinations of the various toxins could also be coupled to one isolated molecule, e.g., an antibody, thereby accommodating variable cytotoxicity. The coupling of one or more toxin molecules to the isolated molecule, e.g., antibody, is envisioned to include many chemical mechanisms, for instance covalent binding, affinity binding, intercalation, coordinate binding, and complexation. 
     Chemotherapeutic agents include the following compounds or classes of compounds: Acivicin; Aclarubicin; Acodazole Hydrochloride; Acronine; Adozelesin; Adriamycin; Aldesleukin; Altretamine; Ambomycin; Ametantrone Acetate; Aminoglutethimide; Amsacrine; Anastrozole; Anthramycin; Asparaginase; Asperlin; Azacitidine; Azetepa; Azotomycin; Batimastat; Buniodepa; Bicalutamide; Bisantrene Hydrochloride; Bisnafide Dimesylate; Bizelesin; Bleomycin Sulfate; Brequinar Sodium; Bropirimine; Busulfan; Cactinomycin; Calusterone; Caracemide; Carbetimer; Carboplatin; Carmustine; Carubicin Hydrochloride; Carzelesin; Cedefingol; Chlorombucil; Cirolemycin; Cisplatin; Cladribine; Crisnatol Mesylate; Cyclophosphamide; Cytarabine; Dacarbazine; DACA (N-[2-(Dimethyl-amino)ethyl]acridine-4-carboxamide); Dactinomycin; Daunorubicin Hydrochloride; Daunomycin; Decitabine; Dexormaplatin; Dezaguanine; Dezaguanine Ifesylate; Diaziquone; Docetaxel; Doxorubicin; Doxorubicin Hydrochloride; Droloxifene; Droloxifene Citrate; Dromostanolone Propionate; Duazomycin; Edatrexate; Eflornithine Hydrochloride; Elsamitrucin; Enloplatin; Enpromate; Epipropidine; Epirubicin Hydrochloride; Erbulozole; Esorubicin Hydrochloride; Estramustine; Estramustine Phosphate Sodium; Etanidazole; Ethiodized Oil I131; Etoposide; Etoposide Phosphate; Etoprine; Fadrozole Hydrochloride; Fazarabine; Fenretinide; Floxuridine; Fludarabine Phosphate; Fluorouracil; 5-FdUMP; Flurocitabine; Fosquidone; Fostriecin Sodium; Gemcitabine; Gemcitabine Hydrochloride; Gold Au 198; Hydroxyurea; Idarubicin Hydrochloride; Ifosfamide; Ilmofosine; Interferon Alfa-2a; Interferon Alfa-2b; Interferon Alfa-n1; Interferon Alfa-n3; Interferon Beta-1a; Interferon Gamma-1b; Iproplatin; Irinotecan Hydrochloride; Lanreotide Acetate; Letrozole; Leuprolide Acetate; Liarozole Hydrochloride; Lometrexol Sodium; Lomustine; Losoxantrone Hydrochloride; Masoprocol; Maytansine; Mechlorethamine Hydrochloride; Megestrol Acetate; Melengestrol Acetate; Melphalan; Menogaril; Mercaptopurine; Methotrexate; Methotrexate Sodium; Metoprine; Meturedepa; Mitindomide; Mitocarcin; Mitocromin; Mitogillin; Mitomalcin; Mitomycin; Mitosper; Mitotane; Mitoxantrone Hydrochloride; Mycophenolic Acid; Nocodazole; Nogalamycin; Ormaplatin; Oxisuran; Paclitaxel Pegaspargase; Peliomycin; Pentamustine; Peplomycin Sulfate; Perfosfamide; Pipobroman; Piposulfan; Piroxantrone Hydrochloride; Plicamycin; Plomestane; Porfimer Sodium; Porfiromycin; Prednimustine; Procarbazine Hydrochloride; Puromycin; Puromycin Hydrochloride; Pyrazofurin; Riboprine; Rogletimide; Safingol; Safingol Hydrochloride; Semustine; Simtrazene; Sparfosate Sodium; Sparsomycin; Spirogermanium Hydrochloride; Spiromustine; Spiroplatin; Streptonigrin; Streptozocin; Strontium Chloride Sr 89; Sulofenur; Talisomycin; Taxane; Taxoid; Tecogalan Sodium; Tegafur; Teloxantrone Hydrochloride; Temoporfin; Teniposide; Teroxirone; Testolactone; Thiamiprine; Thioguanine; Thiotepa; Thymitaq; Tiazofurin; Tirapazamine; Tomudex; TOP-53; Topotecan Hydrochloride; Toremifene Citrate; Trestolone Acetate; Triciribine Phosphate; Trimetrexate; Trimetrexate Glucuronate; Triptorelin; Tubulozole Hydrochloride; Uracil Mustard; Uredepa; Vapreotide; Verteporfin; Vinblastine; Vinblastine Sulfate; Vincristine; Vincristine Sulfate, Vindesine; Vindesine Sulfate; Vinepidine Sulfate; Vinglycinate Sulfate; Vinleurosine Sulfate; Vinorelbine Tartrate; Vinrosidine Sulfate; Vinzolidine Sulfate; Vorozole; Zeniplatin; Zinostatin; Zorubicin Hydrochloride; 2-Chlorodeoxyadenosine; 2′-Deoxyformycin; 9-aminocamptothecin; raltitrexed; N-propargyl-5,8-dideazafolic acid, 2-chloro-2′-arabino-fluoro-2′-deoxyadenosine; 2-chloro-2′-deoxyadenosine; anisomycin; trichostatin A; hPRL-G129R; CEP-751; linomide; Piritrexim Isethionate; Sitogluside; Tamsulosin Hydrochloride and Pentomone. 
     The invention, in some aspects, provides kits comprising one or more containers housing one or more of the compositions of the invention. The kit may be designed to facilitate use of the methods described herein by researchers and can take many forms. Each of the compositions of the kit, where applicable, may be provided in liquid form (e.g., in solution), or in solid form, (e.g., a dry powder). In certain cases, some of the compositions may be constitutable or otherwise processable (e.g., to an active form), for example, by the addition of a suitable solvent or other species (for example, water or a cell culture medium), which may or may not be provided with the kit. The kits may also include reference samples. As used herein, “instructions” can define a component of instruction and/or promotion, and typically involve written instructions on or associated with packaging of the invention. Instructions also can include any oral or electronic instructions provided in any manner such that a user will clearly recognize that the instructions are to be associated with the kit, for example, audiovisual (e.g., videotape, DVD, etc.), Internet, and/or web-based communications, etc. The written instructions may be in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which instructions can also reflects approval by the agency of manufacture, use or sale for animal administration. 
     The kit may contain any one or more of the components described herein in one or more containers. As an example, in one embodiment, the kit may include instructions for mixing one or more components of the kit and/or isolating and mixing a sample and applying to a individual. The kit may include a container housing agents described herein. The agents may be in the form of a liquid, gel or solid (powder). The agents may be prepared sterilely, packaged in syringe and shipped refrigerated. Alternatively it may be housed in a vial or other container for storage. A second container may have other agents prepared sterilely. Alternatively the kit may include the active agents premixed and shipped in a syringe, vial, tube, or other container. The kit may have one or more or all of the components required to administer the agents to an animal, such as a syringe, topical application devices, or iv needle tubing and bag, particularly in the case of the kits for treating individuals with cancer. 
     The compositions and therapeutic agents may be administered simultaneously or sequentially. When the other therapeutic agents are administered simultaneously they can be administered in the same or separate formulations, but are administered at the same time. The other therapeutic agents are administered sequentially with one another and with the modulators, when the administration of the other therapeutic agents and the modulators is temporally separated. The separation in time between the administration of these compounds may be a matter of minutes or it may be longer. 
     The compositions of the present invention preferably contain a pharmaceutically acceptable carrier or excipient suitable for rendering the compound or mixture administrable orally as a tablet, capsule or pill, or parenterally, intravenously, intradermally, intramuscularly or subcutaneously, or transdermally. The active ingredients may be admixed or compounded with any conventional, pharmaceutically acceptable carrier or excipient. The compositions may be sterile. 
     As used herein, the term “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic agents, absorption delaying agents, and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the compositions of this invention, its use in the therapeutic formulation is contemplated. Supplementary active ingredients can also be incorporated into the pharmaceutical formulations. A composition is said to be a “pharmaceutically acceptable carrier” if its administration can be tolerated by a recipient patient. Sterile phosphate-buffered saline is one example of a pharmaceutically acceptable carrier. Other suitable carriers are well-known in the art. 
     It will be understood by those skilled in the art that any mode of administration, vehicle or carrier conventionally employed and which is inert with respect to the active agent may be utilized for preparing and administering the pharmaceutical compositions of the present invention. Illustrative of such methods, vehicles and carriers are those described, for example, in Remington&#39;s Pharmaceutical Sciences, 18th ed. (1990), the disclosure of which is incorporated herein by reference. Those skilled in the art, having been exposed to the principles of the invention, will experience no difficulty in determining suitable and appropriate vehicles, excipients and carriers or in compounding the active ingredients therewith to form the pharmaceutical compositions of the invention. 
     An effective amount, also referred to as a therapeutically effective amount is an amount sufficient to ameliorate at least one adverse effect associated with expression, or reduced expression, of a CSC-associated gene in a cell or in an individual in need of such inhibition or supplementation. The therapeutically effective amount to be included in pharmaceutical compositions depends, in each case, upon several factors, e.g., the type, size and condition of the patient to be treated, the intended mode of administration, the capacity of the patient to incorporate the intended dosage form, etc. Generally, an amount of active agent is included in each dosage form to provide from about 0.1 to about 250 mg/kg, and preferably from about 0.1 to about 100 mg/kg. One of ordinary skill in the art would be able to determine empirically an appropriate therapeutically effective amount. 
     Combined with the teachings provided herein, by choosing among the various active compounds and weighing factors such as potency, relative bioavailability, patient body weight, severity of adverse side-effects and preferred mode of administration, an effective prophylactic or therapeutic treatment regimen can be planned which does not cause substantial toxicity and yet is entirely effective to treat the particular individual. The effective amount for any particular application can vary depending on such factors as the disease or condition being treated, the particular therapeutic agent being administered, the size of the individual, or the severity of the disease or condition. One of ordinary skill in the art can empirically determine the effective amount of a particular nucleic acid and/or other therapeutic agent without necessitating undue experimentation. 
     The pharmaceutical compositions can be administered by any suitable route for administering medications. A variety of administration routes are available. The particular mode selected will depend, of course, upon the particular agent or agents selected, the particular condition being treated, and the dosage required for therapeutic efficacy. The methods of this invention, generally speaking, may be practiced using any mode of administration that is medically acceptable, meaning any mode that produces effective levels of an immune response without causing clinically unacceptable adverse effects. Preferred modes of administration are discussed herein. For use in therapy, an effective amount of the nucleic acid and/or other therapeutic agent can be administered to an individual by any mode that delivers the agent to the desired surface, e.g., mucosal, systemic. 
     Administering the pharmaceutical composition of the present invention may be accomplished by any means known to the skilled artisan. Routes of administration include but are not limited to oral, parenteral, intravenous, intramuscular, intraperitoneal, intranasal, sublingual, intratracheal, inhalation, subcutaneous, ocular, vaginal, and rectal. Systemic routes include oral and parenteral. Several types of devices are regularly used for administration by inhalation. These types of devices include metered dose inhalers (MDI), breath-actuated MDI, dry powder inhaler (DPI), spacer/holding chambers in combination with MDI, and nebulizers. 
     In some cases, compounds of the invention are prepared in a colloidal dispersion system. Colloidal dispersion systems include lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. A preferred colloidal system of the invention is a liposome. Liposomes are artificial membrane vessels which are useful as a delivery vector in vivo or in vitro. It has been shown that large unilamellar vesicles (LUVs), which range in size from 0.2-4.0 μm can encapsulate large macromolecules. RNA, DNA and intact virions can be encapsulated within the aqueous interior and be delivered to cells in a biologically active form. Fraley et al. (1981) Trends Biochem Sci 6:77. 
     Liposomes may be targeted to a particular tissue by coupling the liposome to a specific binding molecule such as one that binds to a CSC-associated polypeptide. Binding molecules which may be useful for targeting a liposome to, for example, a cancer stem cell include, but are not limited to intact or fragments of molecules, e.g., antibodies or antigen binding fragments, which interact with CSC-associated polypeptides on the surface of cancer stem cells. Such binding molecules may easily be identified by binding assays well known to those of skill in the art. 
     Lipid formulations for transfection are commercially available from QIAGEN, for example, as EFFECTENE™ (a non-liposomal lipid with a special DNA condensing enhancer) and SUPERFECT™ (a novel acting dendrimeric technology). 
     Liposomes are commercially available from Gibco BRL, for example, as LIPOFECTIN™ and LIPOFECTACE™, which are formed of cationic lipids such as N-[1-(2,3 dioleyloxy)-propyl]-N,N,N-trimethylammonium chloride (DOTMA) and dimethyl dioctadecylammonium bromide (DDAB). Methods for making liposomes are well known in the art and have been described in many publications. Liposomes also have been reviewed by Gregoriadis G (1985) Trends Biotechnol 3:235-241. 
     Certain cationic lipids, including in particular N-[1-(2,3 dioleoyloxy)-propyl]-N,N,N-trimethylammonium methyl-sulfate (DOTAP), appear to be especially advantageous when combined with the modified oligonucleotide analogs of the invention. 
     In one embodiment, the vehicle is a biocompatible microparticle or implant that is suitable for implantation or administration to the mammalian recipient. Exemplary bioerodible implants that are useful in accordance with this method are described in PCT International application no. PCT/US/03307 (Publication No. WO95/24929, entitled “Polymeric Gene Delivery System”. PCT/US/0307 describes a biocompatible, preferably biodegradable polymeric matrix for containing an exogenous gene under the control of an appropriate promoter. The polymeric matrix can be used to achieve sustained release of the therapeutic agent in the individual. 
     The polymeric matrix preferably is in the form of a microparticle such as a microsphere (e.g., wherein a therapeutic agent is dispersed throughout a solid polymeric matrix) or a microcapsule (e.g., wherein a therapeutic agent is stored in the core of a polymeric shell). Other forms of the polymeric matrix for containing the therapeutic agent include films, coatings, gels, implants, and stents. The size and composition of the polymeric matrix device is selected to result in favorable release kinetics in the tissue into which the matrix is introduced. The size of the polymeric matrix further is selected according to the method of delivery which is to be used, typically injection into a tissue or administration of a suspension by aerosol into the nasal and/or pulmonary areas. Preferably when an aerosol route is used the polymeric matrix and the therapeutic agent are encompassed in a surfactant vehicle. The polymeric matrix composition can be selected to have both favorable degradation rates and also to be formed of a material which is bioadhesive, to further increase the effectiveness of transfer when the matrix is administered to a nasal and/or pulmonary surface that has sustained an injury. The matrix composition also can be selected not to degrade, but rather, to release by diffusion over an extended period of time. Biocompatible microspheres that are suitable for delivery, such as oral or mucosal delivery, are disclosed in Chickering et al. (1996) Biotech Bioeng 52:96-101 and Mathiowitz E et al. (1997) Nature 386:410-414 and PCT Pat. Application WO97/03702. 
     Both non-biodegradable and biodegradable polymeric matrices can be used to deliver the therapeutic agentsto an individual. Biodegradable matrices are preferred. Such polymers may be natural or synthetic polymers. The polymer is selected based on the period of time over which release is desired, generally in the order of a few hours to a year or longer. Typically, release over a period ranging from between a few hours and three to twelve months is most desirable, particularly for the nucleic acid agents. The polymer optionally is in the form of a hydrogel that can absorb up to about 90% of its weight in water and further, optionally is cross-linked with multi-valent ions or other polymers. 
     Bioadhesive polymers of particular interest include bioerodible hydrogels described by H. S. Sawhney, C. P. Pathak and J. A. Hubell in Macromolecules, (1993) 26:581-587, the teachings of which are incorporated herein. These include polyhyaluronic acids, casein, gelatin, glutin, polyanhydrides, polyacrylic acid, alginate, chitosan, poly(methyl methacrylates), poly(ethyl methacrylates), poly(butylmethacrylate), poly(isobutyl methacrylate), poly(hexylmethacrylate), poly(isodecyl methacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), and poly(octadecyl acrylate). 
     If the therapeutic agent is a nucleic acid, the use of compaction agents may also be desirable. Compaction agents also can be used alone, or in combination with, a biological or chemical/physical vector. A “compaction agent”, as used herein, refers to an agent, such as a histone, that neutralizes the negative charges on the nucleic acid and thereby permits compaction of the nucleic acid into a fine granule. Compaction of the nucleic acid facilitates the uptake of the nucleic acid by the target cell. The compaction agents can be used alone, i.e., to deliver a nucleic acid in a form that is more efficiently taken up by the cell or, more preferably, in combination with one or more of the above-described vectors. 
     Other exemplary compositions that can be used to facilitate uptake of a nucleic acid include calcium phosphate and other chemical mediators of intracellular transport, microinjection compositions, electroporation and homologous recombination compositions (e.g., for integrating a nucleic acid into a preselected location within the target cell chromosome). 
     The compounds may be administered alone (e.g., in saline or buffer) or using any delivery vehicle known in the art. For instance the following delivery vehicles have been described: cochleates; Emulsomes; ISCOMs; liposomes; live bacterial vectors (e.g.,  Salmonella, Escherichia coli, Bacillus  Calmette-Guérin,  Shigella, Lactobacillus ); live viral vectors (e.g., Vaccinia, adenovirus, Herpes Simplex); microspheres; nucleic acid vaccines; polymers (e.g. carboxymethylcellulose, chitosan); polymer rings; proteosomes; sodium fluoride; transgenic plants; virosomes; and, virus-like particles. 
     The formulations of the invention are administered in pharmaceutically acceptable solutions, which may routinely contain pharmaceutically acceptable concentrations of salt, buffering agents, preservatives, compatible carriers, adjuvants, and optionally other therapeutic ingredients. 
     The term pharmaceutically-acceptable carrier means one or more compatible solid or liquid filler, diluents or encapsulating substances which are suitable for administration to a human or other vertebrate animal. The term carrier denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application. The components of the pharmaceutical compositions also are capable of being commingled with the compounds of the present invention, and with each other, in a manner such that there is no interaction which would substantially impair the desired pharmaceutical efficiency. 
     For oral administration, the compounds can be formulated readily by combining the active compound(s) with pharmaceutically acceptable carriers well known in the art. Such carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by an individual to be treated. Pharmaceutical preparations for oral use can be obtained as solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. Optionally the oral formulations may also be formulated in saline or buffers for neutralizing internal acid conditions or may be administered without any carriers. 
     Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses. 
     Pharmaceutical preparations which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. Microspheres formulated for oral administration may also be used. Such microspheres have been well defined in the art. All formulations for oral administration should be in dosages suitable for such administration. 
     For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner. 
     For administration by inhalation, the compounds for use according to the present invention may be conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g. gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch. 
     The compounds, when it is desirable to deliver them systemically, may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. 
     Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions. 
     Alternatively, the active compounds may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use. 
     The compounds may also be formulated in rectal or vaginal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides. 
     In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long-acting formulations may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt. 
     The pharmaceutical compositions also may comprise suitable solid or gel phase carriers or excipients. Examples of such carriers or excipients include but are not limited to calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives, gelatin, and polymers such as polyethylene glycols. 
     Suitable liquid or solid pharmaceutical preparation forms are, for example, aqueous or saline solutions for inhalation, microencapsulated, encochleated, coated onto microscopic gold particles, contained in liposomes, nebulized, aerosols, pellets for implantation into the skin, or dried onto a sharp object to be scratched into the skin. The pharmaceutical compositions also include granules, powders, tablets, coated tablets, (micro)capsules, suppositories, syrups, emulsions, suspensions, creams, drops or preparations with protracted release of active compounds, in whose preparation excipients and additives and/or auxiliaries such as disintegrants, binders, coating agents, swelling agents, lubricants, flavorings, sweeteners or solubilizers are customarily used as described above. The pharmaceutical compositions are suitable for use in a variety of drug delivery systems. For a brief review of methods for drug delivery, see Langer R (1990) Science 249:1527-1533, which is incorporated herein by reference. 
     The compounds may be administered per se (neat) or in the form of a pharmaceutically acceptable salt. When used in medicine the salts should be pharmaceutically acceptable, but non-pharmaceutically acceptable salts may conveniently be used to prepare pharmaceutically acceptable salts thereof. Such salts include, but are not limited to, those prepared from the following acids: hydrochloric, hydrobromic, sulphuric, nitric, phosphoric, maleic, acetic, salicylic, p-toluene sulphonic, tartaric, citric, methane sulphonic, formic, malonic, succinic, naphthalene-2-sulphonic, and benzene sulphonic. Also, such salts can be prepared as alkaline metal or alkaline earth salts, such as sodium, potassium or calcium salts of the carboxylic acid group. 
     Suitable buffering agents include: acetic acid and a salt (1-2% w/v); citric acid and a salt (1-3% w/v); boric acid and a salt (0.5-2.5% w/v); and phosphoric acid and a salt (0.8-2% w/v). Suitable preservatives include benzalkonium chloride (0.003-0.03% w/v); chlorobutanol (0.3-0.9% w/v); parabens (0.01-0.25% w/v) and thimerosal (0.004-0.02% w/v). 
     The compositions may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the art of pharmacy. All methods include the step of bringing the compounds into association with a carrier which constitutes one or more accessory ingredients. In general, the compositions are prepared by uniformly and intimately bringing the compounds into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product. Liquid dose units are vials or ampoules. Solid dose units are tablets, capsules and suppositories. 
     Other delivery systems can include time-release, delayed release or sustained release delivery systems. Such systems can avoid repeated administrations of the compounds, increasing convenience to the individual and the physician. Many types of release delivery systems are available and known to those of ordinary skill in the art. They include polymer base systems such as poly(lactide-glycolide), copolyoxalates, polycaprolactones, polyesteramides, polyorthoesters, polyhydroxybutyric acid, and polyanhydrides. Microcapsules of the foregoing polymers containing drugs are described in, for example, U.S. Pat. No. 5,075,109. Delivery systems also include non-polymer systems that are: lipids including sterols such as cholesterol, cholesterol esters and fatty acids or neutral fats such as mono-, di-, and tri-glycerides; hydrogel release systems; silastic systems; peptide-based systems; wax coatings; compressed tablets using conventional binders and excipients; partially fused implants; and the like. Specific examples include, but are not limited to: (a) erosional systems in which an agent of the invention is contained in a form within a matrix such as those described in U.S. Pat. Nos. 4,452,775, 4,675,189, and 5,736,152, and (b) diffusional systems in which an active component permeates at a controlled rate from a polymer such as described in U.S. Pat. Nos. 3,854,480, 5,133,974 and 5,407,686. In addition, pump-based hardware delivery systems can be used, some of which are adapted for implantation. 
     EXAMPLES 
     Among the numerous CSC-associated genes are genes involved in vasculogenesis and angiogenesis. For example, global gene expression analyses validated by mRNA and protein determinations revealed preferential display of genes for vascular endothelial growth factor receptor-1 (VEGFR-1) and related members of signaling cascades involved in vasculogenesis and angiogenesis in ABCB5 +  MMIC. In vitro, vascular endothelial growth factor (VEGF) induced expression of the endothelial-associated marker CD144 (VE-cadherin) in VEGFR-1-expressing ABCB5 +  MMIC but not VEGFR-1-negative ABCB5 −  melanoma bulk populations, indicating a unique capacity of CSC for VEGF/VEGFR-1 signaling-dependent vasculogenic differentiation. In vivo, tumors initiated from patient-derived melanoma cells or established melanoma cultures by xenotransplantation into the murine subcutis or by intradermal injection into human skin in chimeric murine recipients formed perfused ABCB5 mRNA- and protein-expressing vessel-like channels also detected in clinical melanoma specimens that co-expressed CD144 and the vasculogenic mimicry marker TIE-1 4 . Tumour initiation in human skin by fluorescent transgene-expressing human melanoma cells confirmed CD144 +  channels to be of melanoma origin. Moreover, MMIC depletion in tumour grafts to human skin significantly reduced channel formation and resulted in attenuated tumour growth. Our results identify melanoma vasculogenesis driven by ABCB5 +  MMIC as a novel mechanism by which CSC may promote tumor growth. Furthermore, they suggest that MMIC-dependent vasculogenesis represents a novel CSC target for VEGF/VEGFR-1-directed inhibitors of angiogenesis. 
     Example 1 Materials and Methods 
     Melanoma Cells and Culture Methods. 
     The established human cutaneous melanoma cell lines G3361, A375, MALME-3M, SK-MEL-2, SK-MEL-5, SK-MEL-28, UACC-62, UACC-257, M14 and MDA-MB-435 were cultured as described 3,5,23 . Clinical cutaneous melanoma cells were derived from surgical specimen according to human subjects research protocols approved by the IRBs of the University of Wiirzburg Medical School or the Wistar Institute, Philadelphia, Pa. as described previously 3 . The established human uveal melanoma cell lines MUM-2B and MUM-2C were a gift of Dr. Mary J. Hendrix, Northwestern University, and were cultured as described 16 . 
     Cell Isolation. 
     ABCB5 + -purified (ABCB5 + ) cells were isolated by positive selection and ABCB5 + -depleted (ABCB5 − ) cell populations were generated by removing ABCB5 +  cells using anti-ABCB5 mAb (clone 3C2-1D12 23 ) labeling and magnetic bead cell sorting as described 3 . Briefly, human G3361, A375, MUM-2B or MUM-2C melanoma cells or single cell suspensions derived from clinical melanoma samples were labeled with anti-ABCB5 mAb for 30 min at 4° C., washed twice for excess antibody removal, followed by incubation with secondary anti-mouse IgG mAb-coated magnetic microbeads for 30 min at 4° C. Subsequently, cells were washed twice for excess magnetic microbead removal and then sorted into ABCB5 +  and ABCB5 −  cell fractions by dual-passage cell separation in MidiMACS or MiniMACS separation columns (depending on cell number) according to the manufacturer&#39;s recommendations (Miltenyi Biotec, Auburn, Calif.). Assessment of purity of ABCB5 +  and ABCB5 −  (ABCB5 +  cell-depleted) melanoma cell isolates and determination of cell viability following magnetic cell sorting were performed and yielded similar results as described previously 3 . 
     Global Gene Expression Microarray Analyses. 
     Microarray analyses were performed on purified ABCB5 +  (n=5) and ABCB5 −  (n=5) cell subsets derived from the established human melanoma cell lines G3361 and A375 and from three distinct clinical melanoma specimen previously characterized in our laboratory with regards to ABCB5 expression and MMIC phenotype in human melanoma xenotransplantation assays 3 . Total RNA was extracted, processed and hybridized as described previously 10  onto Affymetrix human HG-U133Plus2 GeneChip microarrays (Affymetrix, Santa Clara, Calif.). Statistical analysis of microarray results was performed as described previously 10 . The expression data set in its entirety will be made available through GEO (gene expression omnibus). Functional gene networks were generated using Ingenuity Pathways Analysis (Ingenuity® Systems, ingenuity.com), by mapping each gene identifier to its corresponding gene object in the Ingenuity Pathways Knowledge Base. These focus genes were overlaid onto a global molecular network developed from information contained in the Ingenuity Pathways Knowledge Base. Focus gene networks were then algorithmically generated based on their connectivity and subsequently analyzed to identify the biological functions that were most significant to the genes in the network. 
     RNA Extraction and Reverse Transcriptase-PCR. 
     Total RNA was isolated from ABCB5 +  and ABCB5 −  human melanoma cells using RNeasy columns (QIAGEN, Valencia, Calif.). Standard cDNA synthesis reactions were performed using 5 μg RNA and the SuperScript First-Strand Synthesis System for reverse transcriptase-PCR (Invitrogen, Carlsbad, Calif.) as per the manufacturer&#39;s instructions. For PCR analysis, 5 μl of diluted first strand product (˜100 ng of cDNA) was added to 45 μl of PCR reaction mixture containing 5 units of Superscript II (Invitrogen) according to the manufacturer&#39;s protocol. The following PCR program was performed: denaturation at 95° C. for 5 min, then cycled 35 times at 94° C. for 1 min, 53° C. for 30 s, and 72° C. for 30 s, and subsequently extended at 72° C. for 10 min. The primer sequences were as follows: PTK2 forward primer, 5′-TGCCTTTTACTTTCGTGTGG-3′(SEQ ID NO:1); PTK2 reverse primer 5′-CCAAATTCCTGTTTTGCTTCA-3′(SEQ ID NO:2); MET forward primer 5′-CCCCACCTTATCCTGACGTA-3′(SEQ ID NO:3); MET reverse primer 5′-CGTGTGTCCACCTCATCATC-3′(SEQ ID NO:4); NRP2 forward primer 5′-GAGGCAGGGGAAAATAGAGG-3′(SEQ ID NO:5); NRP2 reverse primer 5′-TCTCCCGAAAGGTTGAAATG-3′(SEQ ID NO:6); ETS1 forward primer 5′-CGCTTACTCTGTTGGGGTCT-3′(SEQ ID NO:7); ETS1 reverse primer 5′-TCTCCAGCAAAATGATGTGC-3′(SEQ ID NO:8); FLT1 forward primer 5′-TGGCAACTGCTTTTATGTTCTG-3′(SEQ ID NO:9); FLT1 reverse primer 5′-TCCATAGGGTGATGGTCAAA-3′(SEQ ID NO: 10). The reaction products were resolved on a 1% LE agarose gel (Ambion, Austin, Tex.) and photographed. β-Actin primers were used as controls to ensure RNA integrity. 
     RNA Extraction and Real Time Quantitative PCR. 
     Total RNA was isolated from unsegregated or sorted human melanoma cells using the RT 2  qPCR Grade RNA isolation kit (SABiosciences, Frederick, Md.). Standard cDNA synthesis reactions were performed using 1 μg RNA and the RT 2  First Strand Kit for reverse transcriptase-PCR (SABiosciences) as per the manufacturer&#39;s instructions. The reverse transcriptase product (1 μl) was amplified by primer pairs specific for ABCB5 5 . β-actin was used as a normalizing control. The primers for ABCB5 (Genebank accession no. AY234788) detection were 5′-GCTGAGGAATCCACCCAATCT-3′ (forward) (SEQ ID NO:11) and 5′-AGCCTGAATGGCCTTTTGTG-3′ (reverse) (SEQ ID NO:12). The primers for β-actin detection were 5′-CCTGGCACCCAGCACAAT-3′ (SEQ ID NO:13) (forward) and 5′-AGTACTCCGTGTGGATCGGC-3′ (reverse) (SEQ ID NO: 14). Samples were assayed using Sybergreen chemistry and kinetic PCR (ABI 7300 Sequence Detector; Applied Biosystems, Foster City, Calif.). Samples were amplified using the Sybergreen PCR reagent kit (Applied Biosystems) according to the manufacturer&#39;s protocol. Sense and antisense primers were used at a final concentration of 10 nM. The cDNA samples were amplified under following conditions: 50° C. for 2 min and 95° C. for 10 min, followed by 40 cycles of amplification at 94° C. for 15 s and 60° C. for 1 min. All samples were run in triplicate. The relative amounts of transcripts were analyzed using the 2(-Delta Delta C(T)) method as described previously 3,5,10 . Statistical differences between mRNA expression levels were determined using the nonparametric Mann-Whitney test. A two-sided P value of P&lt;0.05 was considered significant. 
     Western Analysis. 
     Total cell lysates were harvested from logarithmically growing cultures of the human melanoma cell lines MALME-3M, SK-MEL-2, SK-MEL-5, SK-MEL-28, UACC-62, UACC-257, M14, and MDA-MB-435 and analyzed by 8% SDS-PAGE and Western assay to detect relative levels of ABCB5 (mAb 3C2-1D12 23 ) and alpha-tubulin (mAb clone DM1A, Sigma-Aldrich, St. Louis, Mo.), using LI-COR Odyssey IR imaging system densitometry. 
     Flow Cytometry. 
     G3361, A375, MUM-2B, or MUM-2C melanoma cells were analyzed for surface ABCB5 expression by incubation with anti-ABCB5 mAb or isotype control mAb for 30 min at 4° C., followed by counterstaining with FITC-conjugated goat anti-mouse Ig or with APC-conjugated donkey anti-mouse IgG secondary Abs and single color flow cytometry at the F11 (FITC) or F14 (APC) emission spectrum on a Becton Dickinson FACScan as described 3,5,23 . Washing was performed twice between each step. Analysis of coexpression of ABCB5 with the VEGFR-1 surface marker in G3361 melanoma cells was performed by dual-color flow cytometry as described 3 . Briefly, melanoma cells were incubated for 30 min at 4° C. with anti-ABCB5 mAb or isotype control mAb, followed by counterstaining with APC-conjugated donkey anti-mouse IgG secondary Ab as above. Subsequently, cells were fixed at 4° C. and then incubated for 30 min at 4° C. with PE-conjugated anti-VEGFR-1 mAb (R&amp;D Systems, Minneapolis, Minn.) or PE-conjugated isotype control mAb (BD PharMingen, San Diego, Calif.). Dual color flow cytometry was subsequently performed with acquisition of fluorescence emission at the F14 (APC) and F12 (PE) spectra on a Becton Dickinson FACScan. Washing was performed twice between each step. Statistical differences between expression levels of markers were determined using the nonparametric Mann-Whitney test. A two-sided P value of P&lt;0.05 was considered significant. 
     In Vitro Vasculogenic Differentiation and Tube Formation Assays. 
     VEGF-dependent induction of CD144 expression and formation of capillary-like tube structures by human G3361 melanoma cells was assayed on growth factor reduced Matrigel, a basement membrane matrix preparation (BD Biosciences, San Jose, Calif.). Growth factor reduced Matrigel was added to eight-chamber polystyrene vessel tissue culture-treated glass slides and allowed to gelatinize for 20 min at 37° C. Purified ABCB5 +  or ABCB5 −  or unsegregated human melanoma cells were seeded into culture slide wells at densities of 5×10 4  cells/cm 2  in medium 199 containing 5% FCS 11  in the presence or absence of VEGF (100 ng/ml). After 48-hour incubation, cells were fixed with 4% paraformaldehyde/PBS for 20 min at room temperature, and after extensive washing with PBS the cells were blocked in 5% donkey serum/0.01% Tween 20/PBS for 1 hr at room temperature. Cells were then incubated with rabbit anti-CD144 polyclonal Ab (diluted 1:100; Bethyl Laboratories, Montgomery, Tex.) overnight at 4° C. After extensive washing with 0.01% Tween 20/PBS, the cells were incubated with goat anti-rabbit Texas red-conjugated secondary Ab (diluted 1:250; Jackson ImmunoResearch Laboratories, West Grove, Pa.) for 1 hr at room temperature. Following washing with 1×PBS/0.01% Tween 20, cells were then mounted in Vectashield (Vecta Laboratories, Burlingame, Calif.) supplemented with 100 ng/ml DAPI to visualize nuclei. Cells were analyzed by fluorescent microscopy using a Mercury-100 Watts fluorescent light source (Microvideo Instruments, Avon, Mass.) attached to a Nikon Eclipse TE 300 microscope (Nikon Instruments, Melville, N.Y.) with the use of separate filters for each fluorochrome. The images were obtained using a Spot digital camera (Diagnostic Instruments Inc., Sterling Heights, Mich.), and the Spot 3.3.2. software package was imported into Adobe Photoshop (Adobe Systems, Mountain View, Calif.). For tube formation assays, unsegregated human melanoma cells were seeded into culture slide wells at densities of 5×10 4  cells/cm 2  in medium 199 containing 5% FCS 11 . Immediately, cells were pretreated with medium alone, rabbit anti-VEGFR1 Ab (10 μg/ml; Santa Cruz Biotechnology, Santa Cruz, Calif.) or rabbit isotype control Ab (10 μg/ml; BD Biosciences) at 37° C. for 2 hrs prior to stimulation with VEGF (100 ng/ml). Tube formation was detected by phase contrast microscope (Nikon Eclipse TE 300 microscope) after 24 hrs of incubation. For quantitative analysis of tube formation and length and for determination of CD144 expression at 48 hrs, n=3 three randomly selected microscopy fields were photographed per experimental condition. Images were acquired as described above and tube formation was analyzed using Image J software available from the National Institutes of Health web site as described previously 24 . For quantification of CD144 expression, positive cells were counted using Neurolucida 8.10 software (MBF Bioscience, Williston, Vt.). Differences among groups were analyzed by one-way ANOVA followed by Bonferroni post hoc tests. Differences with P values&lt;0.05 were considered statistically significant. 
     In Vitro Adipogenic, Osteogenic and Myogenic Differentiation Assays. 
     For adipogenic, osteogenic and myogenic differentiation assays purified ABCB5 +  and ABCB5 −  G3361 melanoma cells were seeded in triplicate at 3×10 3  cells/well in 96-well culture plates. Adipogenic and osteogenic differentiation was assessed using commercially available differentiation kits and Oil Red O and Alizarin Red staining, respectively, according to the manufacturer&#39;s instructions (Chemicon International, Temecula, Calif.). Myogenic differentiation assays were performed as described previously 10 . Briefly, melanoma subpopulations were incubated in growth medium consisting of DMEM with 4% glucose, 20% fetal bovine serum (vol/vol), 1% (vol/vol) penicillin-streptomycin (10,000 UI/ml-10,000 μg/ml, Invitrogen) for 10 days. The medium was exchanged every 2 days. At day 14, cells were fixed in ice cold methanol for 3 min on ice and incubated with 1:50 diluted anti-myogenin mouse monoclonal Ab (Dako, Carpinteria, Calif.) overnight at 4° C. Plates were then washed, incubated with goat anti-mouse FITC-conjugated secondary Ab (Jackson ImmunoResearch Laboratories, diluted 1:100) and then mounted with Vectashield mounting medium (Vector) supplemented with 100 ng/ml DAPI to visualize nuclei. Slides were visualized with the 20× and 40× objective on a Nikon Eclipse TE2000-S microscope, photographed using the Spot 7.4 slider camera and images processed using Spot software version 4.0.9. (Diagnostic Instruments, Sterling Heights, Mich.). For quantification of differentiation marker expression, positive cells were manually counted and statistical differences between expression levels of markers were determined using the nonparametric Mann-Whitney test. A two-sided P value of P&lt;0.05 was considered significant. 
     Immunohistochemistry and Immunofluorescence Double Labeling. 
     The following primary Abs were used: rat anti-Laminin B2, (Abcam, Cambridge, Mass.), rabbit anti-CD144, (Cell Signaling, Beverly, Mass.), goat anti-Tie-1, (Neuromics, Edina, Minn.), and mouse anti-ABCB5 3,5,23 . Isotype matched irrelevant Abs served as negative control. The secondary Abs were horse anti-mouse IgG-HRP, horse anti-goat IgG-HRP, goat anti-rabbit IgG-HRP (VECTOR Laboratories, Burlingame, Calif.) and goat anti-rat IgG-HRP (Biolegend, San Diego, Calif.), and donkey anti-mouse IgG-AF488, donkey anti-rabbit IgG-AF594, and donkey anti-goat IgG-AF594 (Invitrogen, Carlsbad, Calif.). Immunohistochemistry was performed using the 2-step horseradish peroxidase method. Briefly, frozen tissue sections were fixed with −20° C. acetone for 5 min, then incubated with primary Ab at 4° C. overnight. After washing out unbound primary Ab with phosphate-buffered saline (PBS), the tissue sections were incubated with secondary Ab at room temperature for 30 min, then washed with PBS 3×5 min. Immunoreactivity was detected using NovaRed peroxidase substrate (VECTOR Laboratories, Burlingame, Calif.). For immunofluorescence double labeling, the frozen tissue sections were fixed with −20° C. acetone for 5 min, then incubated with the mix of 2 primary Abs (for example ABCB5 Ab+CD144 Ab) at 40° C. overnight. After washing with PBS, the tissue sections were incubated with the mix of 2 secondary Abs (for example donkey anti-mouse IgG-AF488+donkey anti-rabbit IgG-AF594) at room temperature for 1 hour, then washed with PBS 3×5 min, and the sections were then mounted with ProLong Gold antifade reagent with DAPI (Invitrogen, Carlsbad, Calif.). The sections were viewed under a Olympus BX51 System fluorescence microscope (Olympus Corporation, Tokyo, Japan). For HLA-2A immunohistochemistry of SK-MEL-5 melanoma xenografts to chimeric mouse/human skin, frozen sections were incubated with 5 μg/ml mouse anti-human HLA-2A Ab (BD Pharmingen, San Jose, Calif.) at 4° C. overnight. After washing out unbound primary Ab with phosphate buffered saline (PBS), sections were incubated with 1:200 peroxidase-conjugated horse anti-mouse IgG Ab (Vector Laboratories, Burlingame, Calif.) at room temperature for 30 min. Unbound secondary Ab was washed out with PBS. Color was developed using the NovRed peroxidase substrate kit (Vector Laboratories) and sections were counterstained with hematoxylin Gill&#39;s No. 1 (Fisher Scientific, Pittsburgh, Pa.). 
     In Situ Hybridization. 
     RNA probes were prepared as follows: PCR-derived RNA probe templates were synthesized by introducing the T7 promoter into the antisense strand and the SP6 promoter into the sense strand. The primer pair, AB5T7AS (5′-TAATACGACTCACTATAGGGATGTCTGGCTTTTTCCCTTCTTGAC-3′) (SEQ ID NO:15) and AB5SP6S (5′-GATTTAGGTGACACTATAGAAATTCAAGCTGGACGAATGACCCCA-3′) (SEQ ID NO:16), was used to generate the DNA template for antisense and sense RNA probes spanning 200 base pairs of human ABCB5 cDNA. This sequence encodes ABCB5 amino acids 499-564 (GI:34539755). The primer pair CD133T7AS (5′-TAATACGACTCACTATAGGGAGCAGCCCCAGGACACAGCATA-3′) (SEQ ID NO:17) and CD133SP6S (5′-GATTTAGGTGACACTATAGAGACCCAAGACTCCCATAAAGC-3′) (SEQ ID NO:18) was used to generate the DNA template for antisense and sense RNA probes spanning 200 base pairs of human CD133 cDNA, wherein this sequence encodes CD133 amino acid 42-108 (GI: 5174386). The sequence specificities for ABCB5 and CD133 were confirmed using the Genbank database BLAST program. The RNA probes were labeled with digoxigenin (DIG) using the DIG RNA labeling kit (Roche Applied Science, Indianapolis, Ind.). For in situ hybridization, 8 μM frozen tissue sections were baked at 50° C. for 15 min, then fixed in 4% paraformaldehyde at room temperature (RT) for 20 min. The sections were treated with 1 μg/ml proteinase K/PBS at 37° C. for 20 min and inactivated proteinase K with 0.2% glucine/PBS at RT for 5 min. Upon washes with PBS 2×2 min, the tissue sections were fixed in 4% paraformadehyde at RT for 15 min, washed with PBS 2×5 min, and then treated with 0.25% acetic anhydride/0.1M triethanolamine at RT for 10 min. The tissue sections were placed in 2×SSC and then hybridized with 500 ng/ml antisense or sense probe in hybridization buffer (0.3M NaCl, 10 mM Tris-HCl pH 7.6, 5 mM EDTA, 1× Denharts, 50% formamide, 100 μg/ml tRNA and 10% dectran sulphate) at 42° C. overnight. Post hybridization sections were treated with 0.2×SSC at 55° C. for 2×20 min, 20 g/ml RNaseA in 0.5M NaCl, 10 mM Tris-HCl pH 7.5 at 37° C. for 30 min, and 0.2×SSC at 55° C. for 20 min. The hybridized probes were immunodetected using the DIG detection kit (Roche) and the Tyramide Signal Amplification (TSA) kit (PerkinElmer, Boston, Mass.) as follows: 1×DIG block buffer for 30 min, 1:100 anti-DIG Ab peroxidase conjugate at RT for 1 hour, 1×DIG wash 3×5 min, TSA reagent 10 min at RT, PBS 2×5 min, 1:100 streptavidin-horseradish peroxidase 30 min at RT, PBS 3×5 min. The labeling was visualized with NovaRed substrate (Vector Laboratories). 
     Animals. 
     BALB/c nude mice and NOD/SCID mice were purchased from The Jackson Laboratory (Bar Harbor, Me.). SCID mice (C.B-17) and BALB/c Rag2 −/−  mice were purchased from Taconic (Germantown, N.Y.). The animals were housed in autoclaved microisolator cages and were fed sterilized food and water. Mice were maintained in accordance with the institutional guidelines of Children&#39;s Hospital Boston and Harvard Medical School and experiments were performed according to approved experimental protocols. 
     Human to Mouse Melanoma Xenotransplantation and Human to Chimeric Mouse/Human Skin Melanoma Xenotransplantation. 
     Human to mouse melanoma xenografts were established by subcutaneous injection of human G3361, A375, SK-MEL-5 or clinical patient-derived human melanoma cells in BALB/c nude or NOD/SCID mice as described previously 3 . For human to chimeric mouse/human skin melanoma xenotransplantation, single donor-derived split human skin was obtained in accordance with the Partners HealthCare Research Management Institutional Review Board by cutting abdominal skin with a 0.016-inch gauge dermatome. Human skin was subsequently xenografted onto immunodeficient Rag2 −/−  mice as described previously 13 , under a protocol approved by the institutional animal committee. Briefly, two circular graft beds, each, 1.5 cm 2  were prepared on bilateral dorsa of 4-8 week old Rag2 −/−  micetreated with antibiotics (1 tablet of additional food per week containing Amoxicillin (3 mg), Flagyl (0.69 mg) and Bismuth (0.185 mg)) to prevent  Helicobacter pylorii  infection. Human donor skin was trimmed to conform to the bed and held in place with staples until 10 days following surgery. Unsegregated or ABCB5 + -depleted A375, MUM-2B or MUM-2C melanoma cells (2×10 6  in 20 μl PBS) were intradermally microinjected into grafts after 6 weeks stabilization. All skin grafts were harvested in their entirety 3 weeks after tumour cell inoculation, fixed in formalin, serially sectioned and stained with H&amp;E using standard methods for histological analysis of tumour formation. Sections representing maximum cross-sectional tumour area and thus best approximating the size of the generally spherical to ovoid tumour nodules were evaluated. Tumour volume (TV) was histologically determined and calculated as described 3 . Statistically significant differences in histological tumour formation were assessed using the Fisher&#39;s Exact test. Differences in tumour volume were statistically compared using the nonparametric Mann-Whitney Test, with a two-sided P value of P&lt;0.05 considered significant. 
     Stable Green Fluorescence Protein (GFP)-Transfected Melanoma Xenografts to Human-SCID Chimeras. 
     Recombinant lentiviral vectors harboring GFP cDNA were obtained from Dr. M. Herlyn at the Wistar Institute and used to infect human A375 melanoma cells by lentiviral gene transfer. Two days after infection, cells were selected with puromycin (1 μg/ml) for a period of 7 days. Transgene expression was verified by fluorescence microscopy and flow cytometry. Melanoma xenografts were generated in human-SCID chimeras according to the protocol previously described 13 . SCID mice (C.B-17) between 4-6 weeks of age were purchased from Taconic (Germantown, N.Y.). Mice were anesthetized and prepared for transplantation by shaving the hair from a 2 cm 2  area on the dorsal torso followed by removal of full thickness skin down to the fascia. Full thickness human foreskin grafts of the same size were placed onto the wound beds. The skin grafts were then covered by Vaseline-saturated gauze and secured with band aids and 3M sports tapes. After 10 days, the dressings were removed and the mice allowed to recover for approximately 4-5 weeks before melanoma inoculation. GFP-labeled A375 melanoma cells were harvested and suspended in PBS at a density of 10 8  cells/ml. One hundred μl each of cell suspension were injected intradermally into the human skin grafts. The tumour xenografts were then harvested in 3 weeks or when the tumour reaches 1 cm 3  in size, and processed for frozen section. For double immunofluorescence, frozen sections (5 μm thick) of melanoma xenografts were fixed in 4% paraformaldehyde, blocked with donkey serum, and incubated sequentially with anti-CD144 (Cell Signaling, Danvers, Mass.), Texas red-conjugated donkey anti-rabbit (Invitrogen, Carlsbad, Calif.), anti-GFP (Novus Biologicals, Littleton, Colo.), and FITC-conjugated donkey anti-goat Abs (Jackson ImmunoResearch, West Grove, Pa.). After washing in PBS, the sections were coverslipped using an antiquench mountant containing DAPI (VectaShield, Vector Laboratories, Burlingame, Calif.). Irrelevant isotype-matched primary Abs were included as controls. 
     Example 2 
     The mechanisms through which ABCB5 +  MMIC or CSC in other cancers trigger and promote neoplastic progression are currently unknown. We hypothesized that ABCB5 +  MMIC possess vasculogenic differentiation plasticity and selectively drive melanoma growth through a specific role in providing nutritional support to growing tumours based on preferential co-expression in vivo of the vasculogenic differentiation markers CD144 (VE-cadherin) and TIE-1 3  by the ABCB5 +  tumourigenic minority population. 
     To further characterize the repertoire of genes differentially expressed in MMIC compared to tumour bulk populations, we first performed microarray analyses on purified ABCB5 +  (n=5) and ABCB5 −  (n=5) cell subsets derived from the established human melanoma cell lines G3361 and A375 and from three separate patient-derived melanoma specimens, all previously characterized in our laboratory with regard to ABCB5 expression and MMIC phenotype in human melanoma xenotransplantation assays 3 . Using this approach 10 , 399 genes were identified that were differentially expressed (P&lt;0.05) between ABCB5 +  MMIC and ABCB5 −  melanoma bulk populations (Table 5), in addition to ABCB5 shown overexpressed in ABCB5 +  purified populations by real-time PCR (P&lt;0.05). One identified functional gene network, validated by PCR-based gene expression analyses in ABCB5 +  melanoma cell subsets, showed key molecules of vasculogenesis (the ability to differentiate along endothelial lines), FLT1 (VEGFR-1) and PTK2 (FAK), and of angiogenesis (the ability to induce ingrowth and proliferation of mature stromal blood vessels), FLT1 (VEGFR-1), PTK2 (FAK), MET (HGFR), NRP2, and ETS1, to be specifically overexpressed in ABCB5 +  MMIC ( FIG. 1 a,b   ). 
     Another set of genes differentially expressed in ABCB+ melanoma stem cells vs. ABCB5-melanoma bulk population cells was identified using RT-PCR. The data is shown in Table 6. The fold-expression levels are shown in the 7 th  column and can be compared to the control values shown in the last few rows of the table. A positive value indicates that the gene had higher expression levels in ABCB5+ cells and a negative value indicates that the gene had higher expression levels in ABCB5− cells. Some of the genes exhibited a greater than 100-fold and some even greater 1000-fold increase in expression in ABCB5+ versus ABCB5− cells. The highly expressed genes include factors that are likely secreted by the stem cells which may act on cells in a tumor either in an autocrine fashion on tumor stem cells, or in a paracrine fashion also on bulk population cancer cells. Appropriate therapies can be designed to treat cancers by inhibiting the expression or activity of such factors. 
     Preferential expression of VEGFR-1 by ABCB5 +  MMIC vs. ABCB5 −  subpopulations was also demonstrated by dual-color flow cytometry at the protein level (15.6±5.3% vs. 4.4±2.0% of cells, respectively, mean±s.e.m., n=6, P&lt;0.05) ( FIG. 1 c   ). To determine whether VEGF/VEGFR-1 interaction in MMIC influenced expression of the vasculogenic differentiation marker CD144, we evaluated functionally the effects of VEGF signaling in purified ABCB5 +  MMIC or ABCB5 −  melanoma subpopulations. VEGF (100 ng/ml 11 ) selectively induced expression of CD144 at high levels in VEGFR-1-expressing ABCB5 +  but not VEGFR-1-negative ABCB5 −  melanoma cells, to 36.2±5.7% vs. 4.8±2.7% of cells (mean±s.e.m., n=3), respectively (P&lt;0.01) ( FIG. 1 d   ). Preincubation with a blocking monoclonal antibody (mAb) to VEGFR-1 abrogated the ability of VEGF to induce CD144 expression in human melanoma cells (0.0±0.0% in VEGFR-1 mAb-treated vs. 64±1% or 57±3% in untreated or isotype control mAb-treated cultures, respectively, mean±s.e.m., n=3, P&lt;0.01) ( FIG. 1 e   ). Moreover, VEGFR-1 mAb strongly inhibited VEGF-induced multicellular capillary-like tube formation by human melanoma cells in established in vitro vasculogenic differentiation assays 11 , with significantly reduced numbers of tubes formed/microscopy field (6.7±0.9 in VEGFR-1 mAb-treated vs. 99.0±24.0 or 76.7±3.3% in untreated or isotype control mAb-treated cultures, respectively, mean±s.e.m., n=3, P&lt;0.05), and significantly lower average tube length (33.2±4.5 μm in VEGFR-1 mAb-treated vs. 92.1±1.6 μm or 86.5±1.7 μm in untreated or isotype control mAb-treated cultures, respectively, mean±s.e.m., n=3, P&lt;0.001) ( FIG. 1 f   ). In contrast, both ABCB5 +  MMIC and ABCB5 −  melanoma bulk population exhibited similar adipogenic and osteogenic differentiation capacity previously detected in human melanoma cells 12  (adipogenesis: 100.0±0.0% vs. 93.2±6.9% of cells Oil Red-positive, respectively; mean±s.e.m., n=3, NS; osteogenesis: 90.8±9.2% vs. 98.3±1.7% of cells Alizarin Red-positive, respectively; mean±s.e.m., n=3, NS) ( FIG. 1 g,h   ), and neither ABCB5 +  MMIC nor ABCB5 −  melanoma bulk population exhibited capacity for myogenic differentiation 10  (0.0±0.0% vs. 0.0±0.0% of cells myogenin-positive, respectively; mean±s.e.m., n=3, NS) ( FIG. 1 h   ). The selective in vitro vasculogenic differentiation capacity of ABCB5 +  MMIC in response to VEGF/VEGFR-1 signaling indicated a potential role of this CSC subset in tumour vasculogenesis. 
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Differentially expressed genes between ABCB5 +  MMIC and 
               
               
                 ABCB5 −  melanoma bulk populations (P &lt; 0.05). 
               
            
           
           
               
               
               
               
            
               
                   
                 Molecules 
                 ID 
                 Fold Change 
               
               
                   
                   
               
            
           
           
               
               
               
               
            
               
                   
                 AABHD7 
                 239579_at 
                 0.661 
               
               
                   
                 ACBD6 
                 225317_at 
                 0.83 
               
               
                   
                 AK3 
                 224655_at 
                 0.845 
               
               
                   
                 AKAP9 
                 215483_at 
                 2.168 
               
               
                   
                 AKR1CL2 
                 1559982_s_at 
                 1.732 
               
               
                   
                 AMZ2 
                 227567_at 
                 1.377 
               
               
                   
                 ANAPC5 
                 235926_at 
                 2.631 
               
               
                   
                 ANK2 
                 202921_s_at 
                 4.162 
               
               
                   
                 ANKH 
                 229176_at 
                 0.776 
               
               
                   
                 ANKRD28 
                 241063_at 
                 2.297 
               
               
                   
                 ANKRD44 
                 226641_at 
                 1.218 
               
               
                   
                 ANKRD52 
                 228257_at 
                 0.762 
               
               
                   
                 ANXA4 
                 201302_at 
                 0.83 
               
               
                   
                 AOC3 
                 204894_s_at 
                 1.894 
               
               
                   
                 APBB2 
                 40148_at 
                 1.139 
               
               
                   
                 ARS2 
                 201679_at 
                 1.307 
               
               
                   
                 ASCC3L1 
                 214982_at 
                 3.009 
               
               
                   
                 (includes EG:23020) 
               
               
                   
                 ASPM 
                 232238_at 
                 1.411 
               
               
                   
                 ATAD2 
                 235266_at 
                 1.304 
               
               
                   
                 ATP5I 
                 207335_x_at 
                 0.737 
               
               
                   
                 ATXN2L 
                 207798_s_at 
                 1.656 
               
               
                   
                 BARD1 
                 205345_at 
                 1.559 
               
               
                   
                 BAT3 
                 230513_at 
                 0.697 
               
               
                   
                 BCL9L 
                 227616_at 
                 1.291 
               
               
                   
                 BDP1 
                 224227_s_at 
                 1.632 
               
               
                   
                 BLID 
                 239672_at 
                 1.91 
               
               
                   
                 BRI3 
                 223376_s_at 
                 0.792 
               
               
                   
                 BUB1 
                 216277_at 
                 1.856 
               
               
                   
                 (includes EG:699) 
               
               
                   
                 BUB1 
                 233445_at 
                 3.209 
               
               
                   
                 (includes EG:699) 
               
               
                   
                 C10ORF18 
                 244165_at 
                 2.046 
               
               
                   
                 C12ORF45 
                 226349_at 
                 0.688 
               
               
                   
                 C12ORF48 
                 220060_s_at 
                 1.216 
               
               
                   
                 C12ORF51 
                 230216_at 
                 2.874 
               
               
                   
                 C12ORF51 
                 1557529_at 
                 3.632 
               
               
                   
                 C14ORF135 
                 1563259_at 
                 1.353 
               
               
                   
                 C14ORF156 
                 221434_s_at 
                 0.867 
               
               
                   
                 C16ORF63 
                 225087_at 
                 0.872 
               
               
                   
                 C18ORF10 
                 213617_s_at 
                 0.754 
               
               
                   
                 C18ORF10 
                 212055_at 
                 0.737 
               
               
                   
                 C19ORF42 
                 219097_x_at 
                 0.813 
               
               
                   
                 C20ORF4 
                 234654_at 
                 1.731 
               
               
                   
                 C22ORF28 
                 200042_at 
                 0.829 
               
               
                   
                 C22ORF30 
                 216555_at 
                 1.521 
               
               
                   
                 C2ORF30 
                 224630_at 
                 0.851 
               
               
                   
                 C5ORF24 
                 229098_s_at 
                 1.531 
               
               
                   
                 C9ORF78 
                 218116_at 
                 0.789 
               
               
                   
                 C9ORF85 
                 244160_at 
                 1.52 
               
               
                   
                 CABIN1 
                 1557581_x_at 
                 3.052 
               
               
                   
                 CAMK2D 
                 225019_at 
                 0.823 
               
               
                   
                 CAMK2D 
                 228555_at 
                 0.758 
               
               
                   
                 CANX 
                 238034_at 
                 0.8 
               
               
                   
                 CAPZB 
                 201949_x_at 
                 0.764 
               
               
                   
                 CASC5 
                 228323_at 
                 1.144 
               
               
                   
                 CBS 
                 240517_at 
                 1.818 
               
               
                   
                 CCDC127 
                 226515_at 
                 0.835 
               
               
                   
                 CCDC14 
                 240884_at 
                 1.771 
               
               
                   
                 CCDC52 
                 234995_at 
                 1.166 
               
               
                   
                 CCDC57 
                 214818_at 
                 1.703 
               
               
                   
                 CCDC73 
                 239848_at 
                 1.294 
               
               
                   
                 CCDC93 
                 219774_at 
                 1.208 
               
               
                   
                 CDC14B 
                 234605_at 
                 2.512 
               
               
                   
                 CDC16 
                 242359_at 
                 6.261 
               
               
                   
                 CENPJ 
                 234023_s_at 
                 1.22 
               
               
                   
                 CENPJ 
                 220885_s_at 
                 1.64 
               
               
                   
                 CEP27 
                 228744_at 
                 0.651 
               
               
                   
                 CEP55 
                 218542_at 
                 1.096 
               
               
                   
                 CGGBP1 
                 224600_at 
                 0.913 
               
               
                   
                 CHD2 
                 244443_at 
                 1.757 
               
               
                   
                 CHD8 
                 212571_at 
                 1.27 
               
               
                   
                 CLN8 
                 229958_at 
                 1.344 
               
               
                   
                 CNIH3 
                 232758_s_at 
                 1.451 
               
               
                   
                 COBRA1 
                 1556434_at 
                 1.985 
               
               
                   
                 COIL 
                 203653_s_at 
                 1.259 
               
               
                   
                 COL4A2 
                 211966_at 
                 0.729 
               
               
                   
                 COQ4 
                 218328_at 
                 1.328 
               
               
                   
                 CPEB2 
                 226939_at 
                 1.251 
               
               
                   
                 CPNE3 
                 202119_s_at 
                 0.833 
               
               
                   
                 CREB1 
                 204313_s_at 
                 0.791 
               
               
                   
                 CREB3L2 
                 237952_at 
                 2.013 
               
               
                   
                 CRIPAK 
                 228318_s_at 
                 1.486 
               
               
                   
                 CROP 
                 242389_at 
                 2.121 
               
               
                   
                 CSE1L 
                 201112_s_at 
                 0.911 
               
               
                   
                 CSE1L 
                 210766_s_at 
                 0.885 
               
               
                   
                 CUL4A 
                 232466_at 
                 2.607 
               
               
                   
                 CYB5R3 
                 1554574_a_at 
                 0.793 
               
               
                   
                 DARS 
                 201624_at 
                 0.928 
               
               
                   
                 DCLRE1C 
                 242927_at 
                 1.187 
               
               
                   
                 DCUN1D2 
                 240478_at 
                 1.76 
               
               
                   
                 DDX17 
                 213998_s_at 
                 1.528 
               
               
                   
                 DDX52 
                 212834_at 
                 0.771 
               
               
                   
                 DEGS1 
                 209250_at 
                 0.804 
               
               
                   
                 DEPDC1 
                 232278_s_at 
                 1.119 
               
               
                   
                 DHX40 
                 218277_s_at 
                 0.812 
               
               
                   
                 DNAJC21 
                 230893_at 
                 0.829 
               
               
                   
                 DNM1L 
                 236032_at 
                 1.503 
               
               
                   
                 DTX3 
                 49051_g_at 
                 1.32 
               
               
                   
                 ECHDC1 
                 233124_s_at 
                 0.943 
               
               
                   
                 EIF2S1 
                 201142_at 
                 0.717 
               
               
                   
                 EIF2S1 
                 201144_s_at 
                 0.824 
               
               
                   
                 EIF4G3 
                 201935_s_at 
                 1.174 
               
               
                   
                 ELOVL2 
                 213712_at 
                 0.699 
               
               
                   
                 EMP2 
                 225079_at 
                 0.781 
               
               
                   
                 ENAH 
                 222433_at 
                 0.783 
               
               
                   
                 ENDOD1 
                 212573_at 
                 0.775 
               
               
                   
                 ENTPD5 
                 231676_s_at 
                 0.867 
               
               
                   
                 ERBB3 
                 1563253_s_at 
                 0.691 
               
               
                   
                 ERRFI1 
                 224657_at 
                 0.881 
               
               
                   
                 ETS1 
                 241435_at 
                 1.797 
               
               
                   
                 EWSR1 
                 229966_at 
                 1.686 
               
               
                   
                 EXT1 
                 242126_at 
                 2.116 
               
               
                   
                 FAM62C 
                 239770_at 
                 1.551 
               
               
                   
                 FAM98A 
                 212333_at 
                 0.767 
               
               
                   
                 FHL3 
                 218818_at 
                 0.546 
               
               
                   
                 FLJ10357 
                 241627_x_at 
                 2.31 
               
               
                   
                 FLJ31306 
                 239432_at 
                 1.753 
               
               
                   
                 FLT1 
                 232809_s_at 
                 1.861 
               
               
                   
                 FOXN3 
                 218031_s_at 
                 0.721 
               
               
                   
                 FUBP1 
                 240307_at 
                 2.087 
               
               
                   
                 GABARAPL2 
                 209046_s_at 
                 0.863 
               
               
                   
                 GABPA 
                 243498_at 
                 2.03 
               
               
                   
                 GALNT1 
                 201722_s_at 
                 0.926 
               
               
                   
                 GBF1 
                 233114_at 
                 2.03 
               
               
                   
                 GGT1 
                 211417_x_at 
                 1.555 
               
               
                   
                 GHITM 
                 1554510_s_at 
                 0.764 
               
               
                   
                 GMFB 
                 202544_at 
                 0.904 
               
               
                   
                 GNPDA1 
                 202382_s_at 
                 0.787 
               
               
                   
                 GOLGA8A 
                 213650_at 
                 2.289 
               
               
                   
                 GPD2 
                 243598_at 
                 2.13 
               
               
                   
                 GPR107 
                 211979_at 
                 0.843 
               
               
                   
                 GPR135 
                 241085_at 
                 1.851 
               
               
                   
                 HDAC3 
                 240482_at 
                 2.062 
               
               
                   
                 HEATR2 
                 241352_at 
                 0.784 
               
               
                   
                 HECW1 
                 237295_at 
                 11.843 
               
               
                   
                 HELLS 
                 242890_at 
                 1.359 
               
               
                   
                 HERC5 
                 219863_at 
                 1.156 
               
               
                   
                 HIAT1 
                 225222_at 
                 0.832 
               
               
                   
                 HNRNPC 
                 235500_at 
                 1.769 
               
               
                   
                 HNRPD 
                 235999_at 
                 1.92 
               
               
                   
                 HNRPD 
                 241702_at 
                 1.962 
               
               
                   
                 HNRPH1 
                 213472_at 
                 2.332 
               
               
                   
                 HOXA2 
                 228642_at 
                 1.44 
               
               
                   
                 HOXB9 
                 216417_x_at 
                 0.766 
               
               
                   
                 HOXD3 
                 206601_s_at 
                 1.897 
               
               
                   
                 HPS1 
                 239382_at 
                 1.749 
               
               
                   
                 HSD17B1 
                 228595_at 
                 0.753 
               
               
                   
                 HSDL2 
                 209513_s_at 
                 0.803 
               
               
                   
                 HSPA4L 
                 205543_at 
                 0.786 
               
               
                   
                 HUWE1 
                 214673_s_at 
                 1.858 
               
               
                   
                 IDS 
                 1559136_s_at 
                 2.001 
               
               
                   
                 IFNGR1 
                 242903_at 
                 2.171 
               
               
                   
                 IGHMBP2 
                 215980_s_at 
                 0.893 
               
               
                   
                 IL13RA1 
                 201887_at 
                 0.775 
               
               
                   
                 INSIG2 
                 209566_at 
                 0.872 
               
               
                   
                 IPO7 
                 200993_at 
                 0.875 
               
               
                   
                 IPW 
                 213447_at 
                 1.399 
               
               
                   
                 IRS2 
                 236338_at 
                 2.162 
               
               
                   
                 JARID1A 
                 226367_at 
                 1.192 
               
               
                   
                 JARID2 
                 232835_at 
                 2.139 
               
               
                   
                 KIAA0841 
                 36888_at 
                 1.389 
               
               
                   
                 KIAA0907 
                 230028_at 
                 1.83 
               
               
                   
                 KIAA1267 
                 224489_at 
                 1.355 
               
               
                   
                 KIAA1618 
                 231956_at 
                 2.27 
               
               
                   
                 KIAA1737 
                 225623_at 
                 0.837 
               
               
                   
                 KIAA2013 
                 1555933_at 
                 2.18 
               
               
                   
                 KIDINS220 
                 1557246_at 
                 2.97 
               
               
                   
                 KPNA6 
                 226976_at 
                 0.814 
               
               
                   
                 KRTAP19-1 
                 1556410_a_at 
                 2.07 
               
               
                   
                 KSR2 
                 230551_at 
                 3.211 
               
               
                   
                 LBA1 
                 213261_at 
                 1.225 
               
               
                   
                 LIMS1 
                 212687_at 
                 0.822 
               
               
                   
                 LOC126917 
                 225615_at 
                 0.819 
               
               
                   
                 LOC137886 
                 212934_at 
                 0.886 
               
               
                   
                 LOC145757 
                 1558649_at 
                 2.779 
               
               
                   
                 LOC145786 
                 229178_at 
                 1.907 
               
               
                   
                 LOC146325 
                 1553826_a_at 
                 3.943 
               
               
                   
                 LOC203547 
                 225556_at 
                 0.802 
               
               
                   
                 LOC219731 
                 1557208_at 
                 0.419 
               
               
                   
                 LOC254128 
                 1557059_at 
                 2.164 
               
               
                   
                 LOC283888 
                 1559443_s_at 
                 2.56 
               
               
                   
                 LOC285147 
                 236166_at 
                 2.377 
               
               
                   
                 LOC338799 
                 226369_at 
                 1.137 
               
               
                   
                 LOC388135 
                 230475_at 
                 1.979 
               
               
                   
                 LOC388969 
                 232145_at 
                 1.555 
               
               
                   
                 LOC389203 
                 225014_at 
                 0.79 
               
               
                   
                 LOC641298 
                 208118_x_at 
                 1.419 
               
               
                   
                 LOC645166 
                 228158_at 
                 0.823 
               
               
                   
                 LOC645513 
                 239556_at 
                 2.24 
               
               
                   
                 LOC729397 
                 236899_at 
                 2.231 
               
               
                   
                 LRCH3 
                 229387_at 
                 1.793 
               
               
                   
                 LRRFIP1 
                 239379_at 
                 1.796 
               
               
                   
                 MAEA 
                 207922_s_at 
                 0.765 
               
               
                   
                 MALAT1 
                 224568_x_at 
                 1.699 
               
               
                   
                 MALAT1 
                 223940_x_at 
                 1.659 
               
               
                   
                 MAP1LC3B 
                 208785_s_at 
                 0.808 
               
               
                   
                 MAP2K4 
                 203266_s_at 
                 0.881 
               
               
                   
                 MAP3K15 
                 200979_at 
                 0.741 
               
               
                   
                 6-Mar 
                 201737_s_at 
                 1.219 
               
               
                   
                 MBNL1 
                 201152_s_at 
                 0.867 
               
               
                   
                 MDM4 
                 235589_s_at 
                 1.629 
               
               
                   
                 MECR 
                 218664_at 
                 0.832 
               
               
                   
                 MED19 
                 226300_at 
                 0.782 
               
               
                   
                 MEF2C 
                 236395_at 
                 2.104 
               
               
                   
                 MET 
                 213816_s_at 
                 1.283 
               
               
                   
                 MIA3 
                 1569057_s_at 
                 0.759 
               
               
                   
                 MLL 
                 212079_s_at 
                 1.599 
               
               
                   
                 MOBKL1B 
                 214812_s_at 
                 0.762 
               
               
                   
                 MRPL42 
                 217919_s_at 
                 0.866 
               
               
                   
                 (includes EG:28977) 
               
               
                   
                 MRPL51 
                 224334_s_at 
                 0.846 
               
               
                   
                 MTERFD3 
                 225341_at 
                 1.422 
               
               
                   
                 MTUS1 
                 239576_at 
                 1.975 
               
               
                   
                 MYO10 
                 243159_x_at 
                 2.528 
               
               
                   
                 MYO10 
                 244350_at 
                 1.677 
               
               
                   
                 N4BP2L1 
                 213375_s_at 
                 2.01 
               
               
                   
                 N4BP2L2 
                 235547_at 
                 1.631 
               
               
                   
                 N4BP2L2 
                 242576_x_at 
                 2.349 
               
               
                   
                 NAALAD2 
                 1554506_x_at 
                 0.464 
               
               
                   
                 NANP 
                 228073_at 
                 0.817 
               
               
                   
                 NAPA 
                 239362_at 
                 1.624 
               
               
                   
                 NAPE-PLD 
                 242635_s_at 
                 1.216 
               
               
                   
                 NARG1 
                 1556381_at 
                 2.827 
               
               
                   
                 NAT8B 
                 206964_at 
                 2.513 
               
               
                   
                 NBPF16 
                 201104_x_at 
                 1.411 
               
               
                   
                 NBR1 
                 1568856_at 
                 1.957 
               
               
                   
                 NCKAP1L 
                 209734_at 
                 2.071 
               
               
                   
                 NDFIP1 
                 217800_s_at 
                 0.815 
               
               
                   
                 NDUFAF2 
                 228355_s_at 
                 0.722 
               
               
                   
                 NDUFB6 
                 203613_s_at 
                 0.712 
               
               
                   
                 NEK1 
                 213328_at 
                 1.381 
               
               
                   
                 NFATC2IP 
                 217527_s_at 
                 1.272 
               
               
                   
                 NPAS2 
                 1557690_x_at 
                 1.76 
               
               
                   
                 NPTN 
                 228723_at 
                 2.086 
               
               
                   
                 NRP2 
                 210841_s_at 
                 1.106 
               
               
                   
                 NUCB2 
                 203675_at 
                 0.812 
               
               
                   
                 NUDT4 
                 212183_at 
                 0.685 
               
               
                   
                 NUPL1 
                 241425_at 
                 2.179 
               
               
                   
                 OCIAD1 
                 235537_at 
                 1.794 
               
               
                   
                 ORMDL1 
                 223187_s_at 
                 1.171 
               
               
                   
                 OSBPL5 
                 233734_s_at 
                 1.261 
               
               
                   
                 OSGEP 
                 242930_at 
                 1.541 
               
               
                   
                 PABPN1 
                 213046_at 
                 2.228 
               
               
                   
                 PAK1 
                 226507_at 
                 0.869 
               
               
                   
                 PAPD4 
                 222282_at 
                 3.39 
               
               
                   
                 PDE4B 
                 215671_at 
                 3.457 
               
               
                   
                 PDHB 
                 211023_at 
                 0.827 
               
               
                   
                 PDHB 
                 208911_s_at 
                 0.807 
               
               
                   
                 PDK1 
                 239798_at 
                 1.654 
               
               
                   
                 PDLIM5 
                 212412_at 
                 0.752 
               
               
                   
                 PDSS1 
                 236298_at 
                 1.64 
               
               
                   
                 PDXDC1 
                 1560014_s_at 
                 2.105 
               
               
                   
                 PGRMC2 
                 213227_at 
                 0.686 
               
               
                   
                 PHC1 
                 218338_at 
                 1.123 
               
               
                   
                 PHF20L1 
                 219606_at 
                 2.3 
               
               
                   
                 PIGY 
                 224660_at 
                 0.793 
               
               
                   
                 (includes EG:84992) 
               
               
                   
                 PIP5K3 
                 1557719_at 
                 2.227 
               
               
                   
                 PITPNA 
                 201190_s_at 
                 0.863 
               
               
                   
                 PMP22 
                 210139_s_at 
                 0.865 
               
               
                   
                 PMS2L3 
                 214473_x_at 
                 1.159 
               
               
                   
                 POFUT2 
                 207448_at 
                 1.759 
               
               
                   
                 POLR2J2 
                 1552622_s_at 
                 1.828 
               
               
                   
                 POLR2J2 
                 1552621_at 
                 1.652 
               
               
                   
                 POP4 
                 202868_s_at 
                 0.847 
               
               
                   
                 PPP1R3D 
                 204554_at 
                 0.805 
               
               
                   
                 PPP1R7 
                 201213_at 
                 0.698 
               
               
                   
                 PPP3CA 
                 202457_s_at 
                 0.867 
               
               
                   
                 PRO1073 
                 228582_x_at 
                 1.607 
               
               
                   
                 PRPF38B 
                 230270_at 
                 1.888 
               
               
                   
                 PSEN1 
                 242875_at 
                 1.851 
               
               
                   
                 PSMA2 
                 201316_at 
                 0.839 
               
               
                   
                 PSMA3 
                 201532_at 
                 0.798 
               
               
                   
                 PTK2 
                 234211_at 
                 2.539 
               
               
                   
                 PTPMT1 
                 229535_at 
                 0.769 
               
               
                   
                 RAB11FIP3 
                 228613_at 
                 2.546 
               
               
                   
                 RAB11FIP3 
                 216043_x_at 
                 0.551 
               
               
                   
                 RAB14 
                 200927_s_at 
                 0.772 
               
               
                   
                 RAB1A 
                 213440_at 
                 0.81 
               
               
                   
                 RAD54L 
                 204558_at 
                 1.483 
               
               
                   
                 RADIL 
                 223693_s_at 
                 2.126 
               
               
                   
                 RBM25 
                 1557081_at 
                 1.57 
               
               
                   
                 RBM26 
                 229433_at 
                 1.43 
               
               
                   
                 RBM4 
                 213718_at 
                 1.53 
               
               
                   
                 RBM5 
                 209936_at 
                 2.249 
               
               
                   
                 RFT1 
                 240281_at 
                 1.426 
               
               
                   
                 RHOA 
                 240337_at 
                 2.143 
               
               
                   
                 RHOBTB2 
                 1556645_s_at 
                 1.538 
               
               
                   
                 RLBP1L1 
                 224996_at 
                 0.835 
               
               
                   
                 RNF43 
                 228826_at 
                 1.401 
               
               
                   
                 RP11-139H14.4 
                 1569124_at 
                 11.472 
               
               
                   
                 RPE 
                 221770_at 
                 0.766 
               
               
                   
                 RPE 
                 225039_at 
                 0.787 
               
               
                   
                 RPL7L1 
                 225515_s_at 
                 0.899 
               
               
                   
                 RUNX3 
                 204198_s_at 
                 1.233 
               
               
                   
                 SDAD1 
                 242190_at 
                 3.009 
               
               
                   
                 SDCCAG8 
                 243963_at 
                 2.67 
               
               
                   
                 SEC16B 
                 1552880_at 
                 1.877 
               
               
                   
                 SEPHS1 
                 208940_at 
                 0.875 
               
               
                   
                 11-Sep 
                 201307_at 
                 0.784 
               
               
                   
                 SF1 
                 210172_at 
                 2.452 
               
               
                   
                 SF3B1 
                 201070_x_at 
                 1.35 
               
               
                   
                 SF3B1 
                 214305_s_at 
                 1.359 
               
               
                   
                 SFRS15 
                 222311_s_at 
                 1.818 
               
               
                   
                 SFRS15 
                 243759_at 
                 2.028 
               
               
                   
                 SGCA 
                 1562729_at 
                 2.395 
               
               
                   
                 SGOL2 
                 235425_at 
                 1.591 
               
               
                   
                 SH2B3 
                 203320_at 
                 0.806 
               
               
                   
                 SKP1 
                 200718_s_at 
                 0.898 
               
               
                   
                 SLC16A1 
                 202235_at 
                 0.83 
               
               
                   
                 SLC20A1 
                 230494_at 
                 1.884 
               
               
                   
                 SLC2A11 
                 232167_at 
                 1.529 
               
               
                   
                 SLC2A8 
                 239426_at 
                 2.012 
               
               
                   
                 SLC30A9 
                 237051_at 
                 2.063 
               
               
                   
                 SMA4 
                 238446_at 
                 2.035 
               
               
                   
                 SMC6 
                 218781_at 
                 1.203 
               
               
                   
                 SMYD2 
                 212922_s_at 
                 0.867 
               
               
                   
                 SNORA28 
                 241843_at 
                 1.628 
               
               
                   
                 SNRPA1 
                 242146_at 
                 3.54 
               
               
                   
                 SON 
                 201085_s_at 
                 1.144 
               
               
                   
                 SPOPL 
                 225659_at 
                 0.828 
               
               
                   
                 SQLE 
                 213577_at 
                 1.502 
               
               
                   
                 SRP72 
                 208801_at 
                 0.751 
               
               
                   
                 SRP72 
                 208803_s_at 
                 0.766 
               
               
                   
                 SRPRB 
                 218140_x_at 
                 0.767 
               
               
                   
                 STK36 
                 234005_x_at 
                 1.335 
               
               
                   
                 STK36 
                 231806_s_at 
                 1.362 
               
               
                   
                 STRAP 
                 1558002_at 
                 2.189 
               
               
                   
                 STX11 
                 235670_at 
                 0.778 
               
               
                   
                 STX8 
                 204690_at 
                 0.819 
               
               
                   
                 SUPT7L 
                 201838_s_at 
                 0.865 
               
               
                   
                 SVIL 
                 215279_at 
                 2.228 
               
               
                   
                 SYNE2 
                 202761_s_at 
                 1.356 
               
               
                   
                 TAF15 
                 227891_s_at 
                 1.971 
               
               
                   
                 TAF1B 
                 239046_at 
                 1.468 
               
               
                   
                 TAOK3 
                 220761_s_at 
                 1.195 
               
               
                   
                 TBC1D5 
                 201814_at 
                 0.782 
               
               
                   
                 TBC1D8 
                 221592_at 
                 1.246 
               
               
                   
                 TBC1D8 
                 204526_s_at 
                 1.373 
               
               
                   
                 TBXA2R 
                 207554_x_at 
                 0.877 
               
               
                   
                 TBXA2R 
                 336_at 
                 0.73 
               
               
                   
                 TCAG7.907 
                 238678_at 
                 1.546 
               
               
                   
                 TCOF1 
                 202385_s_at 
                 1.169 
               
               
                   
                 (includes EG:6949) 
               
               
                   
                 TFB1M 
                 228075_x_at 
                 0.87 
               
               
                   
                 THRAP3 
                 217847_s_at 
                 1.464 
               
               
                   
                 TIMM23 
                 218119_at 
                 0.723 
               
               
                   
                 TM6SF1 
                 1558102_at 
                 0.704 
               
               
                   
                 TMEM126B 
                 221622_s_at 
                 0.843 
               
               
                   
                 TMEM165 
                 1560622_at 
                 1.756 
               
               
                   
                 TMEM30A 
                 232591_s_at 
                 0.771 
               
               
                   
                 TNFAIP1 
                 201207_at 
                 0.88 
               
               
                   
                 TNPO1 
                 1556116_s_at 
                 1.739 
               
               
                   
                 TNRC6A 
                 234734_s_at 
                 1.268 
               
               
                   
                 TOX4 
                 201685_s_at 
                 0.73 
               
               
                   
                 TPM4 
                 235094_at 
                 2.079 
               
               
                   
                 TRAPPC2 
                 219351_at 
                 0.821 
               
               
                   
                 TRAPPC2L 
                 218354_at 
                 0.837 
               
               
                   
                 TRIM33 
                 239716_at 
                 2.496 
               
               
                   
                 TRIM46 
                 238147_at 
                 1.96 
               
               
                   
                 TRIO 
                 240773_at 
                 2.607 
               
               
                   
                 TRNT1 
                 243236_at 
                 2.295 
               
               
                   
                 TRPV1 
                 1556229_at 
                 2.636 
               
               
                   
                 TSPAN31 
                 203227_s_at 
                 0.744 
               
               
                   
                 TTC26 
                 233999_s_at 
                 1.184 
               
               
                   
                 TTC3 
                 208664_s_at 
                 1.396 
               
               
                   
                 TTC9C 
                 1569189_at 
                 1.55 
               
               
                   
                 TTLL4 
                 1557611_at 
                 2.092 
               
               
                   
                 TXNDC12 
                 223017_at 
                 0.849 
               
               
                   
                 TXNL1 
                 243664_at 
                 1.98 
               
               
                   
                 UBE2E3 
                 210024_s_at 
                 0.758 
               
               
                   
                 UBE3C 
                 1560739_a_at 
                 0.815 
               
               
                   
                 UBXD7 
                 212840_at 
                 0.754 
               
               
                   
                 UGT1A6 
                 206094_x_at 
                 3.86 
               
               
                   
                 UNK 
                 1562434_at 
                 1.637 
               
               
                   
                 UQCC 
                 229672_at 
                 1.451 
               
               
                   
                 USP36 
                 224979_s_at 
                 1.393 
               
               
                   
                 USP8 
                 229501_s_at 
                 0.808 
               
               
                   
                 VPS37B 
                 236889_at 
                 2.85 
               
               
                   
                 VTI1B 
                 209452_s_at 
                 0.821 
               
               
                   
                 WDR41 
                 218055_s_at 
                 0.789 
               
               
                   
                 WDR68 
                 233782_at 
                 1.924 
               
               
                   
                 WFS1 
                 1555270_a_at 
                 1.315 
               
               
                   
                 WIPF2 
                 216006_at 
                 2.916 
               
               
                   
                 WTAP 
                 1560274_at 
                 1.747 
               
               
                   
                 XRCC5 
                 232633_at 
                 2.106 
               
               
                   
                 YY1 
                 224711_at 
                 0.821 
               
               
                   
                 ZFHX3 
                 215828_at 
                 1.737 
               
               
                   
                 ZFR 
                 238970_at 
                 2.655 
               
               
                   
                 ZFX 
                 207920_x_at 
                 1.625 
               
               
                   
                 ZMYND8 
                 209049_s_at 
                 1.102 
               
               
                   
                 ZNF154 
                 242170_at 
                 2.667 
               
               
                   
                 ZNF224 
                 216983_s_at 
                 2.986 
               
               
                   
                 ZNF226 
                 219603_s_at 
                 1.332 
               
               
                   
                 ZNF251 
                 226754_at 
                 1.313 
               
               
                   
                 ZNF292 
                 236435_at 
                 3.201 
               
               
                   
                 ZNF326 
                 241720_at 
                 1.418 
               
               
                   
                 ZNF337 
                 1565614_at 
                 2.096 
               
               
                   
                 ZNF536 
                 233890_at 
                 3.303 
               
               
                   
                 ZNF567 
                 242429_at 
                 2.103 
               
               
                   
                 ZNF618 
                 226590_at 
                 0.75 
               
               
                   
                 ZNF668 
                 219047_s_at 
                 0.691 
               
               
                   
                 ZNF800 
                 227101_at 
                 1.484 
               
               
                   
                 ZUFSP 
                 228330_at 
                 1.205 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Differentially expressed genes between ABCB5 +  and ABCB5 −   
               
               
                 cells as detected by RT-PCR. PCR Array Catalog #: PAHS-024 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 ABCB5+/ 
               
               
                   
                   
                   
                   
                   
                   
                 ABCB5− 
               
               
                   
                   
                   
                   
                   
                   
                 Fold 
               
               
                 Position 
                 Unigene 
                 Refseq 
                 Symbol 
                 Description 
                 Gname 
                 change 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 A01 
                 Hs.525622 
                 NM_005163 
                 AKT1 
                 V-akt murine thymoma 
                 AKT/PKB 
                 1.2687 
               
               
                   
                   
                   
                   
                 viral oncogene homolog 1 
               
               
                 A02 
                 Hs.369675 
                 NM_001146 
                 ANGPT1 
                 Angiopoietin 1 
                 AGP1/AGPT 
                 1.2953 
               
               
                 A03 
                 Hs.583870 
                 NM_001147 
                 ANGPT2 
                 Angiopoietin 2 
                 AGPT2/ANG2 
                 2.7007 
               
               
                 A04 
                 Hs.209153 
                 NM_014495 
                 ANGPTL3 
                 Angiopoietin-like 3 
                 ANGPT5 
                 3.0596 
               
               
                 A05 
                 Hs.9613 
                 NM_001039667 
                 ANGPTL4 
                 Angiopoietin-like 4 
                 ANGPTL2/ARP4 
                 1.6974 
               
               
                 A06 
                 Hs.1239 
                 NM_001150 
                 ANPEP 
                 Alanyl (membrane) 
                 APN/CD13 
                 1.3597 
               
               
                   
                   
                   
                   
                 aminopeptidase 
               
               
                   
                   
                   
                   
                 (aminopeptidase N, 
               
               
                   
                   
                   
                   
                 aminopeptidase M, 
               
               
                   
                   
                   
                   
                 microsomal 
               
               
                   
                   
                   
                   
                 aminopeptidase, CD13, 
               
               
                   
                   
                   
                   
                 p150) 
               
               
                 A07 
                 Hs.194654 
                 NM_001702 
                 BAI1 
                 Brain-specific 
                 FLJ41988 
                 3.0596 
               
               
                   
                   
                   
                   
                 angiogenesis inhibitor 1 
               
               
                 A08 
                 Hs.54460 
                 NM_002986 
                 CCL11 
                 Chemokine (C-C motif) 
                 SCYA11 
                 1.8834 
               
               
                   
                   
                   
                   
                 ligand 11 
               
               
                 A09 
                 Hs.303649 
                 NM_002982 
                 CCL2 
                 Chemokine (C-C motif) 
                 GDCF- 
                 2.0326 
               
               
                   
                   
                   
                   
                 ligand 2 
                 2/GDCF-2HC11 
               
               
                 A10 
                 Hs.76206 
                 NM_001795 
                 CDH5 
                 Cadherin 5, type 2, VE- 
                 7B4/CD144 
                 3.0596 
               
               
                   
                   
                   
                   
                 cadherin (vascular 
               
               
                   
                   
                   
                   
                 epithelium) 
               
               
                 A11 
                 Hs.517356 
                 NM_030582 
                 COL18A1 
                 Collagen, type XVIII, 
                 KNO 
                 1.9634 
               
               
                   
                   
                   
                   
                 alpha 1 
               
               
                 A12 
                 Hs.570065 
                 NM_000091 
                 COL4A3 
                 Collagen, type IV, alpha 
                 TUMSTATIN 
                 2.1634 
               
               
                   
                   
                   
                   
                 3 (Goodpasture antigen) 
               
               
                 B01 
                 Hs.789 
                 NM_001511 
                 CXCL1 
                 Chemokine (C—X—C 
                 FSP/GRO1 
                 1.2086 
               
               
                   
                   
                   
                   
                 motif) ligand 1 
               
               
                   
                   
                   
                   
                 (melanoma growth 
               
               
                   
                   
                   
                   
                 stimulating activity, 
               
               
                   
                   
                   
                   
                 alpha) 
               
               
                 B02 
                 Hs.632586 
                 NM_001565 
                 CXCL10 
                 Chemokine (C—X—C 
                 C7/IFI10 
                 −2.1987 
               
               
                   
                   
                   
                   
                 motif) ligand 10 
               
               
                 B03 
                 Hs.89690 
                 NM_002090 
                 CXCL3 
                 Chemokine (C—X—C 
                 CINC- 
                 2.061 
               
               
                   
                   
                   
                   
                 motif) ligand 3 
                 2b/GRO3 
               
               
                 B04 
                 Hs.89714 
                 NM_002994 
                 CXCL5 
                 Chemokine (C—X—C 
                 ENA- 
                 1.8834 
               
               
                   
                   
                   
                   
                 motif) ligand 5 
                 78/SCYB5 
               
               
                 B05 
                 Hs.164021 
                 NM_002993 
                 CXCL6 
                 Chemokine (C—X—C 
                 CKA-3/GCP-2 
                 2.1936 
               
               
                   
                   
                   
                   
                 motif) ligand 6 
               
               
                   
                   
                   
                   
                 (granulocyte chemotactic 
               
               
                   
                   
                   
                   
                 protein 2) 
               
               
                 B06 
                 Hs.77367 
                 NM_002416 
                 CXCL9 
                 Chemokine (C—X—C 
                 CMK/Humig 
                 −1.1225 
               
               
                   
                   
                   
                   
                 motif) ligand 9 
               
               
                 B07 
                 Hs.592212 
                 NM_001953 
                 TYMP 
                 Thymidine 
                 ECGF1/MNGIE 
                 1.5837 
               
               
                   
                   
                   
                   
                 phosphorylase 
               
               
                 B08 
                 Hs.154210 
                 NM_001400 
                 EDG1 
                 Endothelial 
                 CHEDG1/D1S3362 
                 1.0377 
               
               
                   
                   
                   
                   
                 differentiation, 
               
               
                   
                   
                   
                   
                 sphingolipid G-protein- 
               
               
                   
                   
                   
                   
                 coupled receptor, 1 
               
               
                 B09 
                 Hs.516664 
                 NM_182685 
                 EFNA1 
                 Ephrin-A1 
                 B61/ECKLG 
                 1.4573 
               
               
                 B10 
                 Hs.516656 
                 NM_004952 
                 EFNA3 
                 Ephrin-A3 
                 EFL2/EPLG3 
                 1.3692 
               
               
                 B11 
                 Hs.149239 
                 NM_004093 
                 EFNB2 
                 Ephrin-B2 
                 EPLG5/HTKL 
                 1.1355 
               
               
                 B12 
                 Hs.419815 
                 NM_001963 
                 EGF 
                 Epidermal growth factor 
                 HOMG4/URG 
                 187.8365 
               
               
                   
                   
                   
                   
                 (beta-urogastrone) 
               
               
                 C01 
                 Hs.76753 
                 NM_000118 
                 ENG 
                 Endoglin (Osler-Rendu- 
                 CD105/END 
                 1.1514 
               
               
                   
                   
                   
                   
                 Weber syndrome 1) 
               
               
                 C02 
                 Hs.437008 
                 NM_004444 
                 EPHB4 
                 EPH receptor B4 
                 HTK/MYK1 
                 1.3692 
               
               
                 C03 
                 Hs.115263 
                 NM_001432 
                 EREG 
                 Epiregulin 
                 ER 
                 1.8834 
               
               
                 C04 
                 Hs.483635 
                 NM_000800 
                 FGF1 
                 Fibroblast growth factor 
                 AFGF/ECGF 
                 1.5511 
               
               
                   
                   
                   
                   
                 1 (acidic) 
               
               
                 C05 
                 Hs.284244 
                 NM_002006 
                 FGF2 
                 Fibroblast growth factor 
                 BFGF/FGFB 
                 1.1355 
               
               
                   
                   
                   
                   
                 2 (basic) 
               
               
                 C06 
                 Hs.1420 
                 NM_000142 
                 FGFR3 
                 Fibroblast growth factor 
                 ACH/CD333 
                 1.7092 
               
               
                   
                   
                   
                   
                 receptor 3 
               
               
                   
                   
                   
                   
                 (achondroplasia, 
               
               
                   
                   
                   
                   
                 thanatophoric dwarfism) 
               
               
                 C07 
                 Hs.11392 
                 NM_004469 
                 FIGF 
                 C-fos induced growth 
                 VEGF- 
                 3.5884 
               
               
                   
                   
                   
                   
                 factor (vascular 
                 D/VEGFD 
               
               
                   
                   
                   
                   
                 endothelial growth factor 
               
               
                   
                   
                   
                   
                 D) 
               
               
                 C08 
                 Hs.654360 
                 NM_002019 
                 FLT1 
                 Fms-related tyrosine 
                 FLT/VEGFR1 
                 2.4172 
               
               
                   
                   
                   
                   
                 kinase 1 (vascular 
               
               
                   
                   
                   
                   
                 endothelial growth 
               
               
                   
                   
                   
                   
                 factor/vascular 
               
               
                   
                   
                   
                   
                 permeability factor 
               
               
                   
                   
                   
                   
                 receptor) 
               
               
                 C09 
                 Hs.388245 
                 NM_021973 
                 HAND2 
                 Heart and neural crest 
                 DHAND2/Hed 
                 2.0186 
               
               
                   
                   
                   
                   
                 derivatives expressed 2 
               
               
                 C10 
                 Hs.396530 
                 NM_000601 
                 HGF 
                 Hepatocyte growth factor 
                 F- 
                 4.542 
               
               
                   
                   
                   
                   
                 (hepapoietin A; scatter 
                 TCF/HGFB 
               
               
                   
                   
                   
                   
                 factor) 
               
               
                 C11 
                 Hs.654600 
                 NM_001530 
                 HIF1A 
                 Hypoxia-inducible factor 
                 HIF- 
                 −1.0918 
               
               
                   
                   
                   
                   
                 1, alpha subunit (basic 
                 1alpha/HIF1 
               
               
                   
                   
                   
                   
                 helix-loop-helix 
               
               
                   
                   
                   
                   
                 transcription factor) 
               
               
                 C12 
                 Hs.44227 
                 NM_006665 
                 HPSE 
                 Heparanase 
                 HPA/HPR1 
                 286.6871 
               
               
                 D01 
                 Hs.504609 
                 NM_002165 
                 ID1 
                 Inhibitor of DNA binding 
                 ID 
                 −1.0329 
               
               
                   
                   
                   
                   
                 1, dominant negative 
               
               
                   
                   
                   
                   
                 helix-loop-helix protein 
               
               
                 D02 
                 Hs.76884 
                 NM_002167 
                 ID3 
                 Inhibitor of DNA binding 
                 HEIR-1 
                 −1.3535 
               
               
                   
                   
                   
                   
                 3, dominant negative 
               
               
                   
                   
                   
                   
                 helix-loop-helix protein 
               
               
                 D03 
                 Hs.37026 
                 NM_024013 
                 IFNA1 
                 Interferon, alpha 1 
                 IFL/IFN 
                 1.8834 
               
               
                 D04 
                 Hs.93177 
                 NM_002176 
                 IFNB1 
                 Interferon, beta 1, 
                 IFB/IFF 
                 1.8834 
               
               
                   
                   
                   
                   
                 fibroblast 
               
               
                 D05 
                 Hs.856 
                 NM_000619 
                 IFNG 
                 Interferon, gamma 
                 IFG/IFI 
                 1.8834 
               
               
                 D06 
                 Hs.160562 
                 NM_000618 
                 IGF1 
                 Insulin-like growth factor 
                 IGFI 
                 4.7022 
               
               
                   
                   
                   
                   
                 1 (somatomedin C) 
               
               
                 D07 
                 Hs.126256 
                 NM_000576 
                 IL1B 
                 Interleukin 1, beta 
                 IL-1/IL1- 
                 2.0898 
               
               
                   
                   
                   
                   
                   
                 BETA 
               
               
                 D08 
                 Hs.654458 
                 NM_000600 
                 IL6 
                 Interleukin 6 (interferon, 
                 BSF2/HGF 
                 1.7331 
               
               
                   
                   
                   
                   
                 beta 2) 
               
               
                 D09 
                 Hs.624 
                 NM_000584 
                 IL8 
                 Interleukin 8 
                 3- 
                 1.1674 
               
               
                   
                   
                   
                   
                   
                 10C/AMCF-I 
               
               
                 D10 
                 Hs.436873 
                 NM_002210 
                 ITGAV 
                 Integrin, alpha V 
                 CD51/DKFZp686A08142 
                 1.217 
               
               
                   
                   
                   
                   
                 (vitronectin receptor, 
               
               
                   
                   
                   
                   
                 alpha polypeptide, 
               
               
                   
                   
                   
                   
                 antigen CD51) 
               
               
                 D11 
                 Hs.218040 
                 NM_000212 
                 ITGB3 
                 Integrin, beta 3 (platelet 
                 CD61/GP3A 
                 −1.0619 
               
               
                   
                   
                   
                   
                 glycoprotein IIIa, antigen 
               
               
                   
                   
                   
                   
                 CD61) 
               
               
                 D12 
                 Hs.224012 
                 NM_000214 
                 JAG1 
                 Jagged 1 (Alagille 
                 AGS/AHD 
                 1566.5046 
               
               
                   
                   
                   
                   
                 syndrome) 
               
               
                 E01 
                 Hs.479756 
                 NM_002253 
                 KDR 
                 Kinase insert domain 
                 CD309/FLK1 
                 1.234 
               
               
                   
                   
                   
                   
                 receptor (a type III 
               
               
                   
                   
                   
                   
                 receptor tyrosine kinase) 
               
               
                 E02 
                 Hs.473256 
                 NM_005560 
                 LAMA5 
                 Laminin, alpha 5 
                 KIAA1907 
                 3.8727 
               
               
                 E03 
                 Hs.421391 
                 NM_007015 
                 LECT1 
                 Leukocyte cell derived 
                 BRICD3/CHM-I 
                 1.8834 
               
               
                   
                   
                   
                   
                 chemotaxin 1 
               
               
                 E04 
                 Hs.194236 
                 NM_000230 
                 LEP 
                 Leptin 
                 OB/OBS 
                 2.1485 
               
               
                 E05 
                 Hs.82045 
                 NM_002391 
                 MDK 
                 Midkine (neurite growth- 
                 MK/NEGF2 
                 1.4573 
               
               
                   
                   
                   
                   
                 promoting factor 2) 
               
               
                 E06 
                 Hs.513617 
                 NM_004530 
                 MMP2 
                 Matrix metallopeptidase 
                 CLG4/CLG4A 
                 1.674 
               
               
                   
                   
                   
                   
                 2 (gelatinase A, 72 kDa 
               
               
                   
                   
                   
                   
                 gelatinase, 72 kDa type 
               
               
                   
                   
                   
                   
                 IV collagenase) 
               
               
                 E07 
                 Hs.297413 
                 NM_004994 
                 MMP9 
                 Matrix metallopeptidase 
                 CLG4B/GELB 
                 1.9097 
               
               
                   
                   
                   
                   
                 9 (gelatinase B, 92 kDa 
               
               
                   
                   
                   
                   
                 gelatinase, 92 kDa type 
               
               
                   
                   
                   
                   
                 IV collagenase) 
               
               
                 E08 
                 Hs.436100 
                 NM_004557 
                 NOTCH4 
                 Notch homolog 4 
                 INT3/NOTCH3 
                 1.2002 
               
               
                   
                   
                   
                   
                 ( Drosophila ) 
               
               
                 E09 
                 Hs.131704 
                 NM_003873 
                 NRP1 
                 Neuropilin 1 
                 CD304/DKFZp686A03134 
                 1.1755 
               
               
                 E10 
                 Hs.471200 
                 NM_003872 
                 NRP2 
                 Neuropilin 2 
                 NP2/NPN2 
                 1.4373 
               
               
                 E11 
                 Hs.707991 
                 NM_002607 
                 PDGFA 
                 Platelet-derived growth 
                 PDGF- 
                 1.2002 
               
               
                   
                   
                   
                   
                 factor alpha polypeptide 
                 A/PDGF1 
               
               
                 E12 
                 Hs.514412 
                 NM_000442 
                 PECAM1 
                 Platelet/endothelial cell 
                 CD31/PECAM-1 
                 11.9037 
               
               
                   
                   
                   
                   
                 adhesion molecule 
               
               
                   
                   
                   
                   
                 (CD31 antigen) 
               
               
                 F01 
                 Hs.81564 
                 NM_002619 
                 PF4 
                 Platelet factor 4 
                 CXCL4/SCYB4 
                 2.9966 
               
               
                   
                   
                   
                   
                 (chemokine (C—X—C 
               
               
                   
                   
                   
                   
                 motif) ligand 4) 
               
               
                 F02 
                 Hs.252820 
                 NM_002632 
                 PGF 
                 Placental growth factor, 
                 D12S1900/PGFL 
                 −1.1865 
               
               
                   
                   
                   
                   
                 vascular endothelial 
               
               
                   
                   
                   
                   
                 growth factor-related 
               
               
                   
                   
                   
                   
                 protein 
               
               
                 F03 
                 Hs.77274 
                 NM_002658 
                 PLAU 
                 Plasminogen activator, 
                 ATF/UPA 
                 1.6396 
               
               
                   
                   
                   
                   
                 urokinase 
               
               
                 F04 
                 Hs.143436 
                 NM_000301 
                 PLG 
                 Plasminogen 
                 DKFZp779M0222 
                 1.8834 
               
               
                 F05 
                 Hs.125036 
                 NM_020405 
                 PLXDC1 
                 Plexin domain containing 1 
                 DKFZp686F0937/TEM3 
                 3.4184 
               
               
                 F06 
                 Hs.528665 
                 NM_021935 
                 PROK2 
                 Prokineticin 2 
                 BV8/KAL4 
                 1.8446 
               
               
                 F07 
                 Hs.201978 
                 NM_000962 
                 PTGS1 
                 Prostaglandin- 
                 COX1/COX3 
                 1.2086 
               
               
                   
                   
                   
                   
                 endoperoxide synthase 1 
               
               
                   
                   
                   
                   
                 (prostaglandin G/H 
               
               
                   
                   
                   
                   
                 synthase and 
               
               
                   
                   
                   
                   
                 cyclooxygenase) 
               
               
                 F08 
                 Hs.532768 
                 NM_002615 
                 SERPINF1 
                 Serpin peptidase 
                 EPC-1/PEDF 
                 1.1121 
               
               
                   
                   
                   
                   
                 inhibitor, clade F (alpha- 
               
               
                   
                   
                   
                   
                 2 antiplasmin, pigment 
               
               
                   
                   
                   
                   
                 epithelium derived 
               
               
                   
                   
                   
                   
                 factor), member 1 
               
               
                 F09 
                 Hs.68061 
                 NM_021972 
                 SPHK1 
                 Sphingosine kinase 1 
                 SPHK 
                 1.192 
               
               
                 F10 
                 Hs.301989 
                 NM_015136 
                 STAB1 
                 Stabilin 1 
                 CLEVER- 
                 4.357 
               
               
                   
                   
                   
                   
                   
                 1/FEEL-1 
               
               
                 F11 
                 Hs.89640 
                 NM_000459 
                 TEK 
                 TEK tyrosine kinase, 
                 CD202B/TIE-2 
                 −1.2805 
               
               
                   
                   
                   
                   
                 endothelial (venous 
               
               
                   
                   
                   
                   
                 malformations, multiple 
               
               
                   
                   
                   
                   
                 cutaneous and mucosal) 
               
               
                 F12 
                 Hs.170009 
                 NM_003236 
                 TGFA 
                 Transforming growth 
                 TFGA 
                 3549.3357 
               
               
                   
                   
                   
                   
                 factor, alpha 
               
               
                 G01 
                 Hs.645227 
                 NM_000660 
                 TGFB1 
                 Transforming growth 
                 CED/DPD1 
                 1.1837 
               
               
                   
                   
                   
                   
                 factor, beta 1 
               
               
                 G02 
                 Hs.133379 
                 NM_003238 
                 TGFB2 
                 Transforming growth 
                 TGF-beta2 
                 1.3787 
               
               
                   
                   
                   
                   
                 factor, beta 2 
               
               
                 G03 
                 Hs.494622 
                 NM_004612 
                 TGFBR1 
                 Transforming growth 
                 AAT5/ACVRLK4 
                 1.7695 
               
               
                   
                   
                   
                   
                 factor, beta receptor I 
               
               
                   
                   
                   
                   
                 (activin A receptor type 
               
               
                   
                   
                   
                   
                 II-like kinase, 53 kDa) 
               
               
                 G04 
                 Hs.164226 
                 NM_003246 
                 THBS1 
                 Thrombospondin 1 
                 THBS/TSP 
                 −1.0619 
               
               
                 G05 
                 Hs.371147 
                 NM_003247 
                 THBS2 
                 Thrombospondin 2 
                 TSP2 
                 −1.203 
               
               
                 G06 
                 Hs.522632 
                 NM_003254 
                 TIMP1 
                 TIMP metallopeptidase 
                 CLGI/EPA 
                 −1.1147 
               
               
                   
                   
                   
                   
                 inhibitor 1 
               
               
                 G07 
                 Hs.633514 
                 NM_003255 
                 TIMP2 
                 TIMP metallopeptidase 
                 CSC-21K 
                 1.2864 
               
               
                   
                   
                   
                   
                 inhibitor 2 
               
               
                 G08 
                 Hs.701968 
                 NM_000362 
                 TIMP3 
                 TIMP metallopeptidase 
                 HSMRK222/ 
                 1.8834 
               
               
                   
                   
                   
                   
                 inhibitor 3 (Sorsby 
                 K222 
               
               
                   
                   
                   
                   
                 fundus dystrophy, 
               
               
                   
                   
                   
                   
                 pseudoinflammatory) 
               
               
                 G09 
                 Hs.241570 
                 NM_000594 
                 TNF 
                 Tumor necrosis factor 
                 DIF/TNF- 
                 4.0652 
               
               
                   
                   
                   
                   
                 (TNF superfamily, 
                 alpha 
               
               
                   
                   
                   
                   
                 member 2) 
               
               
                 G10 
                 Hs.525607 
                 NM_006291 
                 TNFAIP2 
                 Tumor necrosis factor, 
                 B94 
                 1.8834 
               
               
                   
                   
                   
                   
                 alpha-induced protein 2 
               
               
                 G11 
                 Hs.73793 
                 NM_003376 
                 VEGFA 
                 Vascular endothelial 
                 VEGF/VEGF-A 
                 2.4509 
               
               
                   
                   
                   
                   
                 growth factor A 
               
               
                 G12 
                 Hs.435215 
                 NM_005429 
                 VEGFC 
                 Vascular endothelial 
                 Flt4-L/VRP 
                 446.7529 
               
               
                   
                   
                   
                   
                 growth factor C 
               
               
                 H01 
                 Hs.534255 
                 NM_004048 
                 B2M 
                 Beta-2-microglobulin 
                 B2M 
                 −1.2983 
               
               
                 H02 
                 Hs.412707 
                 NM_000194 
                 HPRT1 
                 Hypoxanthine 
                 HGPRT/HPRT 
                 −1.2894 
               
               
                   
                   
                   
                   
                 phosphoribosyltransferase 
               
               
                   
                   
                   
                   
                 1 (Lesch-Nyhan 
               
               
                   
                   
                   
                   
                 syndrome) 
               
               
                 H03 
                 Hs.523185 
                 NM_012423 
                 RPL13A 
                 Ribosomal protein L13a 
                 RPL13A 
                 1.1837 
               
               
                 H04 
                 Hs.544577 
                 NM_002046 
                 GAPDH 
                 Glyceraldehyde-3- 
                 G3PD/GAPD 
                 −1.146 
               
               
                   
                   
                   
                   
                 phosphate dehydrogenase 
               
               
                 H05 
                 Hs.520640 
                 NM_001101 
                 ACTB 
                 Actin, beta 
                 PS1TP5BP1 
                 −1.0329 
               
               
                 H06 
                 N/A 
                 SA_00105 
                 HGDC 
                 Human Genomic DNA 
                 HIGX1A 
                 1.8834 
               
               
                   
                   
                   
                   
                 Contamination 
               
               
                 H07 
                 N/A 
                 SA_00104 
                 RTC 
                 Reverse Transcription 
                 RTC 
                 1.7451 
               
               
                   
                   
                   
                   
                 Control 
               
               
                 H08 
                 N/A 
                 SA_00104 
                 RTC 
                 Reverse Transcription 
                 RTC 
                 1.7451 
               
               
                   
                   
                   
                   
                 Control 
               
               
                 H09 
                 N/A 
                 SA_00104 
                 RTC 
                 Reverse Transcription 
                 RTC 
                 1.7695 
               
               
                   
                   
                   
                   
                 Control 
               
               
                 H10 
                 N/A 
                 SA_00103 
                 PPC 
                 Positive PCR Control 
                 PPC 
                 1.8067 
               
               
                 H11 
                 N/A 
                 SA_00103 
                 PPC 
                 Positive PCR Control 
                 PPC 
                 1.7818 
               
               
                 H12 
                 N/A 
                 SA_00103 
                 PPC 
                 Positive PCR Control 
                 PPC 
                 36695.9527 
               
               
                   
               
            
           
         
       
     
     Example 3 
     We therefore tested the hypothesis that MMIC, as defined by the novel marker ABCB5 3 , specifically relate to the phenomenon of vasculogenic mimicry whereby melanoma cells form channels capable of conducting nutrients from peripheral blood and thus serving as surrogates for mature tumour vessels 4 . Because we posited that this phenomenon may be more robust during early stages of tumour formation before cancer angiogenesis fully develops, we evaluated experimentally-induced human-derived melanomas grown as tumour xenografts in the subcutis of immunodeficient mice and in the dermis of human skin xenografted to immunodeficient mice ( FIG. 2 ), the latter a humanized model whereby human melanoma develops in the context of the human stromal microenvironment 13 . While only peripheral tumour vessels expressed the mature endothelial marker, CD31, more interior regions of the melanomas exhibited formation of CD31− negative anastomosing channels with histologic, histochemical (PAS-D and laminin reactivity), and ultrastructural findings consistent with established features of vasculogenic mimicry 4  ( FIG. 2 a - d   ). By electron microscopy, lumen-like spaces in these regions were lined by basement membrane-like material and viable melanoma cells and contained erythrocytes surrounded by finely granular matrix consistent with plasma, suggesting communication with the systemic circulation 4 . By immunohistochemistry and in situ hybridization, channels expressed ABCB5 protein and mRNA, respectively ( FIG. 2 f - h   ), which also correlated in vitro when assayed across a panel of human melanoma cell lines ( FIG. 4 ), and the architecture of ABCB5 +  channels in xenografted tumours was identical to that focally detected in patient-derived melanomas ( FIG. 2 f   , inset). An identical pattern was also observed for CD133 mRNA (not illustrated), an additional marker for tumourigenic melanoma cells 14  and melanoma progression 15 . Anti-ABCB5 mAb systemically administered in vivo localized to channels, further confirming their systemic perfusion as well as the intimate association of ABCB5 +  melanoma cells with channel lumens ( FIG. 2 i   ). Double-labeling demonstrated co-localization of the human endothelial markers CD144 and TIE-1 with ABCB5 +  cells forming channels ( FIG. 2 j,k   ). Tumours initiated by melanoma cell lines expressing the green fluorescence protein (GFP) transgene confirmed the presence of melanoma cells lining channels that co-expressed melanoma-associated GFP and CD144 ( FIG. 2 e   ), as well as human melanoma—but not human xenograft-associated class I major histocompatibility complex (MHC) antigens (not illustrated). These data show that the formation of perfused vessel-like channels in human melanoma is mediated by the ABCB5 +  MMIC subpopulation found to selectively display gene profiles and differentiation capacity consistent with its participation in tumour vasculogenesis. 
     Example 4 
     We next reasoned that if vasculogenic channel formation mediated by ABCB5 +  MMIC was functionally required for their capacity to efficiently initiate and drive melanoma growth, depletion of MMIC to low levels should inhibit the melanoma-associated vasculogenic response. To evaluate tumourigenesis and vasculogenesis in a bioassay most relevant to human primary melanoma, we again utilized a human skin/murine xenograft model whereby melanomas develop in the relevant dermal microenvironment of human skin and express architectural features and evolutionary growth patterns more akin to naturally occurring lesions 13 . Intradermal orthotopic transplantation of 2×10 6  unsegregated A375 cutaneous melanoma cells (ABCB5 positivity: 5.2±5.1%; mean±s.e.m., n=9) ( FIG. 3 a   ) or heterotopic transplantation of 2×10 6  unsegregated uveal melanoma cells previously assayed for vasculogenic differentiation 4,16  (MUM-2B and MUM-2C, ABCB5 positivity: 2.46±0.46% and 3.81±1.04%, respectively; mean±s.e.m., n=3-4) ( FIG. 3 a   ) to human skin resulted in tumour formation three weeks following microinjections in 14 of 14 recipient skin grafts (A375: n=6, MUM-2B: n=4, MUM-2C: n=4 replicates) when assessed histologically in serial sections of each human skin xenograft in its entirety ( FIG. 3 b,c   ). In contrast, intradermal transplantation of equal numbers of ABCB5 + -depleted melanoma cells resulted in histologically-assessed tumour formation in only 6 of 14 recipient skin grafts (P&lt;0.002) ( FIG. 3 b,c   ) and histologically-determined mean tumour volumes (TV) were significantly reduced in recipients of ABCB5 + -depleted vs. unsegregated melanoma inocula (TV=2.8±1.8 mm 3  vs. 10.9±6.9 mm 3 , respectively; mean±s.e.m., P&lt;0.005) ( FIG. 3 d   ). When vasculogenic channel formation within tumours was evaluated using quantitative image analysis technology to assess the pixilated density of laminin immunoreactivity, significantly fewer channels per cross-sectional area were detected in tumours that formed from MMIC-depleted inocula compared to those that originated from unsegregated tumour cell grafts (A375, P&lt;0.0032; MUM-2B, P&lt;0.0005; MUM-2C, P&lt;0.0059) ( FIG. 3 e,f   ). In aggregate, these findings show in relevant xenograft models of early melanoma development the participation of ABCB5 +  MMIC in the genesis of vasculogenic channels, and the interdependency of MMIC-derived channel formation and tumour growth. 
     Discovery of MMIC-driven vasculogenesis identifies selective differentiation plasticity as a novel CSC-specific function through which these tumourigenic cancer subpopulations may provide a specific growth advantage to developing tumours. Our finding of a propensity of MMIC to differentiate selectively into cells capable of serving a defined tissue function required for more efficient tumour growth parallels hallmark characteristics of physiological stem cells, which similarly give rise to cell lineages capable of serving specific roles required for maintenance of tissue homeostasis through defined differentiation programs. Importantly, we find that MMIC-dependent tumourigenesis and vasculogenesis are operative not only in human melanoma to murine skin xenotransplantation models but also upon human melanoma to human skin transplantation. Therefore, our results provide initial evidence that the tumour-sustaining role of human CSC identified in xenotransplantation assays does not merely reflect the limited ability of human tumour cells to adapt to growth in a foreign (mouse) milieu, as has been postulated based on the results of murine tumour transplantation experiments utilizing histocompatible murine hosts 17    
     The now widely-accepted concept of cancer angiogenesis advanced by Folkman in 1971 states that human cancers are critically dependent upon tumour-related blood-vessel growth and development 18 . In addition to classical angiogenesis whereby cancer cells, including CSC 19 , induce in-growth of mature, CD31-positive vessels from surrounding stroma 20 , evidence has been generated that cancer cells may also directly form surrogate vessel-like spaces by the process of vasculogenic mimicry whereby aggressive human melanomas develop patterned networks composed of periodic acid-Schiff (PAS)- and laminin-reactive basement membranes and associated perfusable channels formed by tumour cells that express some but not all endothelium-related genes and proteins 4 . The present study identifies the cells and underlying mechanisms responsible for vasculogenic mimicry, and establishes that in addition to self-renewal, MMIC selectively express vasculogenic genes and form channels consistent with the function of promoting nutrition to rapidly growing tumours. Thus, cancer angiogenesis and MMIC-driven vasculogenesis may represent independent yet potentially interrelated mechanisms whereby aggressive and metabolically-active tumours obtain those nutrients requisite for critical stages of growth and evolution. This may be particularly important during tumour initiation and early phases of tumourigenic growth when hypoxia-dependent, mTOR-driven angiogenesis from surrounding stroma has not fully evolved 21 . 
     Recently, proof-of-principle has been established for the potential therapeutic utility of the CSC concept 3,22 . Therefore, identification of a vasculogenic mechanism whereby MMIC may contribute to tumour growth has potentially important therapeutic implications. Previous studies revealed that normally resistant human melanoma cells are rendered sensitive in vitro to the effects of chemotherapeutic agents by mAb- or siRNA-mediated blockade of ABCB5 5,6 , and that mAb binding to ABCB5 is sufficient to induce an effective anti-melanoma immune response via antibody-dependent cell-mediated cytotoxicity (ADCC) in vivo 3 . Now, recognition of the role of MMIC in tumour vasculogenesis will also permit development of strategies focused on inhibition of the relevant molecular pathways integral to endothelial-directed CSC plasticity. Moreover, the spatial localization of the MMIC component to channels that communicate with the systemic circulation may render this important determinant of cancer virulence particularly vulnerable to therapeutic targeting. 
     Example 5: Vasculogenic/Angiogenic Pathways in Human Melanoma 
     We investigated gene relationships based on Ingenuity Pathway Analysis. We prepared a graphical representation of pathway activation across ABCB5 +  MMIC. Genes that were overexpressed in ABCB5 +  relative to ABCB5 −  human melanoma cells were represented by red nodes (circles) and those expressed at lower levels were represented by black nodes. Black lines were drawn between genes to show known interactions. Known gene functions in vasculogenesis and angiogenesis, and genes known as relevant drug targets were annotated (red lines) ( FIG. 1 a   ). We examined expression of vasculogenic/angiogenic pathway members by RT-PCR in ABCB5 +  MMIC. Results of this anaylsis are shown in  FIG. 1 b   . We used dual color flow cytometry using ABCB5 phenotype-specific cell gating to determining FLT1 (VEGFR-1) protein expression of ABCB5+ MMIC ( FIG. 1 c   , top) and ABCB5− melanoma cells ( FIG. 1 c   , bottom). We examined CD144 expression in ABCB5 +  MMIC or ABCB5 −  melanoma cell subpopulations by immunofluorescence staining prior to (t=0 h) and upon 48h of culture (t=48h) in the presence of 100 ng/ml VEGF 11 . Representative immunofluorescence staining for CD144 expression (Texas red) are shown in  FIG. 1 d   , with nuclei counterstained in blue (DAPI). Mean percentages (mean±s.e.m., n=3 replicate experiments) of cells staining positively for CD144 in each sample are shown on the right. We examined CD144 expression in melanoma cells in the presence of 100 ng/ml VEGF as in above, but in the presence or absence of anti-FLT1 (VEGFR-1) blocking mAb or isotype control mAb. Representative immunofluorescence staining for CD144 expression (Texas red) by melanoma cells cultured for 48h (t=48h) are shown in  FIG. 1 e   , with nuclei counterstained in blue (DAPI). Mean percentages (mean±s.e.m., n=3 replicate experiments) of cells staining positively for CD144 in each sample are shown in the far right panel. We examined tube formation by phase contrast light microscopy of melanoma cells cultured for 24h (t=24h) in the presence of 100 ng/ml VEGF and the presence or absence of anti-FLT1 (VEGFR-1) blocking mAb or isotype control mAb ( FIG. 1 f   ). Number of tubes/microscopy field (mean±s.e.m., n=3 replicate experiments) and tube length (μm) (mean±s.e.m., n=3 replicate experiments) are illustrated for the different experimental conditions on the far right panels, respectively. We examined the differentiation potential of ABCB5 +  and ABCB5 −  human melanoma cells along a adipogenic pathway ( FIG. 1 h   , Oil Red O staining, nuclei are counterstained with hematoxylin) and osteogenic pathway ( FIG. 1 i   , Alizarin Red staining). Myogenic differentiation potential of ABCB5 +  and ABCB5 −  human melanoma cells was also examined ( FIG. 1 j   ). Absence of myogenin staining (FITC, green) was detected in ABCB5 +  or ABCB5 −  human melanoma cells (nuclei are counterstained with DAPI). 
     Example 6: MMIC-Driven In Vivo Vasculogenesis 
     We investigated MMIC driven vasculogenesis in vivo. Sections of human melanoma growing at melanoma cell injection site within human dermis of skin xenograft to NOD/SCID mouse were conventionally-stained by hematoxylin and eosin ( FIG. 2 a   ). We also examined by immunohistochemistry the expression of human CD31 which indicated angiogenic response at perimeter of melanoma within human xenograft. ( FIG. 2 b   , broken line represents interface of tumour nodule with dermal connective tissue). We used periodic-acid Schiff (PAS) stain (with diastase), an immunochemical stain of CD31-negative interior regions of melanoma xenografts, to reveal numerous anastomosing channels ( FIG. 2 c   , inset is laminin immunohistochemistry indicating identical pattern). We conducted transmission electron micrographs of interior regions of melanoma xenografts ( FIG. 2 d   ), and found that lumenal spaces containing blood products (erythrocytes) are lined by melanoma cells and associated basement membrane-like extracellular matrix. We examined the interior zone of melanoma xenograft derived from cells expressing GFP transgene and immunohistochemically stained for endothelial marker CD144 (red chromogen); results are shown in ( FIG. 2 e   ). We found that CD144 expression is confined to cells forming lumen-like spaces lined by cells that co-express GFP and CD144 (indicated as yellow-orange). We also performed immunohistochemistry, at low ( FIG. 2 f   ) and high ( FIG. 2 g   ) magnification, for ABCB5 protein; our results show that reactivity is restricted to anastomosing channels identical to those seen in  FIG. 2 c   . The inset in  FIG. 2 f    depicts similar formation of ABCB5-reactive channels in a patient-derived melanoma biopsy. We performed in situ hybridization for ABCB5 mRNA ( FIG. 2 h   ). Our results reveal a channel pattern corresponding to that of ABCB5 protein expression (compare with  FIG. 2 f   ; inset is sense control). We examined the expression of ABCB5 in melanoma xenografts after intravenous administration in vivo ( FIG. 2 h   ). Detection of anti-ABCB5 mAb was accomplished using anti-mouse Ig immunohistochemistry; note localization to channels (inset represents anti-mouse Ig staining after intravenous administration of irrelevant isotype-matched control mAb). Dual-labeling immunofluorescence microscopy was performed for both ABCB5 (green), CD144 (red), and ABCB5 &amp; CD144 (mix) ( FIG. 2 j   ) and ABCB5 (green), TIE-1 (red), and ABCB5 &amp; TIE-1 (mix) ( FIG. 2 j   ). 
     Example 7: Interdependency of MMIC-Driven Vasculogenesis and Tumourigenesis 
     We examined ABCB5 expression by flow cytometry; ABCB5 or control staining (FITC, F11) was plotted against forward scatter (FSC) for human A375, MUM-2B, and MUM-2C melanoma cell inocula. Representative data is shown in  FIG. 3 a   . We examined histologic sections of melanomas that developed from three unsegregated and ABCB5-depleted melanoma cell lines injected intradermally into human skin xenografts. Representative sections are shown in  FIG. 3 b   . We used histology to determine tumour formation rate (%) 3 weeks following intradermal transplantation of unsegregated vs. ABCB5 + -depleted human A375, MUM-2B or MUM-2C melanoma cells (2×10 6 /inoculum) into human skin/Rag2 −/−  chimeric mice (n=5, respectively). ( FIG. 3 c   ). We determined histological tumour volumes (mean±s.e.m.) 3 weeks following intradermal transplantation of unsegregated vs. ABCB5 + -depleted human A375, MUM-2B or MUM-2C melanoma cells (2×10 6 /inoculum) into human skin/Rag2 −/−  chimeric mice. ( FIG. 3 d   ). We performed immunohistochemistry for laminin. Our results showed the extent of channel formation in melanomas that developed from unsegregated or ABCB5 + -depleted melanoma cell inocula derived from A375, MUM-2B or MUM-2C lines injected intradermally into human skin xenografts (arrows=necrosis). ( FIG. 3 e   ). We performed image analysis of laminin immunoreactivity for melanomas derived from unsegregated and ABCB5 + -depleted cell inocula. Data are shown in  FIG. 3 f   ; y-axis is percent of pixelated area with reactivity (mean±s.e.m.); solid bar represents tumours derived from unsegregated melanoma cells, open bars represent tumours derived from ABCB5 + -depleted cells (A375, P&lt;0.0032; MUM-2B, P&lt;0.0005; MUM-2C, P&lt;0.0059). 
     Example 8: Correlation of ABCB5 Protein and mRNA Expression Across Human Melanoma Cell Lines 
     We examined ABCB5 and tubulin expression in a panel of human melanoma cell lines by western blot analysis ( FIG. 4 a   ). We examined relative ABCB5 mRNA expression (log 2 ) in a panel of human melanoma cell lines plotted against ABCB5 protein expression as determined by ratios of ABCB5 89 kD western blot band intensity and tubulin western blot band intensity for each human melanoma cell line. ( FIG. 4 b   ). Data points are as follows: 1, SK-MEL-2; 2, SK-MEL-5; 3, SK-MEL-28; 4, MDA-MB-435; 5, UACC-62; 6, UACC-257; 7, M14; 8, MALME-3M. Spearman Rank Correlation r (corrected for ties). 
     Example 9: CSC-Associated Genes Identified at the Protein Level 
     Using cell surface immunostaining and flow cytometry we identified additional genes to be differentially regulated at the protein level in ABCB5+ CSC versus ABCB5− cancer bulk populations. These are all immunomodulatory molecules and the ones upregulated in ABCB5+ cells may be relevant to the escape from immunosurveillance and be resposible for resistance to immunotherapy in malignant melanoma, i.e. when the genes overexpressed on ABCB5+ cells are targeted, melanoma is predicted to be sensitized to immune attack and therapy. 
     
       
         
           
               
             
               
                 TABLE 8 
               
               
                   
               
               
                 Upregulated in ABCB5+ CSC compared to 
               
               
                 ABCB5− bulk cancer populations: 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                   
                 MHC class II 
               
               
                   
                 CD28 
               
               
                   
                 CD86 
               
               
                   
                 PD-1 
               
               
                   
                 CD40-L 
               
               
                   
                 4-1BB-L 
               
               
                   
                 B7-H4 
               
               
                   
                 GITR 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 7 
               
               
                   
               
               
                 Downregulated in ABCB5+ CSC compared to 
               
               
                 ABCB5− cancer bulk populations 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                   
                 MHC class I 
               
               
                   
                 CD80 
               
               
                   
                 PD-L1 
               
               
                   
                 ICOS-L 
               
               
                   
                   
               
            
           
         
       
     
     REFERENCES FOR DETAILED DESCRIPTION AND EXAMPLES 
     
         
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     Having thus described several aspects of at least one embodiment of this invention, it is to be appreciated various alterations, modifications, and improvements will readily occur to those skilled in the art. Such alterations, modifications, and improvements are intended to be part of this disclosure, and are intended to be within the spirit and scope of the invention. Accordingly, the foregoing description and drawings are by way of example only.