High-throughput technology enables the genome-wide study in almost every field of biology. However, the majority of current researches are focused on the “single gene” approach, neglecting the information about the correlation structures across genes. In this study, we take into account the correlation structure using modules as our study units. We first find the functional gene modules and then identify the corresponding SNPs by Sparse Partial Least Square method for each module. Finally, the Bayesian network is built on both the genes within the modules and the SNPs underlying the modules to re-construct the pathways associated with the well-known cancer genes in order to realize the causal relationships within the gene regulatory network.

1. Abell, K., A. Bilancio, et al. (2005). "Stat3-induced apoptosis requires a molecular switch in PI(3)K subunit composition." Nat Cell Biol 7(4): 392-398.
2. Al-Moundhri, M. S., M. Al-Kindi, et al. (2007). "NAT2 polymorphism in Omani gastric cancer patients-risk predisposition and clinicopathological associations." World Journal of Gastroenterology 13(19): 2697-2702.
3. Banchio, C., L. M. Schang, et al. (2003). "Activation of CTP : phosphocholine cytidylyltransferase alpha expression during the S phase of the cell cycle is mediated by the transcription factor Sp1." Journal of Biological Chemistry 278(34): 32457-32464.
4. Bigelow, R. L., N. S. Chari, et al. (2004). "Transcriptional regulation of bcl-2 mediated by the sonic hedgehog signaling pathway through gli-1." Journal of Biological Chemistry 279(2): 1197-1205.
5. Bilic, J., Y. L. Huang, et al. (2007). "Wnt induces LRP6 signalosomes and promotes dishevelled-dependent LRP6 phosphorylation." Science 316(5831): 1619-1622.
6. Boccaccio, C., M. Ando, et al. (1998). "Induction of epithelial tubules by growth factor HGF depends on the STAT pathway." Nature 391(6664): 285-288.
7. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res. 2008 Jan;36(Database issue) :637-40. Epub 2007 Nov 13.
8. Brizzi, M. F., P. Defilippi, et al. (1999). "Integrin-mediated adhesion of endothelial cells induces JAK2 and STAT5A activation: role in the control of c-fos gene expression." Mol Biol Cell 10(10): 3463-3471.
9. Brizzi, M. F., P. Dentelli, et al. (2002). "STAT5 activation induced by diabetic LDL depends on LDL glycation and occurs via src kinase activity." Diabetes 51(11): 3311-3317.
10. Brown, D. M. and E. Ruoslahti (2004). "Metadherin, a cell surface protein in breast tumors that mediates lung metastasis." Cancer Cell 5(4): 365-374.
11. Burkhart, D. L., L. K. Ngai, et al. (2010). "Regulation of RB Transcription In Vivo by RB Family Members." Molecular and Cellular Biology 30(7): 1729-1745.
12. Cabusora, L., E. Sutton, et al. (2005). "Differential network expression during drug and stress response." Bioinformatics 21(12): 2898-2905.
13. Califano, D., S. Pignata, et al. (2010). "FEZ1/LZTS1 Protein Expression in Ovarian Cancer." Journal of Cellular Physiology 222(2): 382-386.
14. Cappuzzo, F., M. Varella-Garcia, et al. (2009). "MYC and EIF3H Coamplification Significantly Improve Response and Survival of Non-small Cell Lung Cancer Patients (NSCLC) Treated with Gefitinib." Journal of Thoracic Oncology 4(4): 472-478.
15. Charles, A., X. R. Tang, et al. (2001). "Retinoblastoma protein complexes with C/EBP proteins and activates C/EBP-mediated transcription." Journal of Cellular Biochemistry 83(3): 414-425.
16. Chattopadhyay, I., A. Singh, et al. (2010). "Genome-wide analysis of chromosomal alterations in patients with esophageal squamous cell carcinoma exposed to tobacco and betel quid from high-risk area in India." Mutation Research-Genetic Toxicology and Environmental Mutagenesis 696(2): 130-138.
17. Chen, C., S. Ricks, et al. (2001). "N-Acetyltransferase 2 polymorphisms, cigarette smoking and alcohol consumption, and oral squamous cell cancer risk." Carcinogenesis 22(12): 1993-1999.
18. Chen, H. H., S. Q. Wang, et al. (2008). "[Clinical significance of angiopoietin-2 expression in oral squamous cell carcinoma]." Zhonghua Zhong Liu Za Zhi 30(8): 606-609.
19. Chen, J. and B. Yuan (2006). "Detecting functional modules in the yeast protein-protein interaction network." Bioinformatics 22(18): 2283-2290.
20. Chen, L., Z. M. Zhu, et al. (2009). "Down-regulation of tumor suppressor gene FEZ1/LZTS1 in breast carcinoma involves promoter methylation and associates with metastasis." Breast Cancer Research and Treatment 116(3): 471-478.
21. Cheranov, S. Y., M. Karpurapu, et al. (2008). "An essential role for SRC-activated STAT-3 in 14,15-EET-induced VEGF expression and angiogenesis." Blood 111(12): 5581-5591.
22. Cho, M. L., J. W. Kang, et al. (2006). "STAT3 and NF-kappaB signal pathway is required for IL-23-mediated IL-17 production in spontaneous arthritis animal model IL-1 receptor antagonist-deficient mice." J Immunol 176(9): 5652-5661.
23. Chotani, M. A., K. Touhalisky, et al. (2000). "The small GTPases Ras, Rac, and Cdc42 transcriptionally regulate expression of human fibroblast growth factor 1." Journal of Biological Chemistry 275(39): 30432-30438.
24. Chou, J. L., H. Y. Su, et al. (2010). "Promoter hypermethylation of FBXO32, a novel TGF-beta/SMAD4 target gene and tumor suppressor, is associated with poor prognosis in human ovarian cancer." Laboratory Investigation 90(3): 414-425.
25. Chow, E. K., R. M. O'Connell, et al. (2005). "TLR agonists regulate PDGF-B production and cell proliferation through TGF-beta/type IIFN crosstalk." Embo Journal 24(23): 4071-4081.
26. Chuang, H. Y., E. Lee, et al. (2007). "Network-based classification of breast cancer metastasis." Molecular Systems Biology 3: -.
27. Chun, H. and S. Keles (2009). "Expression Quantitative Trait Loci Mapping With Multivariate Sparse Partial Least Squares Regression." Genetics 182(1): 79-90.
28. Coqueret, O. and H. Gascan (2000). "Functional interaction of STAT3 transcription factor with the cell cycle inhibitor p21WAF1/CIP1/SDI1." Journal of Biological Chemistry 275(25): 18794-18800.
29. Dittrich, M. T., G. W. Klau, et al. (2008). "Identifying functional modules in protein-protein interaction networks: an integrated exact approach." Bioinformatics 24(13): I223-I231.
30. Dong, X., G. Zhou, et al. (2009). "Association of DLC1 gene polymorphism with susceptibility to hepatocellular carcinoma in Chinese hepatitis B virus carriers." Cancer Epidemiol 33(3-4): 265-270.
31. Drake, K. M., E. C. Ruteshouser, et al. (2009). "Loss of Heterozygosity at 2q37 in Sporadic Wilms' Tumor: Putative Role for miR-562." Clinical Cancer Research 15(19): 5985-5992.
32. Eisen, M. B., P. T. Spellman, et al. (1998). "Cluster analysis and display of genome-wide expression patterns." Proceedings of the National Academy of Sciences of the United States of America 95(25): 14863-14868.
33. Emdad, L., S. G. Lee, et al. (2009). "Astrocyte elevated gene-1 (AEG-1) functions as an oncogene and regulates angiogenesis." Proceedings of the National Academy of Sciences of the United States of America 106(50): 21300-21305.
34. Emdad, L., D. Sarkar, et al. (2010). "Astrocyte Elevated Gene-1: A Novel Target for Human Glioma Therapy." Molecular Cancer Therapeutics 9(1): 79-88.
35. Fang, X. H., E. K. Stachowiak, et al. (2005). "Control of CREB-binding protein signaling by nuclear fibroblast growth factor receptor-1 - A novel mechanism of gene regulation." Journal of Biological Chemistry 280(31): 28451-28462.
36. Federici, M., M. L. Giustizieri, et al. (2002). "Impaired IFN-gamma-dependent inflammatory responses in human keratinocytes overexpressing the suppressor of cytokine signaling 1." Journal of Immunology 169(1): 434-442.
37. Fernandez, P. C., S. R. Frank, et al. (2003). "Genomic targets of the human c-Myc protein." Genes & Development 17(9): 1115-1129.
38. Friedman, N., M. Linial, et al. (2000). "Using Bayesian networks to analyze expression data." Journal of Computational Biology 7(3-4): 601-620.
39. Frolov, A., S. Chahwan, et al. (2003). "Response markers and the molecular mechanisms of action of Gleevec in gastrointestinal stromal tumors." Mol Cancer Ther 2(8): 699-709.
40. Frost, J. A., J. L. Swantek, et al. (2000). "Stimulation of NFkappa B activity by multiple signaling pathways requires PAK1." Journal of Biological Chemistry 275(26): 19693-19699.
41. Gnanapragasam, V. J., H. Y. Leung, et al. (2001). "Expression of RAC 3, a steroid hormone receptor co-activator in prostate cancer." Br J Cancer 85(12): 1928-1936.
42. Gupta, S. and R. J. Davis (1994). "MAP kinase binds to the NH2-terminal activation domain of c-Myc." FEBS Lett 353(3): 281-285.
43. Ha, N. C., T. Tonozuka, et al. (2004). "Mechanism of phosphorylation-dependent binding of APC to beta-catenin and its role in beta-catenin degradation." Molecular Cell 15(4): 511-521.
44. Hanisch, D., A. Zien, et al. (2002). "Co-clustering of biological networks and gene expression data." Bioinformatics 18 Suppl 1: S145-154.
45. Hankins, G. R., T. Sasaki, et al. (2008). "Identification of the Deleted in Liver Cancer 1 Gene, Dlc1, as a Candidate Meningioma Tumor Suppressor." Neurosurgery 63(4): 771-780.
46. Hashigasako, A., M. Machide, et al. (2004). "Bi-directional regulation of Ser-985 phosphorylation of c-Met via protein kinase C and protein phosphatase 2A involves c-Met activation and cellular responsiveness to hepatocyte growth factor." Journal of Biological Chemistry 279(25): 26445-26452.
47. Hawkins, G. A., J. C. Mychaleckyj, et al. (2002). "Germline sequence variants of the LZTS1 gene are associated with prostate cancer risk." Cancer Genetics and Cytogenetics 137(1): 1-7.
48. Healy, K. D., L. Hodgson, et al. (2008). "DLC-1 suppresses non-small cell lung cancer growth and invasion by RhoGAP-dependent and independent mechanisms." Molecular Carcinogenesis 47(5): 326-337.
49. Heering, J., P. Erlmann, et al. (2009). "Simultaneous loss of the DLC1 and PTEN tumor suppressors enhances breast cancer cell migration." Exp Cell Res 315(15): 2505-2514.
50. Hein, D. W., M. A. Leff, et al. (2002). "Association of prostate cancer with rapid N-acetyltransferase 1 (NAT1*10) in combination with slow N-acetyltransferase 2 acetylator genotypes in a pilot case-control study." Environ Mol Mutagen 40(3): 161-167.
51. Henshall, S. M., D. E. Afar, et al. (2003). "Survival analysis of genome-wide gene expression profiles of prostate cancers identifies new prognostic targets of disease relapse." Cancer Res 63(14): 4196-4203.
52. Hirokawa, S., H. Sato, et al. (2003). "EBF-regulating Pax5 transcription is enhanced by STAT5 in the early stage of B cells." European Journal of Immunology 33(7): 1824-1829.
53. Hofsli, E., T. E. Wheeler, et al. (2008). "Identification of novel neuroendocrine-specific tumour genes." Br J Cancer 99(8): 1330-1339.
54. Holeiter, G., J. Heering, et al. (2008). "Deleted in Liver Cancer 1 Controls Cell Migration through a Dial-Dependent Signaling Pathway." Cancer Research 68(21): 8743-8751.
55. Hsing, A. W., L. C. Sakoda, et al. (2007). "MSR1 variants and the risks of prostate cancer and benign prostatic hyperplasia: a population-based study in China." Carcinogenesis 28(12): 2530-2536.
56. Huang, H. C. and P. S. Klein (2004). "The Frizzled family: receptors for multiple signal transduction pathways." Genome Biology 5(7): 234.
57. Hubner, N., C. A. Wallace, et al. (2005). "Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease." Nature Genetics 37(3): 243-253.
58. Hwang, T. and T. Park (2009). "Identification of differentially expressed subnetworks based on multivariate ANOVA." Bmc Bioinformatics 10: -.
59. Ideker, T., O. Ozier, et al. (2002). "Discovering regulatory and signalling circuits in molecular interaction networks." Bioinformatics 18 Suppl 1: S233-240.
60. Iguchi, T., S. Sugita, et al. (2009). "MnSOD Genotype and Prostate Cancer Risk as a Function of NAT Genotype and Smoking Status." In Vivo 23(1): 7-12.
61. Jakobsen, A. M., P. Andersson, et al. (2001). "Differential expression of vesicular monoamine transporter (VMAT) 1 and 2 in gastrointestinal endocrine tumours." Journal of Pathology 195(4): 463-472.
62. Jia, Z. Y. and S. Z. Xu (2007). "Mapping quantitative trait loci for expression abundance." Genetics 176(1): 611-623.
63. Jin, Y. L., X. Q. Tian, et al. (2008). "Inhibition of DLC-1 gene expression by RNA interference in the colon cancer LoVo cell line." Oncology Reports 19(3): 669-674.
64. Jin, Z., W. S. May, et al. (2006). "Bcl2 suppresses DNA repair by enhancing c-Myc transcriptional activity." Journal of Biological Chemistry 281(20): 14446-14456.
65. Jourenkova-Mironova, N., H. Wikman, et al. (1999). "Role of arylamine N-acetyltransferase 1 and 2 (NAT1 and NAT2) genotypes in susceptibility to oral/pharyngeal and laryngeal cancers." Pharmacogenetics 9(4): 533-537.
66. Jung, J. E., H. S. Kim, et al. (2008). "STAT3 inhibits the degradation of HIF-1alpha by pVHL-mediated ubiquitination." Exp Mol Med 40(5): 479-485.
67. Jung, Y., J. Park, et al. (2008). "Gene silencing of TSPYL5 mediated by aberrant promoter methylation in gastric cancers." Laboratory Investigation 88(2): 153-160.
68. Kallies, A., J. Hasbold, et al. (2007). "Initiation of plasma-cell differentiation is independent of the transcription factor Blimp-1." Immunity 26(5): 555-566.
69. Kanehisa, M., and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30.
70. Karlseder, J., H. Rotheneder, et al. (1996). "Interaction of Sp1 with the growth- and cell cycle-regulated transcription factor E2F." Molecular and Cellular Biology 16(4): 1659-1667.
71. Katoh, T., S. Kaneko, et al. (1998). "A pilot study testing the association between N-acetyltransferases 1 and 2 and risk of oral squamous cell carcinoma in Japanese people." Carcinogenesis 19(10): 1803-1807.
72. Kendziorski, C. M., M. Chen, et al. (2006). "Statistical methods for expression quantitative trait loci (eQTL) mapping." Biometrics 62(1): 19-27.
73. Kim, E. J., S. Y. Lee, et al. (2010). "TSPYL5 is involved in cell growth and the resistance to radiation in A549 cells via the regulation of p21(WAF1/Cip1) and PTEN/AKT pathway." Biochemical and Biophysical Research Communications 392(3): 448-453.
74. Kim, T. Y., J. W. Lee, et al. (2007). "DLC-1, a GTPase-activating protein for Rho, is associated with cell proliferation, morphology, and migration in human hepatocellular carcinoma." Biochemical and Biophysical Research Communications 355(1): 72-77.
75. Kishida, S., H. Yamamoto, et al. (1999). "DIX domains of Dvl and Axin are necessary for protein interactions and their ability to regulate beta-catenin stability." Molecular and Cellular Biology 19(6): 4414-4422.
76. Kobayashi, M., T. Otani, et al. (2009). "Association between dietary heterocyclic amine levels, genetic polymorphisms of NAT2, CYP1A1, and CYP1A2 and risk of stomach cancer: a hospital-based case-control study in Japan." Gastric Cancer 12(4): 198-205.
77. Kopczynska, E., R. Makarewicz, et al. (2009). "Plasma concentration of angiopoietin-1, angiopoietin-2 and Tie-2 in cervical cancer." Eur J Gynaecol Oncol 30(6): 646-649.
78. Kraus, D. M., G. S. Elliott, et al. (2006). "CSMD1 is a novel multiple domain complement-regulatory protein highly expressed in the central nervous system and epithelial tissues." Journal of Immunology 176(7): 4419-4430.
79. Lee, H. S., D. C. Lee, et al. (2006). "STMN2 is a novel target of beta-catenin/TCF-mediated transcription in human hepatoma cells." Biochemical and Biophysical Research Communications 345(3): 1059-1067.
80. Lee, S. G., Z. Z. Su, et al. (2008). "Astrocyte elevated gene-1 activates cell survival pathways through PI3K-Akt signaling." Oncogene 27(8): 1114-1121.
81. Li, C. M., M. R. Guo, et al. (2002). "Gene expression in Wilms' tumor mimics the earliest committed stage in the metanephric mesenchymal-epithelial transition." American Journal of Pathology 160(6): 2181-2190.
82. Li, J., L. Yang, et al. (2009). "Astrocyte elevated gene-1 is a proliferation promoter in breast cancer via suppressing transcriptional factor FOXO1." Oncogene 28(36): 3188-3196.
83. Liang, Q. W., R. R. Mohan, et al. (1998). "Signaling by HGF and KGF in corneal epithelial cells: Ras/MAP kinase and Jak-STAT pathways." Investigative Ophthalmology & Visual Science 39(8): 1329-1338.
84. Lilla, C., E. Verla-Tebit, et al. (2006). "Effect of NAT1 and NAT2 genetic polymorphisms on colorectal cancer risk associated with exposure to tobacco smoke and meat consumption." Cancer Epidemiol Biomarkers Prev 15(1): 99-107.
85. Loyo, M., M. Brait, et al. (2010). "A survey of methylated candidate tumor suppressor genes in nasopharyngeal carcinoma." Int J Cancer.
86. Ma, C., K. M. Quesnelle, et al. (2009). "Characterization CSMD1 in a large set of primary lung, head and neck, breast and skin cancer tissues." Cancer Biol Ther 8(10): 907-916.
87. Mao, Y. W., X. C. Ge, et al. (2009). "Disrupted in Schizophrenia 1 Regulates Neuronal Progenitor Proliferation via Modulation of GSK3 beta/beta-Catenin Signaling." Cell 136(6): 1017-1031.
88. Maraziotis, I. A., K. Dimitrakopoulou, et al. (2007). "Growing functional modules from a seed protein via integration of protein interaction and gene expression data." Bmc Bioinformatics 8: -.
89. Marques, C. F. S., S. Koifman, et al. (2006). "Influence of CYP1A1, CYP2E1, GSTM3 and NAT2 genetic polymorphisms in oral cancer susceptibility: Results from a case-control study in Rio de Janeiro." Oral Oncology 42(6): 632-637.
90. Massie, C. E., B. Adryan, et al. (2007). "New androgen receptor genomic targets show an interaction with the ETS1 transcription factor." Embo Reports 8(9): 871-878.
91. Mathioudaki, K., T. Leotsakou, et al. (2004). "SR-A1, a member of the human pre-mRNA splicing factor family, and its expression in colon cancer progression." Biol Chem 385(9): 785-790.
92. McKay, J. D., M. Hashibe, et al. (2008). "Sequence variants of NAT1 and NAT2 and other xenometabolic genes and risk of lung and aerodigestive tract cancers in Central Europe." Cancer Epidemiol Biomarkers Prev 17(1): 141-147.
93. Morris, M. R., C. Ricketts, et al. (2010). "Identification of candidate tumour suppressor genes frequently methylated in renal cell carcinoma." Oncogene 29(14): 2104-2117.
94. Moslehi, R., N. Chatterjee, et al. (2006). "Cigarette smoking, N-acetyltransferase genes and the risk of advanced colorectal adenoma." Pharmacogenomics 7(6): 819-829.
95. Nakano, H., H. Oshima, et al. (1996). "TRAF5, an activator of NF-kappaB and putative signal transducer for the lymphotoxin-beta receptor." Journal of Biological Chemistry 271(25): 14661-14664.
96. Nishikata, M., I. Nishimori, et al. (2007). "Carbonic anhydrase-related protein VIII promotes colon cancer cell growth." Mol Carcinog 46(3): 208-214.
97. Noonan-Wheeler, F. C., W. Wu, et al. (2006). "Association of hereditary prostate cancer gene polymorphic variants with sporadic aggressive prostate carcinoma." Prostate 66(1): 49-56.
98. Nothlings, U., J. F. Yamamoto, et al. (2009). "Meat and Heterocyclic Amine Intake, Smoking, NAT1 and NAT2 Polymorphisms, and Colorectal Cancer Risk in the Multiethnic Cohort Study." Cancer Epidemiology Biomarkers & Prevention 18(7): 2098-2106.
99. Oka, D., S. Yamashita, et al. (2009). "The Presence of Aberrant DNA Methylation in Noncancerous Esophageal Mucosae in Association With Smoking History A Target for Risk Diagnosis and Prevention of Esophageal Cancers." Cancer 115(15): 3412-3426.
100. Okamoto, H., K. Yasui, et al. (2003). "PTK2 and EIF3S3 genes may be amplification targets at 8q23-q24 and are associated with large hepatocellular carcinomas." Hepatology 38(5): 1242-1249.
101. Ono, K., K. Uzawa, et al. (2003). "Down-regulation of FEZ1/LZTS1 gene with frequent loss of heterozygosity in oral squamous cell carcinomas." International Journal of Oncology 23(2): 297-302.
102. Ouerhani, S., K. Rouissi, et al. (2009). "Combined effect of NAT2, MTR and MTHFR genotypes and tobacco on bladder cancer susceptibility in Tunisian population." Cancer Detection and Prevention 32(5-6): 395-402.
103. Palla, G., I. Derenyi, et al. (2005). "Uncovering the overlapping community structure of complex networks in nature and society." Nature 435(7043): 814-818.
104. Paris, P. L., A. Andaya, et al. (2004). "Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors." Hum Mol Genet 13(13): 1303-1313.
105. Park, J. I., A. S. Venteicher, et al. (2009). "Telomerase modulates Wnt signalling by association with target gene chromatin." Nature 460(7251): 66-U77.
106. Peng C.H., Liao C.T. et al. “Systems genetics analysis of copy number variation reveals 16 amplicons and 24 genes associated with second primary tumor developement and poor prognosis in oral squamous cell carcinoma.” (manuscript in preparation)
107. Pereira-Leal, J. B., A. J. Enright, et al. (2004). "Detection of functional modules from protein interaction networks." Proteins-Structure Function and Genetics 54(1): 49-57.
108. Peterson, T. R., M. Laplante, et al. (2009). "DEPTOR Is an mTOR Inhibitor Frequently Overexpressed in Multiple Myeloma Cells and Required for Their Survival." Cell 137(5): 873-886.
109. Pils, D., P. Horak, et al. (2005). "Five genes from chromosomal band 8p22 are significantly down-regulated in ovarian carcinoma - N33 and EFA6R have a potential impact on overall survival." Cancer 104(11): 2417-2429.
110. Pircher, T. J., H. Petersen, et al. (1999). "Extracellular signal-regulated kinase (ERK) interacts with signal transducer and activator of transcription (STAT) 5a." Molecular Endocrinology 13(4): 555-565.
111. Pircher, T. J., H. Petersen, et al. (1999). "Extracellular signal-regulated kinase (ERK) interacts with signal transducer and activator of transcription (STAT) 5a." Molecular Endocrinology 13(4): 555-565.
112. Puto, L. A., K. Pestonjamasp, et al. (2003). "p21-activated kinase 1 (PAK1) interacts with the Grb2 adapter protein to couple to growth factor signaling." Journal of Biological Chemistry 278(11): 9388-9393.
113. Radicchi, F., C. Castellano, et al. (2004). "Defining and identifying communities in networks." Proceedings of the National Academy of Sciences of the United States of America 101(9): 2658-2663.
114. Rai, R., H. Dai, et al. (2006). "BRIT1 regulates early DNA damage response, chromosomal integrity, and cancer." Cancer Cell 10(2): 145-157.
115. Rosenzweig, T., S. Aga-Mizrachi, et al. (2004). "Src tyrosine kinase regulates insulin-induced activation of protein kinase C (PKC) delta in skeletal muscle." Cellular Signalling 16(11): 1299-1308.
116. Rual, J. F., K. Venkatesan, et al. (2005). "Towards a proteome-scale map of the human protein-protein interaction network." Nature 437(7062): 1173-1178.
117. Ruckhaberle, E., U. Holtrich, et al. (2009). "Acid ceramidase 1 expression correlates with a better prognosis in ER-positive breast cancer." Climacteric 12(6): 502-513.
118. Sadana, P., Y. Zhang, et al. (2007). "Regulation of carnitine palmitoyltransferase I (CPT-Ialpha) gene expression by the peroxisome proliferator activated receptor gamma coactivator (PGC-1) isoforms." Mol Cell Endocrinol 267(1-2): 6-16.
119. Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H. Recurated protein interaction datasets. Nat Methods. 2009 Jan;6(1):39-46.
120. Sanderson, S., G. Salanti, et al. (2007). "Joint effects of the N-acetyltransferase 1 and 2 (NAT1 and NAT2) genes and smoking on bladder carcinogenesis: a literature-based systematic HuGE review and evidence synthesis." Am J Epidemiol 166(7): 741-751.
121. Savinainen, K. J., M. J. Linja, et al. (2004). "Expression and copy number analysis of TRPS1, EIF3S3 and MYC genes in breast and prostate cancer." British Journal of Cancer 90(5): 1041-1046.
122. Schadt, E. E., J. Lamb, et al. (2005). "An integrative genomics approach to infer causal associations between gene expression and disease." Nature Genetics 37(7): 710-717.
123. Scholnick, S. B. and T. M. Richter (2003). "The role of CSMD1 in head and neck carcinogenesis." Genes Chromosomes Cancer 38(3): 281-283.
124. Seelan, R. S., C. P. Qian, et al. (2000). "Human acid ceramidase is overexpressed but not mutated in prostate cancer." Genes Chromosomes & Cancer 29(2): 137-146.
125. Segal, E., H. Wang, et al. (2003). "Discovering molecular pathways from protein interaction and gene expression data." Bioinformatics 19 Suppl 1: i264-271.
126. Senda, T., A. Iizuka-Kogo, et al. (2007). "Adenomatous polyposis coli (APC) plays multiple roles in the intestinal and colorectal epithelia." Medical Molecular Morphology 40(2): 68-81.
127. Smith, M. W., Z. N. Yue, et al. (2003). "Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma." Cancer Res 63(4): 859-864.
128. Sonoda, J., J. Laganiere, et al. (2007). "Nuclear receptor ERR alpha and coactivator PGC-1 beta are effectors of IFN-gamma-induced host defense." Genes Dev 21(15): 1909-1920.
129. Srirajaskanthan, R., G. Dancey, et al. (2009). "Circulating angiopoietin-2 is elevated in patients with neuroendocrine tumours and correlates with disease burden and prognosis." Endocrine-Related Cancer 16(3): 967-976.
130. Sturm, S., M. Koch, et al. (2001). "Genomic organization of the gene for mouse PIASgamma and analysis of its promoter." Gene 266(1-2): 123-130.
131. Suzuki, H., J. S. Morris, et al. (2008). "Interaction of the cytochrome P4501A2, SULT1A1 and NAT gene polymorphisms with smoking and dietary mutagen intake in modification of the risk of pancreatic cancer." Carcinogenesis 29(6): 1184-1191.
132. Szarvas, T., T. Jager, et al. (2009). "Serum Levels of Angiogenic Factors and their Prognostic Relevance in Bladder Cancer." Pathology & Oncology Research 15(2): 193-201.
133. Takahashi, T., H. Ueno, et al. (1999). "VEGF activates protein kinase C-dependent, but Ras-independent Raf-MEK-MAP kinase pathway for DNA synthesis in primary endothelial cells." Oncogene 18(13): 2221-2230.
134. Tan, P. K., J. Wang, et al. (2007). "Monitoring interactions between receptor tyrosine kinases and their downstream effector proteins in living cells using bioluminescence resonance energy transfer." Molecular Pharmacology 72(6): 1440-1446.
135. Thomassen, M., Q. H. Tan, et al. (2009). "Gene expression meta-analysis identifies chromosomal regions and candidate genes involved in breast cancer metastasis." Breast Cancer Research and Treatment 113(2): 239-249.
136. Tibshirani, R. (1996). "Regression shrinkage and selection via the Lasso." Journal of the Royal Statistical Society Series B-Methodological 58(1): 267-288.
137. Tinel, M., A. Berson, et al. (2003). "Downregulation of cytochromes P450 in growth-stimulated rat hepatocytes: role of c-Myc induction and impaired C/EBP binding to DNA." Journal of Hepatology 39(2): 171-178.
138. Toh, H. and K. Horimoto (2002). "Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling." Bioinformatics 18(2): 287-297.
139. Toomes, C., A. Jackson, et al. (2003). "The presence of multiple regions of homozygous deletion at the CSMD1 locus in oral squamous cell carcinoma question the role of CSMD1 in head and neck carcinogenesis." Genes Chromosomes & Cancer 37(2): 132-140.
140. Ulitsky, I. and R. Shamir (2007). "Identification of functional modules using network topology and high-throughput data." Bmc Systems Biology 1: -.
141. Ushmorov, A., F. Leithauser, et al. (2008). "ABF-1 is frequently silenced by promoter methylation in follicular lymphoma, diffuse large B-cell lymphoma and Burkitt's lymphoma." Leukemia 22(10): 1942-1944.
142. van Duin, M., R. van Marion, et al. (2007). "High-resolution array comparative genomic hybridization of chromosome 8q: evaluation of putative progression markers for gastroesophageal junction adenocarcinomas." Cytogenetic and Genome Research 118(2-4): 130-137.
143. Varzim, G., E. Monteiro, et al. (2002). "Polymorphisms of arylamine N-acetyltransferase (NAT1 and NAT2) and larynx cancer susceptibility." ORL J Otorhinolaryngol Relat Spec 64(3): 206-212.
144. Vert, J. P. and M. Kanehisa (2003). "Extracting active pathways from gene expression data." Bioinformatics 19: Ii238-Ii244.
145. Vervoorts, J., J. M. Luscher-Firzlaff, et al. (2003). "Stimulation of c-MYC transcriptional activity and acetylation by recruitment of the cofactor CBP." Embo Reports 4(5): 484-490.
146. Wakefield, L., J. Robinson, et al. (2008). "Arylamine N-acetyltransferase 1 expression in breast cancer cell lines: a potential marker in estrogen receptor-positive tumors." Genes Chromosomes Cancer 47(2): 118-126.
147. Walker, K., G. Ginsberg, et al. (2009). "Genetic Polymorphism in N-Acetyltransferase (Nat): Population Distribution of Nat1 and Nat2 Activity." Journal of Toxicology and Environmental Health-Part B-Critical Reviews 12(5-6): 440-472.
148. Wong, E. S. M., J. Lim, et al. (2001). "Evidence for direct interaction between sprouty and Cbl." Journal of Biological Chemistry 276(8): 5866-5875.
149. Wu, K. J., M. Mattioli, et al. (2002). "c-MYC activates protein kinase A (PKA) by direct transcriptional activation of the PKA catalytic subunit beta (PKA-C beta) gene." Oncogene 21(51): 7872-7882.
150. Xu, J., S. L. Zheng, et al. (2003). "Common sequence variants of the macrophage scavenger receptor 1 gene are associated with prostate cancer risk." Am J Hum Genet 72(1): 208-212.
151. Yahata, Y., Y. Shirakata, et al. (2003). "Nuclear translocation of phosphorylated STAT3 is essential for vascular endothelial growth factor-induced human dermal microvascular endothelial cell migration and tube formation." Journal of Biological Chemistry 278(41): 40026-40031.
152. Yalcin, A., E. Koulich, et al. (2003). "Apoptosis in cerebellar granule neurons is associated with reduced interaction between CREB-binding protein and NF-kappa B." Journal of Neurochemistry 84(2): 397-408.
153. Yamamoto, F. and M. Yamamoto (2008). "Identification of Genes That Exhibit Changes in Expression on the 8p Chromosomal Arm by the Systematic Multiplex RT-PCR (SM RT-PCR) and DNA Microarray Hybridization Methods." Gene Expression 14(4): 217-227.
154. Yamamoto, G., T. Irie, et al. (2006). "Correlation of invasion and metastasis of cancer cells, and expression of the RAD21 gene in oral squamous cell carcinoma." Virchows Arch 448(4): 435-441.
155. Ye, X., P. Mehlen, et al. (1999). "TRAF family proteins interact with the common neurotrophin receptor and modulate apoptosis induction." Journal of Biological Chemistry 274(42): 30202-30208.
156. Yi, B. Q., B. Zhao, et al. (2008). "[Expression of hRad21 and clinicopathological analysis in gastrointestinal malignant tumors maintained their telomeres by a mechanism of alternative lengthening of telomeres]." Zhonghua Wei Chang Wai Ke Za Zhi 11(1): 67-71.
157. Yu, C. P., K. Chen, et al. (2009). "Overexpression of astrocyte elevated gene-1 (AEG-1) is associated with esophageal squamous cell carcinoma (ESCC) progression and pathogenesis." Carcinogenesis 30(5): 894-901.
158. Yuan, B. Z., X. L. Zhou, et al. (2003). "DLC-1 gene inhibits human breast cancer cell growth and in vivo tumorigenicity." Oncogene 22(3): 445-450.
159. Zhang, L. L., Z. Smit-McBride, et al. (2008). "An oncogenic role for the phosphorylated h-subunit of human translation initiation factor eIF3." Journal of Biological Chemistry 283(35): 24047-24060.
160. Zhang, S. H., X. M. Ning, et al. (2006). "Identification of functional modules in a PPI network by clique percolation clustering." Computational Biology and Chemistry 30(6): 445-451.
161. Zhang, T., J. Zheng, et al. (2009). "Overexpression of DLC-1 induces cell apoptosis and proliferation inhibition in the renal cell carcinoma." Cancer Lett 283(1): 59-67.