Transcriptome network analysis reveals candidate genes for renal cell carcinoma

Journal of Cancer Research and Therapeutics

Volumn 8, Issue 1, 2012, Pages 28-33

  Zhai, Wei ^a   Xu, Yun Fei ^a   Liu, Min ^a   Zheng, Jun Hua ^a  

^a TONGJI UNIVERSITY   (China)

Author keywords

Gene ontology; pathway; regulation network; renal cell carcinoma

Indexed keywords

MYC PROTEIN; STAT1 PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR SP3; TRANSCRIPTOME;

ARTICLE; DISEASE ASSOCIATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENE TARGETING; GENETIC ANALYSIS; GENETIC ASSOCIATION; KIDNEY CARCINOMA;

CARCINOMA, RENAL CELL; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; KIDNEY NEOPLASMS; MOLECULAR SEQUENCE ANNOTATION; NEOPLASM STAGING; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84860435912     PISSN: 09731482     EISSN: 19984138     Source Type: Journal    
DOI: 10.4103/0973-1482.95170     Document Type: Article

References (31)

1. Mulders PF, Brouwers AH, Hulsbergen-van der Kaa CA, van Lin EN, Osanto S, de Mulder PH. Guideline Renal cell carcinoma. Ned Tijdschr Geneeskd 2008;152:376-80.
2. Arai E, Kanai Y. Genetic and epigenetic alterations during renal carcinogenesis. Int J Clin Exp Pathol 2010;4:58-73.
3. Finley DS, Pantuck AJ, Belldegrun AS. Tumor biology and prognostic factors in renal cell carcinoma. Oncologist 2011;16 Suppl 2:4-13.
4. Oya M. Renal cell carcinoma: Biological features and rationale for molecular-targeted therapy. Keio J Med 2009;58:1-11.
5. Suárez, C, Morales R, Muñoz E, Rodón J, Valverde CM, Carles J. Molecular basis for the treatment of renal cell carcinoma. Clin Transl Oncol 2010;12:15-21.
6. Eeckhoute J, Carroll JS, Geistlinger TR, Torres-Arzayus MI, Brown M. A cell-type-specific transcriptional network required for estrogen regulation of cyclin D1 and cell cycle progression in breast cancer. Genes Dev 2006;20:2513-26. (Pubitemid 44396837)
7. Abdollahi A, Schwager C, Kleeff J, Esposito I, Domhan S, Peschke P, et al. Transcriptional network governing the angiogenic switch in human pancreatic cancer. Proc Natl Acad Sci U S A 2007;104:12890-5. (Pubitemid 47255250)
8. Tun HW, Marlow LA, von Roemeling CA, Cooper SJ, Kreinest P, Wu K, et al. Pathway signature and cellular differentiation in clear cell renal cell carcinoma. PLoS One 2010;5:e10696.
9. Kanehisa M. The KEGG database. Novartis Found Symp 2002;247:91-101; discussion 101-3, 119-28, 244-52.
10. Wingender E. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform 2008;9:326-32. (Pubitemid 351894493)
11. Jiang C, Xuan Z, Zhao F, Zhang MQ. TRED: A transcriptional regulatory element database, new entries and other development. Nucleic Acids Res 2007;35:D137-40. (Pubitemid 46056185)
12. Smyth GK. L inear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004;3:3.
13. Maere S, Heymans K, Kuiper M. BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005;21:3448-9. (Pubitemid 41222459)
14. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498-504. (Pubitemid 37428274)
15. Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, et al. A systems biology approach for pathway level analysis. Genome Res 2007;17:1537-45. (Pubitemid 47529438)
16. Campbell CE, Kuriyan NP, Rackley RR, Caulfield MJ, Tubbs R, Finke J, et al. Constitutive expression of the Wilms tumor suppressor gene (WT1) in renal cell carcinoma. Int J Cancer 1998;78:182-8. (Pubitemid 28443175)
17. Sitaram RT, Degerman S, Ljungberg B, Andersson E, Oji Y, Sugiyama H, et al. Wilms' tumour 1 can suppress hTERT gene expression and telomerase activity in clear cell renal cell carcinoma via multiple pathways. Br J Cancer 2010;103:1255-62.
18. Zhang H, Gao P, Fukuda R, Kumar G, Krishnamachary B, Zeller KI, et al. HIF-1 inhibits mitochondrial biogenesis and cellular respiration in VHL-deficient renal cell carcinoma by repression of C-MYC activity. Cancer Cell 2007;11:407-20. (Pubitemid 46670080)
19. Grabmaier K, A de Weijert MC, Verhaegh GW, Schalken JA, Oosterwijk E. Strict regulation of CAIX(G250/MN) by HIF-1alpha in clear cell renal cell carcinoma. Oncogene 2004;23:5624-31. (Pubitemid 39093040)
20. Hui Z, Tretiakova M, Zhang Z, Li Y, Wang X, Zhu JX, et al. Radiosensitization by inhibiting STAT1 in renal cell carcinoma. Int J Radiat Oncol Biol Phys 2009;73:288-95.
21. Tang SW, Chang WH, Su YC, Chen YC, Lai YH, Wu PT, et al. MYC pathway is activated in clear cell renal cell carcinoma and essential for proliferation of clear cell renal cell carcinoma cells. Cancer Lett 2009;273:35-43.
22. Rajandram R, Pat BK, Li J, Johnson DW, Gobe GC. Expression of apoptotic tumour necrosis factor receptor-associated factor, caspase recruitment domain and cell death-inducing DFF-45 effector genes in therapy-treated renal cell carcinoma. Nephrology (Carlton) 2009;14:205-12.
23. Hedberg Y, Davoodi E, Roos G, Ljungberg B, Landberg G. Cyclin-D1 expression in human renal-cell carcinoma. Int J Cancer 1999;84: 268-72. (Pubitemid 29256753)
24. Bindra RS, Vasselli JR, Stearman R, Linehan WM, Klausner RD. VHLmediated hypoxia regulation of cyclin D1 in renal carcinoma cells. Cancer Res 2002;62:3014-9. (Pubitemid 34602387)
25. Atkins DJ, Gingert C, Justenhoven C, Schmahl GE, Bonato MS, Brauch H, et al. Concomitant deregulation of HIF1alpha and cell cycle proteins in VHL-mutated renal cell carcinomas. Virchows Arch 2005;447:634-42. (Pubitemid 41291636)
26. Choi JS, Kim MK, Seo JW, Choi YL, Kim DH, Chun YK, et al. MET expression in sporadic renal cell carcinomas. J Korean Med Sci 2006;21:672-7.
27. Morris MR, Gentle D, Abdulrahman M, Clarke N, Brown M, Kishida T, et al. Functional epigenomics approach to identify methylated candidate tumour suppressor genes in renal cell carcinoma. Br J Cancer 2008;98:496-501. (Pubitemid 351161264)
28. Krishnamachary B, Zagzag D, Nagasawa H, Rainey K, Okuyama H, Baek JH, et al. Hypoxia-inducible factor-1-dependent repression of E-cadherin in von Hippel-Lindau tumor suppressor-null renal cell carcinoma mediated by TCF3, ZFHX1A, and ZFHX1B. Cancer Res 2006;66:2725-31.
29. Haitel A, Wiener HG, Neudert B, Marberger M, Susani M. Expression of the cell cycle proteins p21, p27, and pRb in clear cell renal cell carcinoma and their prognostic significance. Urology 2001;58:477-81. (Pubitemid 32816374)
30. Struckmann K, Schraml P, Simon R, Elmenhorst K, Mirlacher M, Kononen J, et al. Impaired expression of the cell cycle regulator BTG2 is common in clear cell renal cell carcinoma. Cancer Res 2004;64:1632-8. (Pubitemid 38428683)
31. Yang FG, Zhang ZW, Xin DQ, Shi CJ, Wu JP, Guo YL, et al. Peroxisome proliferator-activated receptor gamma ligands induce cell cycle arrest and apoptosis in human renal carcinoma cell lines. Acta Pharmacol Sin 2005;26:753-61.