Gene expression profile analysis of colorectal cancer to investigate potential mechanisms using bioinformatics

OncoTargets and Therapy

Volumn 8, Issue , 2015, Pages 745-752

  Kou, Yubin ^a,b   Zhang, Suya ^c   Chen, Xiaoping ^b   Hu, Sanyuan ^a  

^a SHANDONG UNIVERSITY   (China)

^b Department of General Surgery ^*  (China)

^c Department of Ophthalmology   (China)

Author keywords

Enrichment analysis; Molecular mechanisms; Network module

Indexed keywords

CYTOCHROME P450 2B6; FN1 PROTEIN; PPP1CC PROTEIN; PROTEIN; PROTEIN FOS; RNA; UNCLASSIFIED DRUG;

ALZHEIMER DISEASE; ARTICLE; BIOINFORMATICS; CALCIUM SIGNALING; COLON MUCOSA; COLORECTAL CANCER; COMPUTER PROGRAM; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE ONTOLOGY; HUMAN; MOLECULAR MECHANICS; OXIDATIVE PHOSPHORYLATION; OXIDATIVE STRESS; PARKINSON DISEASE; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; SCORING SYSTEM; STUDENT T TEST; UPREGULATION;

EID: 84929448705     PISSN: 11786930     EISSN: 11786930     Source Type: Journal    
DOI: 10.2147/OTT.S78974     Document Type: Article

References (33)

1. Goel A, Boland CR. Recent insights into the pathogenesis of colorectal cancer. Curr Opin Gastroenterol. 2010;26(1):47–52.
2. Zauber AG, Winawer SJ, O’Brien MJ, et al. Colonoscopic polypectomy and long-term prevention of colorectal-cancer deaths. N Engl J Med. 2012;366(8):687–696.
3. Atkin WS, Edwards R, Kralj-Hans I, et al; UK Flexible Sigmoidoscopy Trial Investigators. Once-only flexible sigmoidoscopy screening in prevention of colorectal cancer: a multicentre randomised controlled trial. Lancet. 2010;375(9726):1624–1633.
4. Rutter CM, Johnson E, Miglioretti DL, Mandelson MT, Inadomi J, Buist DS. Adverse events after screening and follow-up colonoscopy. Cancer Causes Control. 2012;23(2):289–296.
5. Liu Y, Zhou Y, Feng X, et al. Low expression of microRNA-126 is associated with poor prognosis in colorectal cancer. Genes Chromosomes Cancer. 2014;53(4):358–365.
6. Xu L, Li M, Wang M, Yan D, Feng G, An G. The expression of microRNA-375 in plasma and tissue is matched in human colorectal cancer. BMC Cancer. 2014;14:714.
7. Aziz MA, Periyasamy S, Al Yousef Z, et al. Integrated exon level expression analysis of driver genes explain their role in colorectal cancer. PLoS One. 2014;9(10):e110134.
8. Kumar A, Rajendran V, Sethumadhavan R, Purohit R. Evidence of colorectal cancer-associated mutation in MCAK: a computational report. Cell Biochem Biophys. 2013;67(3):837–851.
9. Arthur JC, Gharaibeh RZ, Mühlbauer M, et al. Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer. Nat Commun. 2014;5:4724.
10. Liu YJ, Zhang S, Hou K, et al. Analysis of key genes and pathways associated with colorectal cancer with microarray technology. Asian Pac J Cancer Prev. 2013;14(3):1819–1823.
11. Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets – update. Nucleic Acids Res. 2013;41(Database issue):D991–D995.
12. Hong Y, Ho KS, Eu KW, Cheah PY. A susceptibility gene set for early onset colorectal cancer that integrates diverse signaling pathways: implication for tumorigenesis. Clin Cancer Res. 2007;13(4):1107–1114.
13. Gautier L, Cope L, Bolstad BM, Irizarry RA. Affy – analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004;20(3):307–315.
14. Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2):249–264.
15. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological). 1995;57(1):289–300.
16. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
17. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25–29.
18. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003;31(1):258–261.
19. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431–432.
20. Rhrissorrakrai K, Gunsalus KC. MINE: Module Identification in Networks. BMC Bioinformatics. 2011;12:192.
21. Ely HA, Mellon PL, Coss D. GnRH induces the c-Fos gene via phosphorylation of SRF by the calcium/calmodulin kinase II pathway. Mol Endocrinol. 2011;25(4):669–680.
22. Milde-Langosch K. The Fos family of transcription factors and their role in tumourigenesis. Eur J Cancer. 2005;41(16):2449–2461.
23. Vial E, Sahai E, Marshall CJ. ERK-MAPK signaling coordinately regulates activity of Rac1 and RhoA for tumor cell motility. Cancer Cell. 2003;4(1):67–79.
24. White ES, Muro AF. Fibronectin splice variants: understanding their multiple roles in health and disease using engineered mouse models. IUBMB Life. 2011;63(7):538–546.
25. Gulubova M, Vlaykova T. Immunohistochemical assessment of fibronectin and tenascin and their integrin receptors alpha5beta1 and alpha9beta1 in gastric and colorectal cancers with lymph node and liver metastases. Acta Histochem. 2006;108(1):25–35.
26. Hanamura N, Yoshida T, Matsumoto E, Kawarada Y, Sakakura T. Expression of fibronectin and tenascin-C mRNA by myofibroblasts, vascular cells and epithelial cells in human colon adenomas and carcinomas. Int J Cancer. 1997;73(1):10–15.
27. Gardina PJ, Clark TA, Shimada B, et al. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics. 2006;7:325.
28. Vineetha S, Chandra Shekara Bhat C, Idicula SM. Gene regulatory network from microarray data of colon cancer patients using TSK-type recurrent neural fuzzy network. Gene. 2012;506(2):408–416.
29. Lee JH, Lee JS, Kim SE, et al. Tautomycetin inhibits growth of colorectal cancer cells through p21cip/WAF1 induction via the extracellular signal-regulated kinase pathway. Mol Cancer Ther. 2006;5(12):3222–3231.
30. Guengerich FP, Shimada T. Activation of procarcinogens by human cytochrome P450 enzymes. Mutat Res. 1998;400(1–2):201–213.
31. Kumarakulasingham M, Rooney PH, Dundas SR, et al. Cytochrome p450 profile of colorectal cancer: identification of markers of prognosis. Clin Cancer Res. 2005;11(10):3758–3765.
32. Windmill KF, McKinnon RA, Zhu X, Gaedigk A, Grant DM, McManus ME. The role of xenobiotic metabolizing enzymes in arylamine toxicity and carcinogenesis: functional and localization studies. Mutat Res. 1997;376(1–2):153–160.
33. Bethke L, Webb E, Sellick G, et al. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. BMC Cancer. 2007;7:123.