Genes associated with genotype-specific DNA methylation in squamous cell carcinoma as candidate drug targets

BMC Systems Biology

Volumn 8, Issue 1, 2014, Pages

  Kinoshita, Ryoichi ^a   Iwadate, Mitsuo ^a   Umeyama, Hideaki ^a   Taguchi, Y h ^a  

^a CHUO UNIVERSITY   (Japan)

Author keywords

Cancer; DNA methylation; Gene selection; Genotype; in silico drug discovery; Principal component analysis; Protein tertiary structure

Indexed keywords

ARTICLE; BIOLOGY; DNA METHYLATION; DNA MICROARRAY; ESOPHAGUS TUMOR; GENETICS; GENOTYPE; HUMAN; MOLECULARLY TARGETED THERAPY; SINGLE NUCLEOTIDE POLYMORPHISM; SQUAMOUS CELL CARCINOMA; TUMOR GENE;

CARCINOMA, SQUAMOUS CELL; COMPUTATIONAL BIOLOGY; DNA METHYLATION; ESOPHAGEAL NEOPLASMS; GENES, NEOPLASM; GENOTYPE; HUMANS; MOLECULAR TARGETED THERAPY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84904645440     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-8-S1-S4     Document Type: Article

References (29)

1. Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S, Shu J, Chen X, Waterland RA, Issa JP: Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet. 2007, 3 (10): 2023-2036.
2. McCabe MT, Brandes JC, Vertino PM: Cancer DNA methylation: molecular mechanisms and clinical implications. Clin Cancer Res. 2009, 15 (12): 3927-3937. 10.1158/1078-0432.CCR-08-2784.
3. Pasche B, Yi N: Candidate gene association studies: successes and failures. Curr Opin Genet Dev. 2010, 20 (3): 257-261. 10.1016/j.gde.2010.03.006.
4. Zhou W: Mapping genetic alterations in tumors with single nucleotide polymorphisms. Curr Opin Oncol. 2003, 15: 50-54. 10.1097/00001622-200301000-00007.
5. Scherf DB, Sarkisyan N, Jacobsson H, Claus R, Bermejo JL, Peil B, Gu L, Muley T, Meister M, Dienemann H, Plass C, Risch A: Epigenetic screen identifies genotype-specific promoter DNA methylation and oncogenic potential of CHRNB4. Oncogene. 2012
6. Opavsky R, Wang SH, Trikha P, Raval A, Huang Y, Wu YZ, Rodriguez B, Keller B, Liyanarachchi S, Wei G, Davuluri RV, Weinstein M, Felsher D, Ostrowski M, Leone G, Plass C: CpG island methylation in a mouse model of lymphoma is driven by the genetic configuration of tumor cells. PLoS Genet. 2007, 3 (9): 1757-1769.
7. Abnet CC, Wang Z, Song X, Hu N, Zhou FY, Freedman ND, Li XM, Yu K, Shu XO, Yuan JM, Zheng W, Dawsey SM, Liao LM, Lee MP, Ding T, Qiao YL, Gao YT, Koh WP, Xiang YB, Tang ZZ, Fan JH, Chung CC, Wang C, Wheeler W, Yeager M, Yuenger J, Hutchinson A, Jacobs KB, Giffen CA, Burdett L, Fraumeni JF, Tucker MA, Chow WH, Zhao XK, Li JM, Li AL, Sun LD, Wei W, Li JL, Zhang P, Li HL, Cui WY, Wang WP, Liu ZC, Yang X, Fu WJ, Cui JL, Lin HL, Zhu WL, Liu M, Chen X, Chen J, Guo L, Han JJ, Zhou SL, Huang J, Wu Y, Yuan C, Huang J, Ji AF, Kul JW, Fan ZM, Wang JP, Zhang DY, Zhang LQ, Zhang W, Chen YF, Ren JL, Li XM, Dong JC, Xing GL, Guo ZG, Yang JX, Mao YM, Yuan Y, Guo ET, Zhang W, Hou ZC, Liu J, Li Y, Tang S, Chang J, Peng XQ, Han M, Yin WL, Liu YL, Hu YL, Liu Y, Yang LQ, Zhu FG, Yang XF, Feng XS, Wang Z, Li Y, Gao SG, Liu HL, Yuan L, Jin Y, Zhang YR, et al: Genotypic variants at 2q33 and risk of esophageal squamous cell carcinoma in China: a meta-analysis of genome-wide association studies. Hum Mol Genet. 2012, 21 (9): 2132-2141. 10.1093/hmg/dds029.
8. Maeng CH, Lee J, van Hummelen P, Park SH, Palescandolo E, Jang J, Park HY, Kang SY, MacConaill L, Kim KM, Shim YM: High-throughput genotyping in metastatic esophageal squamous cell carcinoma identifies phosphoinositide-3-kinase and BRAF mutations. PLoS ONE. 2012, 7 (8): e41655-10.1371/journal.pone.0041655.
9. Wang Y, Ji R, Wei X, Gu L, Chen L, Rong Y, Wang R, Zhang Z, Liu B, Xia S: Esophageal squamous cell carcinoma and ALDH2 and ADH1B polymorphisms in Chinese females. Asian Pac J Cancer Prev. 2011, 12 (8): 2065-2068.
10. Yang HH, Hu N, Wang C, Ding T, Dunn BK, Goldstein AM, Taylor PR, Lee MP: Influence of genetic background and tissue types on global DNA methylation patterns. PLoS ONE. 2010, 5 (2): e9355-10.1371/journal.pone.0009355.
11. Ishida S, Umeyama H, Iwadate M, Taguchi YH: Bioinformatic screening of autoimmune disease genes and protein structure prediction with FAMS for drug discovery. Protein Pept Lett.
12. Holm S: A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics. 1979, 6 (2): 65-70.
13. Nakazato T, Bono H, Matsuda H, Takagi T: Gendoo: functional profiling of gene and disease features using MeSH vocabulary. Nucleic Acids Res. 2009, 37 (Web Server): W166-169. 10.1093/nar/gkp483.
14. Gendoo. [ http://gendoo.dbcls.jp/ ]
15. Student S, Fujarewicz K: Stable feature selection and classification algorithms for multiclass microarray data. Biol Direct. 2012, 7: 33-10.1186/1745-6150-7-33.
16. R Core Team: R: A Language and Environment for Statistical Computing. 2013, R Foundation for Statistical Computing Vienna, Austria, [ http://www.R-project.org/ ]
17. Tibshirani R: Regression shrinkage and selection via the lasso. Journal of the Royal Statistical Society. Series B (Methodological). 1996, 267-288.
18. FAMS. [ http://fams.bio.chuo-u.ac.jp/fams/ ]
19. Umeyama H, Iwadate M: FAMS and FAMSBASE for protein structure. Curr Protoc Bioinformatics. 2004, Chapter 5: Unit5.2
20. Phyre2. [ http://www.sbg.bio.ic.ac.uk/phyre2/ ]
21. Kelley LA, Sternberg MJ: Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 2009, 4 (3): 363-371. 10.1038/nprot.2009.2.
22. DrugBank. [ http://www.drugbank.ca/ ]
23. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS: DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res. 2011, 39 (Database): D1035-1041. 10.1093/nar/gkq1126.
24. O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR: Open Babel: An open chemical toolbox. J Cheminform. 2011, 3: 33-10.1186/1758-2946-3-33.
25. Takaya D, Takeda-Shitaka M, Terashi G, Kanou K, Iwadate M, Umeyama H: Bioinformatics based Ligand-Docking and in-silico screening. Chem Pharm. Bull. 2008, 56 (5): 742-744. 10.1248/cpb.56.742.
26. 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, 289-300.
27. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000, 28: 235-242. 10.1093/nar/28.1.235.
28. ChEMBL. [ https://www.ebi.ac.uk/chembl/ ]
29. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP: ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 2012, 40 (Database): D1100-1107.