Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data

Bioinformatics

Volumn 31, Issue 22, 2015, Pages 3561-3568

  Kumar, Runjun D ^a,b   Searleman, Adam C ^a   Swamidass, S Joshua ^a,b   Griffith, Obi L ^a   Bose, Ron ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AREA UNDER THE CURVE; BIOLOGICAL MODEL; DNA SEQUENCE; GENETIC DATABASE; GENETICS; HUMAN; HUMAN GENOME; MUTATION; NEOPLASM; ONCOGENE; PROCEDURES; QUALITY CONTROL; RECEIVER OPERATING CHARACTERISTIC; REPRODUCIBILITY; STATISTICS; TUMOR SUPPRESSOR GENE;

AREA UNDER CURVE; DATABASES, GENETIC; GENES, TUMOR SUPPRESSOR; GENOME, HUMAN; HUMANS; MODELS, GENETIC; MUTATION; NEOPLASMS; ONCOGENES; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; ROC CURVE; SEQUENCE ANALYSIS, DNA; STATISTICS AS TOPIC;

EID: 84947775837     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv430     Document Type: Article

References (31)

1. Bose,R. et al. (2013) Activating HER2 mutations in HER2 gene amplification negative breast Cancer. Cancer Discov., 3, 224-237.
2. Breiman,L. (2001) Random forests. Mach. Learn., 45, 5-32.
3. Cai,Y. et al. (2014) The NuRD complex cooperates with DNMTs to maintain silencing of key colorectal tumor suppressor genes. Oncogene, 33, 2157-2168.
4. Carter,H. et al. (2013) Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics, 14(Suppl 3), S3.
5. Davoli,T. et al. (2013) Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell, 155, 948-962.
6. Dees,N.D. et al. (2012) MuSiC: identifying mutational significance in cancer genomes. Genome Res., 22, 1589-1598.
7. DeLong,E.R. et al. (1988) Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics, 44, 837-845.
8. Fujita,P.A. et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
9. Futreal,P.A. et al. (2004) A census of human cancer genes, Nat. Rev. Cancer, 4, 177-183.
10. Gonzalez-Perez,A. and Lopez-Bigas,N. (2012) Functional impact bias reveals cancer drivers, Nucleic Acids Res., 40, e169.
11. Griffith,M. et al. (2013) DGIdb: mining the druggable genome, Nat. Methods, 10, 1209-1210.
12. Hanahan,D. and Weinberg,R.A. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674.
13. Hua,X. et al. (2013) DrGaP: a powerful tool for identifying driver genes and pathways in cancer sequencing studies. Am. J. Human Genet., 93, 439-451.
14. Kandoth,C. et al. (2013) Mutational landscape and significance across 12 major cancer types. Nature, 502, 333-339.
15. Kato,U. et al. (2013) Role for phospholipid flippase complex of ATP8A1 and CDC50A proteins in cell migration. J. Biol. Chem., 288, 4922-4934.
16. Lawrence,M.S. et al. (2014) Discovery and saturation analysis of cancer genes across 21 tumour types. Nature, 505, 495-501.
17. Lawrence,M.S. et al. (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature, 499, 214-218.
18. Ley,T.J. et al. (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456, 66-72.
19. Nagarajan,P. et al. (2009) Role of chromodomain helicase DNA-binding protein 2 in DNA damage response signaling and tumorigenesis. Oncogene, 28, 1053-1062.
20. Reimand,J. and Bader,G.D. (2013) Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol. Syst. Biol., 9, 637.
21. Schroeder,M.P. et al. (2014) OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action. Bioinformatics, 30, i549-i555.
22. Simonetti,F.L. et al. (2014) Kin-Driver: a database of driver mutations in protein kinases. Database (Oxford), 2014, bau104.
23. Sutherland,L.C., et al. (2010) RBM5 as a putative tumor suppressor gene for lung cancer. J. Thorac. Oncol., 5, 294-298.
24. Tamborero,D. et al. (2013) OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics, 29, 2238-2244.
25. Tamborero,D. et al. (2013) Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci. Rep., 3, 2650.
26. Towhid,S.T. et al. (2013) Inhibition of colonic tumor growth by the selective SGK inhibitor EMD638683. Cell. Physiol. Biochem., 32, 838-848.
27. Vogelstein,B. et al. (2013) Cancer genome landscapes. Science, 339, 1546-1558.
28. Wang,K. et al. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res., 38, e164-e164.
29. Youn,A. and Simon,R. (2011) Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics, 27, 175-181.
30. Zhang,J. et al. (2002) The N-CoR-HDAC3 nuclear receptor corepressor complex inhibits the JNK pathway through the integral subunit GPS2. Mol. Cell, 9, 611-623.
31. Zhao,M. et al. (2013) TSGene: a web resource for tumor suppressor genes, Nucleic Acids Res., 41, D970-D976.