Using MEMo to discover mutual exclusivity modules in cancer

Current Protocols in Bioinformatics

Volumn , Issue SUPPL.41, 2013, Pages

  Ciriello, Giovanni ^a   Cerami, Ethan ^a   Aksoy, Bulent Arman ^a   Sander, Chris ^a   Schultz, Nikolaus ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

Cancer genomics; Mutual exclusivity; Network modules

Indexed keywords

CYCLIN DEPENDENT KINASE 2; PROTEIN P53;

ARTICLE; COMPUTER PROGRAM; COPY NUMBER VARIATION; GENE AMPLIFICATION; GENE DELETION; GENE MUTATION; GENOMICS; HEMIZYGOSITY; HOMOZYGOSITY; HUMAN; MEDICAL INFORMATION SYSTEM; MUTUAL EXCLUSIVITY MODULE IN CANCER; NEOPLASM; PRIORITY JOURNAL; SOMATIC MUTATION;

EID: 84883407913     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi0817s41     Document Type: Article

References (10)

1. Bell, D., Berchuck, A., Birrer, M., Chien, J., Cramer, D.W., Dao, F., Dhir, R., DiSaia, P., Gabra, H., Glenn, P., et al. 2011. Integrated genomic analyses of ovarian carcinoma. Nature 474:609-615.
2. Beroukhim, R., Getz, G.,Nghiemphu, L., Barretina, J., Hsueh, T., Linhart, D., Vivanco, I., Lee, J.C., Huang, J.H., Alexander, S., Du, J., Kau, T., Thomas, R.K., Shah, K., Soto, H., Perner, S., Prensner, J., Debiasi, R.M., Demichelis, F., Hatton, C., Rubin, M.A., Garraway, L.A., Nelson, S.F., Liau, L.,Mischel, P.S., Cloughesy, T.F., Meyerson, M., Golub, T.A., Lander, E.S., Mellinghoff, I.K., and Sellers, W.R. 2007. Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma. Proc.Natl. Acad. Sci.U.S.A. 104:20007- 20012.
3. Ciriello, G., Cerami, E., Sander, C., and Schultz, N. 2012. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. 22:398-406.
4. Dees, N.D., Zhang, Q., Kandoth, C., Wendl, M.C., Schierding, W., Koboldt, D.C., Mooney, T.B., Callaway, M.B., Dooling, D., Mardis, E.R., Wilson, R.K., and Ding, L. 2012. MuSiC: Identifying mutational significance in cancer genomes. Genome Res. 22:1589-1598.
5. Getz, G., Hofling, H., Mesirov, J.P., Golub, T.R., Meyerson, M., Tibshirani, R., and Lander, E.S. 2007. Comment on "The consensus coding sequences of human breast and colorectal cancers". Science 317:1500.
6. Taylor, B.S., Barretina, J., Socci, N.D., Decarolis, P., Ladanyi, M., Meyerson, M., Singer, S., and Sander, C. 2008. Functional copy-number alterations in cancer. PLoS One 3:e3179.
7. TCGA. 2008. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455:1061-1068.
8. TCGA. 2011. Integrated genomic analyses of ovarian carcinoma. Nature 474:609-615.
9. TCGA. 2012a. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487:330-337.
10. TCGA. 2012b. Comprehensive molecular portraits of human breast tumours. Nature 490:61-70.