Finding driver pathways in cancer: models and algorithms

Sjoblom T: The consensus coding sequences of human breast and colorectal cancers. Science. 2006, 314: 268-274. 10.1126/science.1133427

Ding L: Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008, 455: 1069-1075. 10.1038/nature07423

Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008, 455 (7216): 1061-1068. 10.1038/nature07385

Getz G, Hofling H, Mesirov JP, Golub TR, Meyerson M, Tibshirani R, Lander ES: Comment on “The consensus coding sequences of human breast and colorectal cancers”. Science. 2007, 317: 1500.

Hahn WC, Weinberg RA: Modelling the molecular circuitry of cancer. Nat Rev Cancer. 2002, 2: 331-341. 10.1038/nrc795

Vogelstein B, Kinzler KW: Cancer genes and the pathways they control. Nat Med. 2004, 10: 789-799. 10.1038/nm1087

Efroni S, Ben-Hamo R, Edmonson M, Greenblum S, Schaefer CF, Buetow KH: Detecting cancer gene networks characterized by recurrent genomic alterations in a population. PLoS ONE. 2011, 6: e14437. 10.1371/journal.pone.0014437

Boca SM, Kinzler KW, Velculescu VE, Vogelstein B, Parmigiani G: Patient-oriented gene set analysis for cancer mutation data. Genome Biol. 2010, 11: R112. 10.1186/gb-2010-11-11-r112

Cerami E, Demir E, Schultz N, Taylor BS, Sander C: Automated network analysis identifies core pathways in glioblastoma. PLoS ONE. 2010, 5: e8918. 10.1371/journal.pone.0008918

Vandin F, Upfal E, Raphael BJ: Algorithms for detecting significantly mutated pathways in cancer. J Comput Biol. 2011, 18: 507-522. 10.1089/cmb.2010.0265

Vandin F, Upfal E, Raphael BJ: De novo discovery of mutated driver pathways in cancer. Genome Res. 2012, 22 (2): 375-385. 10.1101/gr.120477.111

McCormick F: Signalling networks that cause cancer. Trends Cell Biol. 1999, 9: M53-M56. 10.1016/S0962-8924(99)01668-2

Yeang C, McCormick F, Levine A: Combinatorial patterns of somatic gene mutations in cancer. FASEB J. 2008, 22 (8): 2605-2622. 10.1096/fj.08-108985

Varela I: Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature. 2011, 469: 539-542. 10.1038/nature09639

Deguchi K, Gilliland DG: Cooperativity between mutations in tyrosine kinases and in hematopoietic transcription factors in AML. Leukemia. 2002, 16: 740-744. 10.1038/sj.leu.2402500

Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE: The consensus coding sequences of human breast and colorectal cancers. Science. 2006, 314: 268-274. 10.1126/science.1133427

Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, : Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008, 321: 1801-1806. 10.1126/science.1164368

Benjamini Y, Hochberg Y: Controlling the false discovery rate. J R Stat Soc. 1995, 57: 289-300.

Mitzenmacher M, Upfal E: Probability and Computing: Randomized Algorithms and Probabilistic Analysis. New York: Cambridge University Press, 2005.

Parmigiani G: Response to Comments on “The Consensus Coding Sequences of Human Breast and Colorectal Cancers”. Science. 2007, 317 (5844): 1500.

Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K: Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008, 455: 1069-1075. 10.1038/nature07423

Thomas RK, Baker AC, Debiasi RM, Winckler W, Laframboise T, Lin WM, Wang M, Feng W, Zander T, MacConaill L, Macconnaill LE, Lee JC, Nicoletti R, Hatton C, Goyette M, Girard L, Majmudar K, Ziaugra L, Wong KK, Gabriel S, Beroukhim R, Peyton M, Barretina J, Dutt A, Emery C, Greulich H, Shah K, Sasaki H, Gazdar A, Minna J: High-throughput oncogene mutation profiling in human cancer. Nat Genet. 2007, 39: 347-351. 10.1038/ng1975