Discovery of co-occurring driver pathways in cancer

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Zhang, Junhua ^a   Wu, Ling Yun ^a   Zhang, Xiang Sun ^a   Zhang, Shihua ^a  

^a CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CARCINOGENESIS; COMPUTER PROGRAM; DISEASE COURSE; GENETICS; HUMAN; METHODOLOGY; MUTATION; NEOPLASM; PATHOLOGY; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ALGORITHMS; CARCINOGENESIS; DISEASE PROGRESSION; HUMANS; MUTATION; NEOPLASMS; SIGNAL TRANSDUCTION; SOFTWARE; SYSTEMS BIOLOGY;

EID: 84905985544     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-271     Document Type: Article

References (56)

1. The Cancer, Genome Atlas Research Network Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061-1068. 10.1038/nature07385, 2671642, 18772890, The Cancer, Genome Atlas Research Network.
2. International Cancer Genome Consortium International network of cancer genome projects. Nature 2010, 464:993-998. 10.1038/nature08987, 2902243, 20393554, International Cancer Genome Consortium.
3. Zhang S, Liu CC, Li W, Shen H, Laird P, Zhou XJ. Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Res 2012, 40:9379-9391. 10.1093/nar/gks725, 3479191, 22879375.
4. Liu Z, Zhang XS, Zhang S. Breast tumour subgroups reveal diverse clinical predictive power. Sci Rep 2014, 4:4002.
5. Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S, O'Meara S, Vastrik I, Schmidt EE, Avis T, Barthorpe S, Bhamra G, Buck G, Choudhury B, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, et al. Patterns of somatic mutation in human cancer genomes. Nature 2007, 446:153-158. 10.1038/nature05610, 2712719, 17344846.
6. Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature 2009, 458:719-724. 10.1038/nature07943, 2821689, 19360079.
7. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S, Du J, Kau T, Thomas RK, Shah K, Soto H, Perner S, Prensner J, Debiasi RM, Demichelis F, Hatton C, Rubin MA, Garraway LA, Nelson SF, Liau L, Mischel PS, Cloughesy TF, Meyerson M, Golub TA, Lander ES, Mellinghoff IK, et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci 2007, 104:20007-20012. 10.1073/pnas.0710052104, 2148413, 18077431.
8. 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, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008, 455:1069-1075. 10.1038/nature07423, 2694412, 18948947.
9. Jones S, Zhang X, Parsons DW, Lin JCH, 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, Hruban RH, et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008, 321:1801-1806. 10.1126/science.1164368, 2848990, 18772397.
10. 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, 3156951, 21092299.
11. 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, 3014942, 21283511.
12. Vogelstein B, Kinzler KW. Cancer genes and the pathways they control. Nat Med 2004, 10:789-799. 10.1038/nm1087, 15286780.
13. Yeang CH, McCormick F, Levine A. Combinatorial patterns of somatic gene mutations in cancer. FASEB J 2008, 22:2605-2622. 10.1096/fj.08-108985, 18434431.
14. Ciriello G, Cerami E, Sander C, Schultz N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 2012, 22:398-406. 10.1101/gr.125567.111, 3266046, 21908773.
15. Miller CA, Settle SH, Sulman EP, Aldape KD, Milosavljevic A. Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors. BMC Med Genomics 2011, 4:34. 10.1186/1755-8794-4-34, 3102606, 21489305.
16. Zhang J, Zhang S, Wang Y, Zhang XS. Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data. BMC Syst Biol 2013, 7:S4.
17. Acharya LR, Judeh T, Duan Z, Rabbat MG, Zhu D. GSGS: a computational approach to reconstruct signaling pathway structures from gene sets. IEEE/ACM Trans Comput Biol Bioinformatics 2012, 9:438-450.
18. Vandin F, Upfal E, Raphael BJ. De novo discovery of mutated driver pathways in cancer. Genome Res 2012, 22:375-385. 10.1101/gr.120477.111, 3266044, 21653252.
19. Zhao J, Zhang S, Wu LY, Zhang XS. Efficient methods for identifying mutated driver pathways in cancer. Bioinformatics 2012, 28:2940-2947. 10.1093/bioinformatics/bts564, 22982574.
20. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011, 144:646-674. 10.1016/j.cell.2011.02.013, 21376230.
21. Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, Yang S, Zhang S, Liu L, Lu M, O'Connor-McCourt M, Purisima EO, Wang E. A map of human cancer signaling. Mol Syst Biol 2007, 3:152. 2174632, 18091723.
22. Klijn C, Bot J, Adams DJ, Reinders M, Wessels L, Jonkers J. Identification of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach. PLoS Comput Biol 2010, 6:e1000631. 10.1371/journal.pcbi.1000631, 2791203, 20052266.
23. Kumar N, Rehrauer H, Cai H, Baudis M. Cdcoca: a statistical method to define complexity dependence of co-occuring chromosomal aberrations. BMC Med Genom 2011, 4:21.
24. Forbes S, Clements J, Dawson E, Bamford S, Webb T, Dogan A, Flanagan A, Teague J, Wooster R, Futreal PA, Stratton MR. COSMIC 2005. Br J Cancer 2006, 94:318-322. 10.1038/sj.bjc.6602928, 2361125, 16421597.
25. Gu Y, Zhao W, Xia J, Zhang Y, Wu R, Wang C, Guo Z. Analysis of pathway mutation profiles highlights collaboration between cancer-associated superpathways. Hum Mutat 2011, 32:1028-1035. 10.1002/humu.21541, 21618647.
26. Gu Y, Wang H, Qin Y, Zhang Y, Zhao W, Qi L, Zhang Y, Wang C, Guo Z. Network analysis of genomic alteration profiles reveals co-altered functional modules and driver genes for glioblastoma. Mol Biosyst 2013, 9:467-477. 10.1039/c2mb25528f, 23344900.
27. Gursky S, Olopade OI, Rowley JD. Identification of a 1.2 Kb cDNA fragment from a region on 9p21 commonly deleted in multiple tumor types. Cancer Genet Cytogenet 2001, 129:93-101. 10.1016/S0165-4608(01)00444-7, 11566337.
28. Christopher SA, Diegelman P, Porter CW, Kruger WD. Methylthioadenosine phosphorylase, a gene frequently codeleted with p16(cdkN2a/ARF), acts as a tumor suppressor in a breast cancer cell line. Cancer Res 2002, 62:6639-6644.
29. Wikman H, Nymark P, Vayrynen A, Jarmalaite S, Kallioniemi A, Salmenkivi K, Vainio-Siukola K, Husgafvel-Pursiainen K, Knuutila S, Wolf M, Anttila S. CDK4 is a probable target gene in a novel amplicon at 12q13.3- q14.1 in lung cancer. Gene Chromosome Cancer 2005, 42:193-199.
30. Mays-Hoopes LL. Aging and cell division. Nat Educ 2010, 3:55.
31. Campisis J. Cancer and ageing: rival demons?. Nat Rev Cancer 2003, 3:339-349. 10.1038/nrc1073, 12724732.
32. Kabbarah O, Chin L. Advances in malignant melanoma: genetic insights from mouse and man. Front Biosci 2006, 11:928-942. 10.2741/1849, 16146783.
33. Rahrmann EP, Watson AL, Keng VW, Choi K, Moriarity BS, Beckmann DA, Wolf NK, Sarver A, Collins MH, Moertel CL, Wallace MR, Gel B, Serra E, Ratner N, Largaespada1 DA. Forward genetic screen for malignant peripheral nerve sheath tumor formation identifies new genes and pathways driving tumorigenesis. Nat Genet 2013, 45:756-766. 10.1038/ng.2641, 3695033, 23685747.
34. Chow LML, Endersby R, Zhu X, Rankin S, Qu C, Zhang J, Broniscer A, Ellison DW, Baker SJ. Cooperativity within and among Pten, p53, and Rb pathways induces high-grade astrocytoma in adult brain. Cancer Cell 2011, 19:305-316. 10.1016/j.ccr.2011.01.039, 3060664, 21397855.
35. Xing F, Persaud Y, Pratilas CA, Taylor BS, Janakiraman M, She QB, Gallardo H, Liu C, Merghoub T, Hefter B, Dolgalev I, Viale A, Heguy A, De Stanchina E, Cobrinik D, Bollag G, Wolchok J, Houghton A, Solit DB. Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring (V600E)BRAF. Oncogene 2012, 31:446-457. 10.1038/onc.2011.250, 3267014, 21725359.
36. Beckner ME, Patil S, LeBlanc JF, Katira K, Nanda A, Martin SS, Brunson LE, Truong LN, Nordberg ML. MLPA and REMBRANDT data predict potential modulation of vitamin D via increased CYP27B1 in aggressive primary brain tumors. Cancer Res 2010, 70(8 Suppl):Abstract 1573.
37. Chau YY, Hastie ND. The role of Wt1 in regulating mesenchyme in cancer, development, and tissue homeostasis. Trends Genet 2012, 28:515-524. 10.1016/j.tig.2012.04.004, 22658804.
38. Kim MKH, McGarry TJ, Broin PO, Flatow JM, Golden AAJ, Licht JD. An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1. Proc Natl Acad Sci 2009, 106:11154-11159. 10.1073/pnas.0901591106, 2708714, 19549856.
39. Chehab NH, Malikzay A, Appel M, Halazonetis TD. Chk2/hCds1 functions as a DNA damage checkpoint in G1 by stabilizing p53. Genes Dev 2000, 14:278-288. 316357, 10673500.
40. Greulich H. The genomics of lung adenocarcinoma: opportunities for targeted therapies. Genes cancer 2010, 1:1200-1210. 10.1177/1947601911407324, 3092285, 21779443.
41. Kesanakurti D, Chetty C, Rajasekhar Maddirela D, Gujrati M, Rao JS. Functional cooperativity by direct interaction between PAK4 and MMP-2 in the regulation of anoikis resistance, migration and invasion in glioma. Cell Death Dis 2012, 3:e445. 10.1038/cddis.2012.182, 3542618, 23254288.
42. Solomon H, Buganim Y, Kogan-Sakin I, Pomeraniec L, Assia Y, Madar S, Goldstein I, Brosh R, Kalo E, Beatus T, Goldfinger N, Rotter V. Various p53 mutant proteins differently regulate the Ras circuit to induce a cancer-related gene signature. J Cell Sci 2012, 125:3144-3152. 10.1242/jcs.099663, 22427690.
43. Kosaka T, Yatabe Y, Onozato R, Kuwano H, Mitsudomi T. Prognostic implication of EGFR, KRAS, and TP53 gene mutations in a large cohort of Japanese patients with surgically treated lung adenocarcinoma. J Thorac Oncol 2009, 4:22-29. 10.1097/JTO.0b013e3181914111, 19096302.
44. Leeper NJ, Raiesdana A, Kojima Y, Kundu RK, Cheng H, Maegdefessel L, Toh R, Ahn GO, Ali ZA, Anderson DR, Miller CL, Roberts SC, Spin JM, de Almeida PE, Wu JC, Xu B, Cheng K, Quertermous M, Kundu S, Kortekaas KE, Berzin E, Downing KP, Dalman RL, Tsao PS, Schadt EE, Owens GK, Quertermous T. Loss of CDKN2B promotes p53-dependent smooth muscle cell apoptosis and aneurysm formation. Arterioscler Thromb Vasc Biol 2013, 33:e1-e10. 10.1161/ATVBAHA.112.300399, 3569043, 23162013.
45. Sera¨o NVL, Delfino KR, Southey BR, Beever JE, Rodriguez-Zas SL. Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival. BMC Med Genomics 2011, 4:49. 10.1186/1755-8794-4-49, 3127972, 21649900.
46. The Cancer Genome Atlas Research Network Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474:609-615. 10.1038/nature10166, 3163504, 21720365, The Cancer Genome Atlas Research Network.
47. Plisiecka-Halasa J, Karpinska G, Szymanska T, Ziolkowska I, Madry R, Timorek A, Debniak J, Ulanska M, Jedryka M, Chudecka-Glaz A, Klimek M, Rembiszewska A, Kraszewska E, Dybowski B, Markowska J, Emerich J, Pluzanska A, Goluda M, Rzepka-Gorska I, Urbanski K, Zielinski J, Stelmachow J, Chrabowska M, Kupryjanczyk J. P21WAF1,P27KIP1, TP53 and C-MYC analysis in 204 ovarian carcinomas treated with platinum-based regimens. Ann Oncol 2003, 14:1078-1085. 10.1093/annonc/mdg299, 12853350.
48. Yeung SJ, Pan J, Lee MH. Roles of p53, Myc and HIF-1 in regulating glycolysis - the seventh hallmark of cancer. Cell Mol Life Sci 2008, 65:3981-3999. 10.1007/s00018-008-8224-x, 18766298.
49. Calcagno DQ, Freitas VM, Leal MF, de Souza CRT, Demachki S, Montenegro R, Assumpcao PP, Khayat AS, Smith MAC, dos Santos AKCR, Burbano RR MYC, FBXW7 andTP53 copy number variation and expression in Gastric Cancer. BMC Gastroenterol 2013, 13:141. 10.1186/1471-230X-13-141, 3851138, 24053468, Burbano RR.
50. Kuhn E, Wu RC, Guan B, Wu G, Zhang J, Wang Y, Song L, Yuan X, Wei L, Roden RBS, Kuo KT, Nakayama K, Clarke B, Shaw P, Olvera N, Kurman RJ, Levine DA, Wang TL, Shih IM. Identification of molecular pathway aberrations in uterine serous carcinoma by genome-wide analyses. J Natl Cancer Inst 2012, 104:1503-1513. 10.1093/jnci/djs345, 3692380, 22923510.
51. de Molina AR, Gallego-Ortega D, Sarmentero-Estrada J, Lagares D, del Pulgar TG, Eva Bandre´s E, Garci´a-Foncillas J, Lacal JC. Choline kinase as a link connecting phospholipid metabolism and cell cycle regulation: Implications in cancer therapy. Int J Biochem Cell Biol 2008, 40:1753-1763. 10.1016/j.biocel.2008.01.013, 18296102.
52. Sangha N, Wu R, Kuick R, Powers S, Mu D, Fiander D, Yuen K, Katabuchi H, Tashiro H, Fearon ER, Cho KR. Neurofibromin 1 (NF1) defects are common in human ovarian serous carcinomas and co-occur with TP53 mutations. Neoplasia 2008, 10:1362-1372. 2586687, 19048115.
53. Zhang J, Shi Y, Lalonde E, Li L, Cavallone L, Ferenczy A, Gotlieb WH, Foulkes WD, Majewski J. Exome profiling of primary, metastatic and recurrent ovarian carcinomas in a BRCA1-positive patient. BMC Cancer 2013, 13:146. 10.1186/1471-2407-13-146, 3614563, 23522120.
54. Kalev P, Simicek M, Vazquez I, Munck S, Chen L, Soin T, Danda N, Chen W, Sablina A. Loss of PPP2R2A inhibits homologous recombination DNA repair and predicts tumor sensitivity to PARP inhibition. Cancer Res 2012, 72:6414-6424. 10.1158/0008-5472.CAN-12-1667, 23087057.
55. Youn A, Simon R. Using passenger mutations to estimate the timing of driver mutations and identify mutator alterations. BMC Bioinformatics 2013, 14:363. 10.1186/1471-2105-14-363, 3903072, 24330428.
56. Leiserson MDM, Blokh D, Sharan R, Raphael BJ. Simultaneous identification of multiple driver pathways in cancer. PLoS Comput Biol 2013, 9:e1003054. 10.1371/journal.pcbi.1003054, 3662702, 23717195.