Correction: Inferring the temporal order of cancer gene mutations in individual tumor samples (PLoS ONE (2014) 9, 2 (e89244) DOI: 10.1371/journal.pone.0089244);Inferring the temporal order of cancer gene mutations in individual tumor samples

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Guo, Jun ^a   Guo, Hanliang ^b   Wang, Zhanyi ^c  

^a BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

^b University of Southern California ^*  (United States)

^c China Mobile Research Institute   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ONCOPROTEIN; TUMOR SUPPRESSOR PROTEIN;

APOPTOSIS; ARTICLE; GENE FREQUENCY; GENE FUNCTION; GENE MAPPING; GENE MUTATION; GENETIC REGULATION; HUMAN; MUTATIONAL ANALYSIS; ONCOGENE; POINT MUTATION; SEQUENCE ANALYSIS; SOLID TUMOR; SOMATIC MUTATION; TUMOR SUPPRESSOR GENE;

ALGORITHMS; GENE REGULATORY NETWORKS; GENES, TUMOR SUPPRESSOR; HUMANS; MODELS, BIOLOGICAL; MUTATION; NEOPLASMS; NEURAL NETWORKS (COMPUTER); ONCOGENES;

EID: 84896332517     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0098676     Document Type: Erratum

References (39)

1. Vogelstein B, Kinzler KW (2004) Cancer genes and the pathways they control. Nat. Med. 10: 789-799. (Pubitemid 39070849)
2. Nowell PC (2002) Tumor progression: a brief historical perspective. Semin. Cancer Biol. 12: 261-266.
3. Schaub FX, Looser R, Li S, Shen HH, Lehmann T, et al. (2010) Clonal analysis of TET2 and JAK2 mutations suggests that TET2 can be a late event in the progression of myeloproliferative neoplasms. Blood 115: 2003-2007.
4. V617F/TET2 mutations: does the order matter? Haematologica 96: 638-640.
5. Ding L, Ellis MJ, Li S, Larson DE, Chen K, et al. (2010) Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464: 999-1005.
6. Notta F, Mullighan CM, Wang CY, Poeppl A, Doulatov S, et al. (2011) Evolution of human BCR-ABL1 lymphoblastic leukaemia-initiating cells. Nature 469: 362-367.
7. Harbour JW, Onken MD, Roberson EDO, Duan S, Gao L, et al. (2010) Frequent Mutation of BAP1 in Metastasizing Uveal Melanomas. Science 330: 1410-1413.
8. Fearon E, Vogelstein BA (1990) Genetic model for colorectal tumorigenesis. Cell 61: 759-767.
9. Attolini CS, Cheng YK, Beroukhim R, Getz G, Wahab OA, et al. (2010) A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc. Natl. Acad. Sci. USA 107: 17604-17609.
10. Gerstung M, Eriksson N, Lin J, Vogelstein B, Beerenwinkel N (2011) The Temporal Order of Genetic and Pathway Alterations in Tumorigenesis. PLoS ONE 6(11): e27136. doi:10.1371/journal.pone.0027136.
11. Sprouffske K, Pepper JW, Maley CC (2011) Accurate reconstruction of the temporal order of mutations in neoplastic progression. Cancer Prev Res 4: 1135-1144.
12. Gilad G, Nabet BY, Ragland RL, Schoppy DW, Smith KD, et al. (2010) Combining ATR Suppression with Oncogenic Ras Synergistically Increases Genomic Instability, Causing Synthetic Lethality or Tumorigenesis in a Dosage-Dependent Manner. Cancer Res. 70: 9693-9702.
13. Halazonetis TD, Gorgoulis VG, Bartek J (2008) An Oncogene-Induced DNA Damage Model for Cancer Development. Science 319: 1352-1355. (Pubitemid 351354863)
14. Krejci L, Altmannova V, Spirek M, Zhao X (2012) Homologous recombination and its regulation. Nucleic Acids Res 30: 1-24.
15. Westermark UK, Lindberg N, Roswall P, Brazater D, Helgadottir HR, et al. (2011) RAD51 can inhibit PDGF-B-induced gliomagenesis and genomic instability. Neuro Oncol 13: 1277-1287.
16. Haffner MC, Marzo AMD, Meeker AK, Nelson WG, Yegnasubramanian S (2011) Transcription-Induced DNA Double Strand Breaks: Both Oncogenic Force and Potential Therapeutic Target? Clin Cancer Res 17: 3858-3864.
17. Verhaak RGW, Goudwaard CS, Putten W, Bijl Ma, Sanders MA, et al. (2005) Mutations in nucleophosmin (NPM1) in acute myeloid leukemia (AML): association with other gene abnormalities and previously established gene expression signatures and their favorable prognostic significance. Blood 106: 3747-3754. (Pubitemid 41739008)
18. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, et al. (2008) Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455: 1069-1075.
19. Guo J, Guo H, Wang Z (2011) An Activation Force-based Affinity Measure for Analyzing Complex Networks. Sci. Rep. 1: 113; DOI:10.1038/srep00113.
20. Barzel B, Barabasi A (2013) Network link prediction by global Silencing of indirect correlations. Nat. Biotechnol. 31: 720-725.
21. Feizi S, Marbach D, Medard M, Kellies M (2013) Network deconvolution as a general method to distinguish direct dependencies in networks. Nat. Biotechnol. 31: 726-733.
22. Palla G, Derenyi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435: 814-818. (Pubitemid 40839731)
23. Ahn YY, Bagrow JP, Lehmann S (2010) Link communities reveal multiscale complexity in networks. Nature 466: 761-764.
24. Rual JF, Venkatesan K, Hao T, Kishikawa TH, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178. (Pubitemid 41509356)
25. Bamford S, Dawson E, Forbes S, Clements J, Pettet R, et al. (2004) The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer 91: 355-358. (Pubitemid 39037083)
26. Forbes S, Clements J, Dawson E, Bamford S, Webb T, et al. (2006) COSMIC 2005. Br J Cancer 94: 318-322. (Pubitemid 43151554)
27. Vogelstein B, Lane D, Levine AJ (2000) Surfing the p53 network. Nature 408: 307-310.
28. Albert R, Jeong H, Balabasi AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382. (Pubitemid 30625551)
29. Dhillon A, Hagan S, Rath O, Kolch W (2007) MAP kinase signalling pathways in cancer. Oncogene 26: 3279-3290. (Pubitemid 46763021)
30. Kinzler KW, Vogelstein B (1996) Lessons from Hereditary Colorectal Cancer. Cell 87: 159-170. (Pubitemid 26358996)
31. Hsieh JS, Lin SR, Chang MY, Chen FM, Lu CY, et al. (2005) APC, K-ras, and p53 gene mutations in colorectal cancer patients: correlation to clinicopathologic features and postoperative surveillance. Am Surg. 71(4): 336-43.
32. Martins FC, De S, Almendro V, Gonen M, Park SY, et al. (2012) Evolutionary Pathways in BRCA1-Associated Breast Tumors. Cancer Discov. 2: 503-511.
33. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100: 57-70. (Pubitemid 30046295)
34. Hanahan D, Weinberg RA (2011) Hallmarks of Cancer: The Next Generation. Cell 144: 646-674.
35. Morin PJ, Vogelstein B, Kinzler KW (1996) Apoptosis and APC in colorectal tumorigenesis. Proc. Natl. Acad. Sci. USA 93: 7950-7954. (Pubitemid 26277145)
36. Chen T, Yang I, Irby R, Shain KH, Wang HG, et al. (2003) Regulation of Caspase Expression and Apoptosis by Adenomatous Polyposis Coli. Cancer Res. 63: 4368-4374. (Pubitemid 36951005)
37. Lindstrom MS (2011) NPM1/B23: a multifunctional chaperone in ribosome biogenesis and chromatin remodeling. Biochem Res Int 2011.
38. Herranz H, Xin HX, Cohen SM (2012) Mutual Repression by Bantam miRNA and Capicua Links the EGFR/MAPK and Hippo Pathways in Growth Control. Current Biology 22: 651-657.
39. Adams JM, Cory S (2007) The Bcl-2 apoptotic switch in cancer development and therapy. Oncogene 26: 1324-1337. (Pubitemid 46328466)