Vandin F, Upfal E, Raphael BJ. De novo discovery of mutated driver pathways in cancer. Genome Res. 2011.
Mclendon R, et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455(7216):1061–8.
Article ADS CAS Google Scholar
Bobrow M, Zhao S. International network of cancer genome projects. Nature. 2010;464(7291):993–8.
Article ADS PubMed Google Scholar
Peng J, Xue H, Shao Y, Shang X, Wang Y, Chen J. A novel method to measure the semantic similarity of hpo terms. Int J Data Min Bioinform. 2017;17(2):173–88.
Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature. 2009;458(7239):719–24.
Article ADS CAS PubMed PubMed Central Google Scholar
Bashashati A, et al. DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol. 2012;13(12):1–14.
Shi K, Gao L, Wang B. Discovering potential cancer driver genes by an integrated network-based approach. Mol BioSyst. 2016;12(9):2921–31.
Article CAS PubMed Google Scholar
Tian R, Basu MK, Capriotti E. ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples. Bioinformatics. 2014;30(17):i572–8.
Article CAS PubMed PubMed Central Google Scholar
Dees ND, et al. MuSiC: identifying mutational significance in cancer genomes. Genome Res. 2012;22(8):1589–98.
Article CAS PubMed PubMed Central Google Scholar
Lawrence MS, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499(7457):214–8.
Article ADS CAS PubMed PubMed Central Google Scholar
Ding L, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008;455(7216):1069–75.
Article ADS CAS PubMed PubMed Central Google Scholar
Pon JR, Marra MA. Driver and passenger mutations in cancer. Annu Rev Pathol. 2015;10:25–50.
Article CAS PubMed Google Scholar
Wendl MC, et al. PathScan: a tool for discerning mutational significance in groups of putative cancer genes. Bioinformatics. 2011;27(12):1595–602.
Article CAS PubMed PubMed Central Google Scholar
Youn A, Simon R. Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics. 2011;27(2):175–81.
Article CAS PubMed Google Scholar
Gatza ML, Silva GO, Parker JS, Fan C, Perou CM. An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer. Nat Genet. 2014;46(10):1051–9.
Article CAS PubMed PubMed Central Google Scholar
Dimitrakopoulos CM, Beerenwinkel N. Computational approaches for the identification of cancer genes and pathways. Wiley Interdiscip Rev. 2017;9(1): e1364.
Martincorena I, et al. Universal patterns of selection in cancer and somatic tissues. Cell. 2017;171(5):1029–41.
Article CAS PubMed PubMed Central Google Scholar
Torti D, Trusolino L. Oncogene addiction as a foundational rationale for targeted anti-cancer therapy: promises and perils. EMBO Mol Med. 2011;3(11):623–36.
Article CAS PubMed PubMed Central Google Scholar
Hahn WC, Weinberg RA. Modelling the molecular circuitry of cancer. Nat Rev Cancer. 2002;2(5):331–41.
Article CAS PubMed Google Scholar
Hahn WC, Counter CM, Lundberg AS, Beijersbergen RL, Brooks MW, Weinberg RA. Creation of human tumour cells with defined genetic elements. Nature. 1999;400(6743):464–8.
Article ADS CAS PubMed Google Scholar
Hou P, Ma J. DawnRank: discovering personalized driver genes in cancer. Genome Med. 2014;6:1–16.
Xi J, Wang M, Li A. Discovering mutated driver genes through a robust and sparse co-regularized matrix factorization framework with prior information from mRNA expression patterns and interaction network. BMC Bioinform. 2018;19(1):1–14.
Xi J, Wang M, Li A. Discovering potential driver genes through an integrated model of somatic mutation profiles and gene functional information. Mol BioSyst. 2017;13(10):2135–44.
Article CAS PubMed Google Scholar
Dimitrakopoulos C, et al. Network-based integration of multi-omics data for prioritizing cancer genes. Bioinformatics. 2018;34(14):2441–8.
Article CAS PubMed PubMed Central Google Scholar
Song J, Peng W, Wang F. A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph. BMC Bioinform. 2019;20(1):1–17.
Song J, Peng W, Wang F. An entropy-based method for identifying mutual exclusive driver genes in cancer. IEEE/ACM Trans Comput Biol Bioinform. 2019;17(3):758–68.
Wei T, Fa B, Luo C, Johnston L, Zhang Y, Yu Z. An efficient and easy-to-use network-based integrative method of multi-omics data for cancer genes discovery. Front Genet. 2021;11: 613033.
Article PubMed PubMed Central Google Scholar
Wang C, Shi J, Cai J, Zhang Y, Zheng X, Zhang N. DriverRWH: discovering cancer driver genes by random walk on a gene mutation hypergraph. BMC Bioinform. 2022;23(1):1–19.
Choudhury Y, et al. Attenuated adenosine-to-inosine editing of microRNA-376a* promotes invasiveness of glioblastoma cells. J Clin Investig. 2012;122(11):4059–76.
Article CAS PubMed PubMed Central Google Scholar
Stahlhut C, Slack FJ. MicroRNAs and the cancer phenotype: profiling, signatures and clinical implications. Genome Med. 2013;5:1–12.
Radicchi F, Castellano C, Cecconi F, Loreto V, Parisi D. Defining and identifying communities in networks. Proc Natl Acad Sci. 2004;101(9):2658–63.
Article ADS CAS PubMed PubMed Central Google Scholar
Li M, Zhang H, Wang J-X, Pan Y. A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data. BMC Syst Biol. 2012;6:1–9.
Xiao Q, Wang J, Peng X, Wu F-X. Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles. Proteome Sci. 2013;11(1):1–8.
Bhattacharyya A. On a measure of divergence between two statistical populations defined by their probability distribution. Bull Calcutta Math Soc. 1943;35:99–110.
Tomczak K, Czerwińska P, Wiznerowicz M. Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol/Współczesna Onkologia. 2015;2015(1):68–77.
Patil A, Nakamura H. HINT: a database of annotated protein-protein interactions and their homologs. Biophysics. 2005;1:21–4.
Article CAS PubMed PubMed Central Google Scholar
Huang H-Y, et al. miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database. Nucleic Acids Res. 2020;48(D1):D148–54.
Tate JG, et al. COSMIC: the catalogue of somatic mutations in cancer. Nucleic Acids Res. 2019;47(D1):D941–7.
Article CAS PubMed Google Scholar
Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man(OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005;33(Suppl 1):D514–7.
Ashburner M, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25–9.
Article CAS PubMed PubMed Central Google Scholar
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45(D1):D353–61.
留言 (0)