Characterizing mutation–expression network relationships in multiple cancers

Computational Biology and Chemistry - Tập 63 - Trang 73-82 - 2016
Shila Ghazanfar1,2, Jean Yee Hwa Yang1
1School of Mathematics and Statistics at the University of Sydney, F07, The University of Sydney, NSW 2006, Australia
2Data61, CSIRO, Locked Bag 17, North Ryde, NSW 2113, Australia

Tài liệu tham khảo

An, 2014, NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes, Database: J. Biol. Databases Curation, 2014, bau015, 10.1093/database/bau015

Bashashati, 2012, DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer, Genome Biol., 13, R124, 10.1186/gb-2012-13-12-r124

Bashashati, 2013, Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling, J. Pathol., 231, 21, 10.1002/path.4230

Breitkreutz, 2007, The BioGRID interaction database: 2008 update, Nucleic Acids Res., 36, D637, 10.1093/nar/gkm1001

Carlson, M. KEGG.db: a set of annotation maps for KEGG, r package version 3.1.2.

Cifola, 2013, Comprehensive genomic characterization of cutaneous malignant melanoma cell lines derived from metastatic lesions by whole-exome sequencing and SNP array profiling, PLOS ONE, 8, e63597, 10.1371/journal.pone.0063597

Ciriello, 2012, Mutual exclusivity analysis identifies oncogenic network modules, Genome Res., 398, 10.1101/gr.125567.111

Creixell, 2015, Pathway and network analysis of cancer genomes, Nat. Methods, 12, 615, 10.1038/nmeth.3440

Dittrich, 2008, Identifying functional modules in protein–protein interaction networks: an integrated exact approach, Bioinformatics (Oxf., Engl.), 24, i223, 10.1093/bioinformatics/btn161

Forbes, 2014, COSMIC: exploring the world's knowledge of somatic mutations in human cancer, Nucleic Acids Res., 43, D805, 10.1093/nar/gku1075

Futreal, 2004, A census of human cancer genes, Nat. Rev. Cancer, 4, 177, 10.1038/nrc1299

Hofree, 2013, Network-based stratification of tumor mutations, Nat. Methods, 10, 1108, 10.1038/nmeth.2651

Jia, 2014, VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data, PLoS Comput. Biol., 10, e1003460, 10.1371/journal.pcbi.1003460

Keshava Prasad, 2009, Human protein reference database – 2009 update, Nucleic Acids Res., 37, 767, 10.1093/nar/gkn892

Krauthammer, 2012, Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma, Nat. Genet., 44, 1006, 10.1038/ng.2359

Law, 2014, DrugBank 4.0: shedding new light on drug metabolism, Nucleic Acids Res., 42, 1091, 10.1093/nar/gkt1068

Leiserson, 2013, Simultaneous identification of multiple driver pathways in cancer, PLoS Comput. Biol., 9, e1003054, 10.1371/journal.pcbi.1003054

Leiserson, 2015, PanCancer Network Analysis identifies combinations of rare somatic mutations across pathways and protein complexes, Nat. Genet., 47, 10.1038/ng.3168

Levandowsky, 1971, Distance between sets, Nature, 234, 34, 10.1038/234034a0

Liao, 2013, The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote, Nucleic Acids Res., 41, e108, 10.1093/nar/gkt214

Morgan, M., Carlson, M., Tenenbaum, D., Arora, S. AnnotationHub: client to access AnnotationHub resources, r package version 2.0.2.

Paull, 2013, Discovering causal pathways linking genomic events to transcriptional states using tied diffusion through interacting events (TieDIE), Bioinformatics (Oxf., Engl.), 29, 2757, 10.1093/bioinformatics/btt471

Prickett, 2009, Analysis of the tyrosine kinome in melanoma reveals recurrent mutations in ERBB4, Nat. Genet., 41, 1127, 10.1038/ng.438

Rolland, 2014, A proteome-scale map of the human interactome network, Cell, 159, 1212, 10.1016/j.cell.2014.10.050

Schaefer, 2012, Hippie: integrating protein interaction networks with experiment based quality scores, PLoS ONE, 7, 1, 10.1371/journal.pone.0031826

Schramm, 2013, Molecular interaction networks for the analysis of human disease: utility, limitations, and considerations, Proteomics, 13, 3393, 10.1002/pmic.201200570

Turner, 2010, iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence, Database: J. Biol. Databases Curation, 2010, baq023, 10.1093/database/baq023

Zhang, 2015, New genes drive the evolution of gene interaction networks in the human and mouse genomes, Genome Biol., 16, 202, 10.1186/s13059-015-0772-4