Systematic characterization of pan‐cancer mutation clusters
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Ruedi Aebersold | Michael Boutros | Marija Buljan | R. Aebersold | M. Boutros | M. Buljan | P. Blattmann | Peter Blattmann
[1] Mariano J. Alvarez,et al. Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks , 2014, Cell.
[2] Elizabeth M. Smigielski,et al. dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..
[3] Michael P Snyder,et al. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations , 2015, Nature Genetics.
[4] Joshua F. McMichael,et al. DGIdb - Mining the druggable genome , 2013, Nature Methods.
[5] The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.
[6] J. Li,et al. PCBP1 suppresses the translation of metastasis-associated PRL-3 phosphatase. , 2010, Cancer cell.
[7] W. Klapper,et al. The PCBP1 gene encoding poly(rc) binding protein i is recurrently mutated in Burkitt lymphoma , 2015, Genes, chromosomes & cancer.
[8] U. Moll,et al. Two hot spot mutant p53 mouse models display differential gain of function in tumorigenesis , 2013, Cell Death and Differentiation.
[9] D. Pe’er,et al. Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers , 2014, Cell.
[10] Ludovic C. Gillet,et al. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system , 2013, Nature Methods.
[11] Glenn R Masson,et al. Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110α (PIK3CA) , 2012, Proceedings of the National Academy of Sciences.
[12] Gabor T. Marth,et al. A global reference for human genetic variation , 2015, Nature.
[13] Joshua M. Stuart,et al. The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.
[14] Robert D. Finn,et al. iPfam: a database of protein family and domain interactions found in the Protein Data Bank , 2013, Nucleic Acids Res..
[15] Ralf Herwig,et al. The ConsensusPathDB interaction database: 2013 update , 2012, Nucleic Acids Res..
[16] K. Nakayama,et al. Ubiquitin ligases: cell-cycle control and cancer , 2006, Nature Reviews Cancer.
[17] Hans-Werner Mewes,et al. CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..
[18] Elizabeth Brunk,et al. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework , 2017, Genome Medicine.
[19] Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource , 2003 .
[20] Wolfgang Huber,et al. Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping , 2013, Nature Methods.
[21] K. Henrick,et al. Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.
[22] T. Hubbard,et al. A census of human cancer genes , 2004, Nature Reviews Cancer.
[23] Henning Hermjakob,et al. The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..
[24] J. Miller,et al. Predicting the Functional Effect of Amino Acid Substitutions and Indels , 2012, PloS one.
[25] M. Rubin,et al. SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling. , 2017, Cancer cell.
[26] Ruedi Aebersold,et al. Mass-spectrometric exploration of proteome structure and function , 2016, Nature.
[27] Zsuzsanna Dosztányi,et al. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content , 2005, Bioinform..
[28] Steven J. M. Jones,et al. Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.
[29] M. Boutros,et al. Microscopy-Based High-Content Screening , 2015, Cell.
[30] Benjamin J. Raphael,et al. Mutational landscape and significance across 12 major cancer types , 2013, Nature.
[31] David T. W. Jones,et al. Signatures of mutational processes in human cancer , 2013, Nature.
[32] N. Socci,et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity , 2015, Nature Biotechnology.
[33] Alexander Hoischen,et al. Prioritization of neurodevelopmental disease genes by discovery of new mutations , 2014, Nature Neuroscience.
[34] Laurie J. Gay,et al. Contribution of platelets to tumour metastasis , 2011, Nature Reviews Cancer.
[35] Xiao-Min Wang,et al. Possible novel roles of poly(rC)-binding protein 1 in SH-SY5Y neurocytes: an analysis using a dynamic Bayesian network , 2012, Neuroscience Bulletin.
[36] A. Godzik,et al. Comparison of algorithms for the detection of cancer drivers at subgene resolution , 2017, Nature Methods.
[37] H. Carter,et al. Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces , 2016, PloS one.
[38] Minoru Kanehisa,et al. KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..
[39] Juancarlos Chan,et al. Gene Ontology Consortium: going forward , 2014, Nucleic Acids Res..
[40] Vivien Marx,et al. Cancer genomes: discerning drivers from passengers , 2014, Nature Methods.
[41] Mariano J. Alvarez,et al. Network-based inference of protein activity helps functionalize the genetic landscape of cancer , 2016, Nature Genetics.
[42] P. Aloy,et al. Interactome3D: adding structural details to protein networks , 2013, Nature Methods.
[43] David L. Masica,et al. Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure. , 2016, Cancer research.
[44] B Marshall,et al. Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..
[45] S. Dietmann,et al. Genetic Exploration of the Exit from Self-Renewal Using Haploid Embryonic Stem Cells , 2014, Cell stem cell.
[46] C. Garvie,et al. Structural studies of Ets-1/Pax5 complex formation on DNA. , 2001, Molecular cell.
[47] Toshio Kuroki,et al. Role of Smad4 (DPC4) inactivation in human cancer. , 2003, Biochemical and biophysical research communications.
[48] Bin Zhang,et al. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse , 2011, Nucleic Acids Res..
[49] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[50] Hidetoshi Shimodaira,et al. Pvclust: an R package for assessing the uncertainty in hierarchical clustering , 2006, Bioinform..
[51] Matthew B. Callaway,et al. MuSiC: Identifying mutational significance in cancer genomes , 2012, Genome research.
[52] Andrew M. Gross,et al. Network-based stratification of tumor mutations , 2013, Nature Methods.
[53] Benjamin J. Raphael,et al. Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin , 2014, Cell.
[54] Meifeng Zhou,et al. Downregulated Poly-C binding protein-1 is a novel predictor associated with poor prognosis in Acute Myeloid Leukemia , 2015, Diagnostic Pathology.
[55] A. Barabasi,et al. Uncovering disease-disease relationships through the incomplete interactome , 2015, Science.
[56] B. Ebert,et al. Mutations in G protein beta subunits promote transformation and kinase inhibitor resistance , 2014, Nature Medicine.
[57] Fan Yang,et al. Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations , 2015, PLoS Comput. Biol..
[58] C. Chothia,et al. Evolution of the Protein Repertoire , 2003, Science.
[59] T. Jacks,et al. Targeted point mutations of p53 lead to dominant-negative inhibition of wild-type p53 function , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[60] M. Madan Babu,et al. Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer , 2016, Molecular cell.
[61] James Y. Zou. Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.
[62] Michael C. Heinold,et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing , 2015, Nature Communications.
[63] Mingming Jia,et al. COSMIC: somatic cancer genetics at high-resolution , 2016, Nucleic Acids Res..
[64] Gary D Bader,et al. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers , 2013 .
[65] Cathy H. Wu,et al. UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..
[66] David Tamborero,et al. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes , 2013, Bioinform..
[67] S. Gabriel,et al. Discovery and saturation analysis of cancer genes across 21 tumor types , 2014, Nature.
[68] Jonathan W. Pillow,et al. POSTER PRESENTATION Open Access , 2013 .
[69] Jared C. Roach,et al. Kaviar: an accessible system for testing SNV novelty , 2011, Bioinform..
[70] C. Chothia. The nature of the accessible and buried surfaces in proteins. , 1976, Journal of molecular biology.
[71] B. Clurman,et al. FBW7 ubiquitin ligase: a tumour suppressor at the crossroads of cell division, growth and differentiation , 2008, Nature Reviews Cancer.
[72] Chris Sander,et al. Pan-Cancer Analysis of Mutation Hotspots in Protein Domains. , 2015, Cell systems.
[73] Gary D Bader,et al. International network of cancer genome projects , 2010, Nature.
[74] Daniel R. Zerbino,et al. Ensembl 2016 , 2015, Nucleic Acids Res..
[75] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[76] K. Kinzler,et al. Cancer Genome Landscapes , 2013, Science.
[77] Robert D. Finn,et al. The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..
[78] Søren Brunak,et al. Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics , 2014, Nature Methods.
[79] Benjamin J. Raphael,et al. Pan-Cancer Network Analysis Identifies Combinations of Rare Somatic Mutations across Pathways and Protein Complexes , 2014, Nature Genetics.
[80] C. Sander,et al. 3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets , 2017, Genome Medicine.
[81] Joaquín Dopazo,et al. A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces , 2015, PLoS Comput. Biol..
[82] Syed Haider,et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space , 2011, Database J. Biol. Databases Curation.
[83] J. Valcárcel,et al. Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers , 2014, Cell.
[84] E. Lander,et al. Lessons from the Cancer Genome , 2013, Cell.
[85] P. Bork,et al. A method and server for predicting damaging missense mutations , 2010, Nature Methods.
[86] John G. Collard,et al. Rho GTPases: functions and association with cancer , 2007, Clinical & Experimental Metastasis.
[87] E. Levy. A simple definition of structural regions in proteins and its use in analyzing interface evolution. , 2010, Journal of molecular biology.
[88] E. Lander,et al. Comprehensive assessment of cancer missense mutation clustering in protein structures , 2015, Proceedings of the National Academy of Sciences.
[89] Steven J. M. Jones,et al. Comprehensive molecular profiling of lung adenocarcinoma , 2014, Nature.
[90] Laurence A. Turka,et al. Cancer-Associated PTEN Mutants Act in a Dominant-Negative Manner to Suppress PTEN Protein Function , 2014, Cell.
[91] Amos Bairoch,et al. The ENZYME database in 2000 , 2000, Nucleic Acids Res..
[92] M. Taketo,et al. Gastrointestinal tumorigenesis in Smad4 (Dpc4) mutant mice. , 2000, Human cell.
[93] Haiyuan Yu,et al. Three-dimensional reconstruction of protein networks provides insight into human genetic disease , 2012, Nature Biotechnology.
[94] Steven A. Roberts,et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .
[95] S. Elledge,et al. Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome , 2013, Cell.