Pan-cancer analysis of somatic mutations and transcriptomes reveals common functional gene clusters shared by multiple cancer types
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[1] Steve Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[2] M. Nitti,et al. Role of Glutathione in Cancer Progression and Chemoresistance , 2013, Oxidative medicine and cellular longevity.
[3] Gary D. Bader,et al. An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.
[4] P. Rijken,et al. Checks and balances in membrane phospholipid class and acyl chain homeostasis, the yeast perspective. , 2013, Progress in lipid research.
[5] T. Abaffy. Human Olfactory Receptors Expression and Their Role in Non-Olfactory Tissues A Mini-Review , 2015 .
[6] Angel Ortega,et al. Glutathione in Cancer Biology and Therapy , 2006, Critical reviews in clinical laboratory sciences.
[7] Terence P. Speed,et al. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..
[8] Bronwen L. Aken,et al. GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.
[9] Davide Heller,et al. STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..
[10] Marina Bosch,et al. Molecular Cell Biology 4th Edition , 2016 .
[11] P. A. Futreal,et al. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data , 2016, Genome Biology.
[12] H. Ohtsuki,et al. Accumulation of driver and passenger mutations during tumor progression , 2009, Proceedings of the National Academy of Sciences.
[13] Daniel R. Zerbino,et al. Ensembl 2016 , 2015, Nucleic Acids Res..
[14] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[15] Francesca D. Ciccarelli,et al. NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings , 2015, Nucleic Acids Res..
[16] Jianzhi Zhang,et al. Why Is the Correlation between Gene Importance and Gene Evolutionary Rate So Weak? , 2009, PLoS genetics.
[17] Shihua Zhang,et al. An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures , 2016, Scientific Reports.
[18] C. Hunter,et al. Programmed Necrosis in the Cross Talk of Cell Death and Inflammation , 2016 .
[19] Keith A. Boroevich,et al. Integrated Analysis of Whole Genome and Transcriptome Sequencing Reveals Diverse Transcriptomic Aberrations Driven by Somatic Genomic Changes in Liver Cancers , 2014, PloS one.
[20] J. Valcárcel,et al. Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers , 2014, Cell.
[21] E. Lander,et al. Lessons from the Cancer Genome , 2013, Cell.
[22] M. De la Fuente,et al. Chronic Inflammation and Cytokines in the Tumor Microenvironment , 2014, Journal of immunology research.
[23] S. Lodha,et al. Discordance in the histopathologic diagnosis of difficult melanocytic neoplasms in the clinical setting , 2008, Journal of cutaneous pathology.
[24] S. Pinho,et al. Glycosylation in cancer: mechanisms and clinical implications , 2015, Nature Reviews Cancer.
[25] C. Harris,et al. Radical causes of cancer , 2003, Nature Reviews Cancer.
[26] Matko Bosnjak,et al. REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.
[27] Ensembl , 2020, Definitions.
[28] Zheng Zhao,et al. LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns , 2015, Oncotarget.
[29] David A. Frank,et al. Signal Transduction in Cancer , 2015, Cancer Treatment and Research.
[30] Shihua Zhang,et al. Tumor characterization and stratification by integrated molecular profiles reveals essential pan-cancer features , 2015, BMC Genomics.
[31] P. A. Futreal,et al. Emerging patterns of somatic mutations in cancer , 2013, Nature Reviews Genetics.
[32] Peter C. Scacheri,et al. Mutations in the noncoding genome , 2015, Current opinion in pediatrics.
[33] Setia Pramana,et al. Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival , 2015, Bioinform..
[34] Brad T. Sherman,et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.
[35] J. Esko,et al. The sweet and sour of cancer: glycans as novel therapeutic targets , 2005, Nature Reviews Cancer.
[36] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[37] J. Condeelis,et al. Regulation of the actin cytoskeleton in cancer cell migration and invasion. , 2007, Biochimica et biophysica acta.
[38] Prahlad T. Ram,et al. A pan-cancer proteomic perspective on The Cancer Genome Atlas , 2014, Nature Communications.
[39] Andrew M. Gross,et al. Network-based stratification of tumor mutations , 2013, Nature Methods.
[40] R. Verhaak,et al. The Pan-Cancer Analysis of Pseudogene Expression Reveals Biologically and Clinically Relevant Tumour Subtypes , 2014, Nature Communications.
[41] Benjamin J. Raphael,et al. Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin , 2014, Cell.
[42] Sven Diederichs,et al. The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non‐coding RNA and synonymous mutations , 2016, EMBO molecular medicine.
[43] J. Cohen,et al. Programmed cell death in the immune system. , 1991, Advances in immunology.
[44] Ben Lehner,et al. Differential DNA mismatch repair underlies mutation rate variation across the human genome , 2015, Nature.
[45] A. Børresen-Dale,et al. Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer , 2016, Cell reports.
[46] Jinah Kim,et al. Primary Cilium Depletion Typifies Cutaneous Melanoma In Situ and Malignant Melanoma , 2011, PloS one.
[47] Benjamin J. Raphael,et al. Mutational landscape and significance across 12 major cancer types , 2013, Nature.
[48] Christopher R. Cabanski,et al. Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function , 2015, RNA biology.
[49] Jianzhi Zhang,et al. Significant impact of protein dispensability on the instantaneous rate of protein evolution. , 2005, Molecular biology and evolution.
[50] L. Ouyang,et al. Programmed cell death pathways in cancer: a review of apoptosis, autophagy and programmed necrosis , 2012, Cell proliferation.
[51] A. Chatterjee. Reduced Glutathione: A Radioprotector or a Modulator of DNA-Repair Activity? , 2013, Nutrients.
[52] Akif Uzman,et al. Molecular Cell Biology (4th edition): Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore and James Darnell; Freeman & Co., New York, NY, 2000, 1084 pp., list price $102.25, ISBN 0-7167-3136-3 , 2001 .
[53] Lu Xiao-jie,et al. Pseudogene in cancer: real functions and promising signature , 2014, Journal of Medical Genetics.
[54] Jie Zhang,et al. Integrative analysis of somatic mutations and transcriptomic data to functionally stratify breast cancer patients , 2016, BMC Genomics.
[55] M. Krendel,et al. Non‐muscle myosins in tumor progression, cancer cell invasion, and metastasis , 2014, Cytoskeleton.
[56] G. Dorn. Molecular Mechanisms That Differentiate Apoptosis from Programmed Necrosis , 2013, Toxicologic pathology.
[57] Xuefei Shi,et al. Pseudogene-expressed RNAs: a new frontier in cancers , 2016, Tumor Biology.
[58] A. Barabasi,et al. Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.
[59] Hadley Wickham,et al. ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .