title: Pancancer analysis of DNA methylation-driven genes using MethylMix.
abstract: Aberrant DNA methylation is an important mechanism that contributes to oncogenesis. Yet, few algorithms exist that exploit this vast dataset to identify hypo- and hypermethylated genes in cancer. We developed a novel computational algorithm called MethylMix to identify differentially methylated genes that are also predictive of transcription. We apply MethylMix to 12 individual cancer sites, and additionally combine all cancer sites in a pancancer analysis. We discover pancancer hypo- and hypermethylated genes and identify novel methylation-driven subgroups with clinical implications. MethylMix analysis on combined cancer sites reveals 10 pancancer clusters reflecting new similarities across malignantly transformed tissues.
authors: Biomedical Informatics Research, Department of Medicine, Stanford University, 1265 Welch Road, Stanford, CA, 94305, USA. ogevaert@stanford.edu.
authors: Olivier
authors: O
authors: Gevaert
authors: Departments of Health Research & Policy, and Statistics, Stanford University, Stanford, CA, 94305, USA. tibs@stanford.edu.
authors: Robert
authors: R
authors: Tibshirani
authors: Department of Radiology, Stanford University, Stanford, CA, 94305, USA. sylvia.plevritis@stanford.edu.
authors: Sylvia K
authors: SK
authors: Plevritis
mesh_terms: D016000:Cluster Analysis; D019175:DNA Methylation / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D006801:Humans; D009369:Neoplasms / Q000145:classification / Q000235:genetics*; D012984:Software; D014158:Transcription, Genetic
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