info:eu-repo/semantics/article
MethylMix 2.0: An R package for identifying DNA methylation genes
Fecha
2018-09Registro en:
Cedoz, Pierre Louis; Prunello, Marcos Miguel; Brennan, Kevin; Gevaert, Olivier; MethylMix 2.0: An R package for identifying DNA methylation genes; Oxford University Press; Bioinformatics (Oxford, England); 34; 17; 9-2018; 3044-3046
1367-4803
CONICET Digital
CONICET
Autor
Cedoz, Pierre Louis
Prunello, Marcos Miguel
Brennan, Kevin
Gevaert, Olivier
Resumen
Summary: DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a major mechanism of gene expression deregulation in a wide range of diseases. At the same time, highthroughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. We developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. Here we present a new version of MethylMix that automates the construction of DNA-methylation and gene expression datasets from The Cancer Genome Atlas (TCGA). More precisely, MethylMix 2.0 incorporates two major updates: The automated downloading of DNA methylation and gene expression datasets from TCGA and the automated preprocessing of such datasets: Value imputation, batch correction and CpG sites clustering within each gene. The resulting datasets can subsequently be analyzed with MethylMix to identify transcriptionally predictive methylation states.