MethylMix - MethylMix: Identifying methylation driven cancer genes
MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.
Last updated 4 months ago
dnamethylationstatisticalmethoddifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetwork
4.97 score 44 dependenciesAMARETTO - Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Integrating an increasing number of available multi-omics cancer data remains one of the main challenges to improve our understanding of cancer. One of the main challenges is using multi-omics data for identifying novel cancer driver genes. We have developed an algorithm, called AMARETTO, that integrates copy number, DNA methylation and gene expression data to identify a set of driver genes by analyzing cancer samples and connects them to clusters of co-expressed genes, which we define as modules. We applied AMARETTO in a pancancer setting to identify cancer driver genes and their modules on multiple cancer sites. AMARETTO captures modules enriched in angiogenesis, cell cycle and EMT, and modules that accurately predict survival and molecular subtypes. This allows AMARETTO to identify novel cancer driver genes directing canonical cancer pathways.
Last updated 4 months ago
statisticalmethoddifferentialmethylationgeneregulationgeneexpressionmethylationarraytranscriptionpreprocessingbatcheffectdataimportmrnamicroarraymicrornaarrayregressionclusteringrnaseqcopynumbervariationsequencingmicroarraynormalizationnetworkbayesianexonarrayonechanneltwochannelproprietaryplatformsalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentmultiplecomparisonqualitycontroltimecourse
1.51 score 143 dependencies