EpiMix

EpiMix integrates high-throughput DNA methylation data and gene expression data for population-level analysis using beta mixture modeling to identify functional DNA methylation predictive of gene expression.

Key Features:

• Automated Data Retrieval: Downloads data from TCGA or GEO databases.
• Preprocessing: Processes raw methylation and gene expression data for downstream analysis.
• Methylation Modeling: Uses beta mixture modeling to identify methylation states of each CpG probe.
• Differential Methylation Analysis: Compares methylation between experimental and control groups to identify hypo- or hypermethylated CpG sites across physiological or pathological conditions.
• Functional Annotation: Identifies functional DNA methylation at proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.
• Interactive Visualization: Generates visual outputs for exploring methylation patterns and results.

Scientific Applications:

• Functional Epigenomics: Identifies DNA methylation predictive of gene expression across diverse genetic elements.
• Disease Methylation Profiling: Detects hypo- or hypermethylated CpG sites in pathological conditions.
• Non-coding RNA Epigenetic Regulation: Maps functional methylation at microRNA and lncRNA genes.
• Enhancer Methylation Mapping: Characterizes methylation at distal cis-regulatory enhancer elements.

Methodology:

EpiMix applies beta mixture modeling to identify methylation states of CpG probes, compares experimental and control group methylation levels, and incorporates specialized algorithms to link functional DNA methylation to gene expression at specific genetic elements.