COHCAP

COHCAP analyzes single-nucleotide resolution DNA methylation data from Illumina methylation arrays and targeted bisulfite sequencing to identify CpG islands with consistent methylation patterns and to correlate methylation with gene expression for epigenetic regulation studies.

Key Features:

• CpG Island Analysis: Identifies CpG islands exhibiting consistent methylation patterns across individual CpG sites at single-nucleotide resolution.
• Integration with Gene Expression Data: Integrates methylation data with gene expression profiles to link CpG island methylation to downstream gene expression changes.
• Differential Methylation Identification: Generates lists of differentially methylated CpG islands with approximately 50% concordance with gene expression changes in cell line and heterogeneous patient datasets.
• Visualization Capabilities: Produces visualizations for quality control metrics, regions of differential methylation, and methylation–expression correlations.
• Disease-associated Methylation Detection: Facilitates identification of disease-associated methylation biomarkers, including negative correlations between DNA methylation and gene expression for markers such as the estrogen receptor in breast cancer.

Scientific Applications:

• Epigenetic Regulation Studies: Maps methylation patterns across CpG islands to investigate epigenetic regulation of gene expression.
• Biomarker Discovery in Complex Diseases: Identifies potential epigenetic biomarkers and therapeutic targets in diseases such as breast cancer.
• Integrative Methylation–Expression Analysis: Correlates methylation and gene expression to prioritize regulatory CpG islands for further study.

Methodology:

Processes single-nucleotide resolution DNA methylation data from Illumina methylation arrays or targeted bisulfite sequencing to identify consistent methylation patterns across CpG sites within CpG islands and integrates these results with gene expression data.