COHCAP

"COHCAP" (City of Hope CpG Island Analysis Pipeline) is an algorithm for analyzing DNA methylation data at single-nucleotide resolution. This tool can process data from Illumina methylation arrays and targeted bisulfite sequencing, primarily focusing on identifying CpG islands that exhibit consistent methylation patterns across CpG sites. A distinctive feature of COHCAP is its ability to integrate DNA methylation data with gene expression information, making it unique in pinpointing CpG islands likely to influence downstream gene expression. This integrative approach allows for generating lists of differentially methylated CpG islands that show significant concordance with gene expression changes, demonstrated in cell line experiments and analyses of heterogeneous patient data.

COHCAP stands out for its utility in identifying key biomarkers and regulatory elements in diseases such as breast cancer. It has been used to highlight biomarkers like the estrogen receptor by revealing a negative correlation between DNA methylation and gene expression. Beyond its analytical capabilities, COHCAP also excels in providing comprehensive visualization tools. These tools assist in quality control, showcasing regions of differential methylation and illustrating the relationship between methylation and gene expression, thereby enhancing the interpretability of results.