COHCAP: City of Hope CpG Island Analysis Pipeline

ABSTRACT: COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data. It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. COHCAP is currently the only DNA methylation package that can handle integration with gene expression data, and the results of this study show that COHCAP can identify regions of differential methylation with ~50% concordance with gene expression. COHCAP is scalable for analysis of both cell line data and heterogeneous patient data, and it can identify known cancer biomarkers as well as intriguing new roles of epigenetic regulation in cancer (such as methylation of estrogen rece

ORGANISM(S): Homo sapiens

SUBMITTER: Charles Warden 

PROVIDER: E-GEOD-42310 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress