HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.

ABSTRACT:

Motivation

Cancer cells are often characterized by epigenetic changes, which include aberrant histone modifications. In particular, local or regional epigenetic silencing is a common mechanism in cancer for silencing expression of tumor suppressor genes. Though several tools have been created to enable detection of histone marks in ChIP-seq data from normal samples, it is unclear whether these tools can be efficiently applied to ChIP-seq data generated from cancer samples. Indeed, cancer genomes are often characterized by frequent copy number alterations: gains and losses of large regions of chromosomal material. Copy number alterations may create a substantial statistical bias in the evaluation of histone mark signal enrichment and result in underdetection of the signal in the reg

SUBMITTER: Ashoor H 

PROVIDER: S-EPMC3834794 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature