HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics.

ABSTRACT: Comparing histone modification profiles between cancer and normal states, or across different tumor samples, can provide insights into understanding cancer initiation, progression and response to therapy. ChIP-seq histone modification data of cancer samples are distorted by copy number variation innate to any cancer cell. We present HMCan-diff, the first method designed to analyze ChIP-seq data to detect changes in histone modifications between two cancer samples of different genetic backgrounds, or between a cancer sample and a normal control. HMCan-diff explicitly corrects for copy number bias, and for other biases in the ChIP-seq data, which significantly improves prediction accuracy compared to methods that do not consider such corrections. On in silico simulated ChIP-seq data generate

SUBMITTER: Ashoor H 

PROVIDER: S-EPMC5416852 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature