MMDiff: quantitative testing for shape changes in ChIP-Seq data sets.

ABSTRACT:

Background

Cell-specific gene expression is controlled by epigenetic modifications and transcription factor binding. While genome-wide maps for these protein-DNA interactions have become widely available, quantitative comparison of the resulting ChIP-Seq data sets remains challenging. Current approaches to detect differentially bound or modified regions are mainly borrowed from RNA-Seq data analysis, thus focusing on total counts of fragments mapped to a region, ignoring any information encoded in the shape of the peaks.

Results

Here, we present MMDiff, a robust, broadly applicable method for detecting differences between sequence count data sets. Based on quantifying shape changes in signal profiles, it overcomes challenges imposed by the highly structured nature of the dat

SUBMITTER: Schweikert G 

PROVIDER: S-EPMC4008153 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature