Peak shape clustering reveals biological insights.

ABSTRACT:

Background

ChIP-seq experiments are widely used to detect and study DNA-protein interactions, such as transcription factor binding and chromatin modifications. However, downstream analysis of ChIP-seq data is currently restricted to the evaluation of signal intensity and the detection of enriched regions (peaks) in the genome. Other features of peak shape are almost always neglected, despite the remarkable differences shown by ChIP-seq for different proteins, as well as by distinct regions in a single experiment.

Results

We hypothesize that statistically significant differences in peak shape might have a functional role and a biological meaning. Thus, we design five indices able to summarize peak shapes and we employ multivariate clustering techniques to divide peaks into gr

SUBMITTER: Cremona MA 

PROVIDER: S-EPMC4625869 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature