What it does

CEAS (Cis-regulatory Element Annotation System) is a tool for characterizing genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. It provides statistics on ChIP enrichment at important genome features such as specific chromosome, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor.

CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic features, allowing continuous and broad ChIP enrichment to be perceived which might be too subtle to detect from ChIP peaks alone.

Usage

CEAS takes the following inputs:

• BED file with discrete ChIP regions (for example, the 'summits' output from the MACS peak caller)
• WIG or bigWIG file with a continuous ChIP enrichment signal
• Gene annotation table (provided as reference data)

Optionally it can also take a BED file describing extra regions of interest (for example non-coding regions).

The analysis modules are:

• ChIP region annotation: estimates the relative enrichment level of ChIP regions in each gene feature with respect to the whole genome.
• Gene-centered annotation: identifies genes associated with ChIP regions to infer the direct regulatory gene targets of the binding factor of interest.
• Average signal profiling within/near important genomic features: displays continuous ChIP enrichment signal within/around important gene features to help visualize the average binding patterns.

Background

This tool is compatible with the ceasBW version of CEAS from the Cistrome package obtained from

https://bitbucket.org/cistrome/cistrome-applications-harvard/overview

(commit id d8c0751, datestamp 20140929). The CEAS code is under the published-packages/CEAS/ subdirectory.

Cistrome data files and documentation can be found at

http://liulab.dfci.harvard.edu/CEAS/index.html

The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html