Cis-regulatory Element Annotation System

Summary

We present a tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. As a stand-alone extension of our web application CEAS (Cis-regulatory Element Annotation System), 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.

Introduction

In analysis of cis-regulatory elements using genome-wide ChIP-chip or ChIP-Seq, it is essential to characterize the ChIP signals and identify potential association of ChIP regions with functionally important genomic regions such as gene promoters or exons. Previously, we developed a web server to evaluate GC content and evolutionary conservation of the ChIP regions, conduct sequence motif finding, and map ChIP regions to their nearest genes (Ji, et al., 2006). However, more analytic functions are needed to provide biologists with a more complete perspective. For example, in addition to merely analyzing the identified ChIP regions of a factor, displaying the average ChIP enrichment signal within/near genes helps biologists better visualize the functional loci of factors, especially for broad histone modifications. In addition, biologists often like a visual overview of ChIP peaks' intensity distributions across chromosomes. Nonetheless, such analysis functions often require the ability of manipulate large continuous ChIP enrichment signal files (e.g. WIG files of hundreds of mega bases in size), which are difficult to transfer to a web server. Therefore, as an extension of our current successful web-based CEAS (over 35K analysis queries processed in 2008), we present a stand-alone CEAS extension package with more analysis functions, including drawing average ChIP signal profiles at genes or user-specified loci from a WIG file. This stand-alone CEAS package also provides summary statistics about how the ChIP regions are distributed over important gene features such as promoters, immediate downstream of genes, and exons, and a report on how individual genes are enriched near ChIP regions.

Author

Hyunjin Shin and Tao Liu from Xiaole Shirley Liu's Lab.

Contact

If you have any comments, suggestions, questions, bug reports, etc, feel free to contact Hyunjin Shin. And PLEASE attach your command line and log messages if possible.

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