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Bioinformatics Advance Access originally published online on August 18, 2009
Bioinformatics 2009 25(19):2605-2606; doi:10.1093/bioinformatics/btp479
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CEAS: cis-regulatory element annotation system

Hyunjin Shin 1, Tao Liu 1, Arjun K. Manrai 2 and X. Shirley Liu 1,*

1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115 and 2Harvard-MIT Division of Health Sciences and Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA

*To whom correspondence should be addressed.


  Abstract

Summary: We present a tool designed to characterize genome-wide protein–DNA interaction patterns from ChIP-chip and ChIP-Seq data. This stand-alone extension of our web application CEAS (cis-regulatory element annotation system) provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic regions, particularly allowing observation of continuous and broad ChIP enrichment that might be too subtle to detect from ChIP peaks alone.

Availability: The CEAS Python package is publicly available at http://liulab.dfci.harvard.edu/CEAS.

Contact: shin{at}jimmy.harvard.edu; xsliu{at}jimmy.harvard.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Joaquin Dopazo

Received on May 16, 2009; revised on July 8, 2009; accepted on August 3, 2009

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