Journal Article

CEAS: <i>cis</i>-regulatory element annotation system

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

in Bioinformatics

Volume 25, issue 19, pages 2605-2606
Published in print October 2009 | ISSN: 1367-4803
Published online August 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp479
CEAS: cis-regulatory element annotation system

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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@jimmy.harvard.edu; xsliu@jimmy.harvard.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1473 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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