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Bioinformatics. 2009 Oct 1;25(19):2605-6. doi: 10.1093/bioinformatics/btp479. Epub 2009 Aug 18.

CEAS: cis-regulatory element annotation system.

Author information

1
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA.

Abstract

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.

PMID:
19689956
DOI:
10.1093/bioinformatics/btp479
[Indexed for MEDLINE]

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