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Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W551-4.

CEAS: cis-regulatory element annotation system.

Author information

1
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, People's Republic China 100871.

Abstract

The recent availability of high-density human genome tiling arrays enables biologists to conduct ChIP-chip experiments to locate the in vivo-binding sites of transcription factors in the human genome and explore the regulatory mechanisms. Once genomic regions enriched by transcription factor ChIP-chip are located, genome-scale downstream analyses are crucial but difficult for biologists without strong bioinformatics support. We designed and implemented the first web server to streamline the ChIP-chip downstream analyses. Given genome-scale ChIP regions, the cis-regulatory element annotation system (CEAS) retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes and identifies enriched transcription factor-binding motifs. Biologists can utilize CEAS to retrieve useful information for ChIP-chip validation, assemble important knowledge to include in their publication and generate novel hypotheses (e.g. transcription factor cooperative partner) for further study. CEAS helps the adoption of ChIP-chip in mammalian systems and provides insights towards a more comprehensive understanding of transcriptional regulatory mechanisms. The URL of the server is http://ceas.cbi.pku.edu.cn.

PMID:
16845068
PMCID:
PMC1538818
DOI:
10.1093/nar/gkl322
[Indexed for MEDLINE]
Free PMC Article
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