Article |
CEAS: cis-regulatory element annotation system
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, People's Republic China 100871 1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health Boston, MA 02115, USA
*To whom correspondence should be addressed. Tel +86 10 6276 4970; Fax +86 10 6275 2438; Email: weilp{at}mail.cbi.pku.edu.cn
Received February 14, 2006. Revised March 11, 2006. Accepted April 13, 2006.
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.
*Correspondence may also be addressed to X. Shirley Liu. Tel +1 617 632-2472; Fax +1 617 632-2444; Email: xsliu{at}jimmy.harvard.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors