title: CEAS: cis-regulatory element annotation system.
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.
authors.affiliation: Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, People's Republic China 100871.
authors.forename: Xuwo
authors.initials: X
authors.lastname: Ji
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Jun
authors.initials: J
authors.lastname: Song
authors.forename: Liping
authors.initials: L
authors.lastname: Wei
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors