CEAS: Cis-regulatory element annotation system

Xuwo Ji, Wei Li, Jun Song, Liping Wei, X. Shirley Liu

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)W551-W554
JournalNucleic acids research
Volume34
Issue numberWEB. SERV. ISS.
DOIs
StatePublished - Jul 2006
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

Fingerprint

Dive into the research topics of 'CEAS: Cis-regulatory element annotation system'. Together they form a unique fingerprint.

Cite this