Published in

Oxford University Press (OUP), Bioinformatics, 19(25), p. 2605-2606

DOI: 10.1093/bioinformatics/btp479

Oxford University Press, Nucleic Acids Research, Web Server(34), p. W551-W554, 2006

DOI: 10.1093/nar/gkl322

Links

Tools

Export citation

Search in Google Scholar

CEAS: cis-regulatory element annotation system

Journal article published in 2009 by X. Ji, J. Song, L. Wei, Hyunjin Shin, W. Li, Tao Liu, Arjun K. Manrai ORCID, X. Shirley Liu
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

Full text: Download

Green circle
Preprint: archiving allowed
Upload
Green circle
Postprint: archiving allowed
Upload
Red circle
Published version: archiving forbidden
Policy details
Data provided by SHERPA/RoMEO

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 .