CREME [electronic resource] : Cis-Regulatory Module Explorer for the Human Genome
- Washington, D.C. : United States. Dept. of Energy, 2004.
Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy.
- Physical Description:
- PDF-file: 14 pages; size: 0.3 Mbytes
- Additional Creators:
- Lawrence Berkeley National Laboratory
United States. Department of Energy
United States. Department of Energy. Office of Scientific and Technical Information
- The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription factors, whose binding sites are tightly clustered and form cis-regulatory modules. In this paper we present a web-server, CREME, for identifying and visualizing cis-regulatory modules in the promoter regions of a given set of potentially co-regulated genes. CREME relies on a database of putative transcription factor binding sites that have been annotated across the human genome using a library of position weight matrices and evolutionary conservation with the mouse and rat genomes. A search algorithm is applied to this dataset to identify combinations of transcription factors whose binding sites tend to co-occur in close proximity in the promoter regions of the input gene set. The identified cis-regulatory modules are statistically scored and significant combinations are reported and graphically visualized. Our web-server is available at http://creme.dcode.org/.
- Published through SciTech Connect.
Published in: Nucleic Acid Research, vol. 32, Web Server, July 1, 2004, pp. 253-56 32 ISSN 0305-1048; NARHAD FT
Ovcharenko, I; Loots, G G; Sharan, R; Ben-Hur, A.
- Funding Information:
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