CREME: Cis-Regulatory Module Explorer for the Human Genome

Journal Article · Wed Feb 11 04:00:00 EST 2004 · Nucleic Acids Research

OSTI ID:15013997

Loots, G G; Sharan, R; Ovcharenko, I; Ben-Hur, A

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/.

• Research Organization: Lawrence Livermore National Laboratory (LLNL), Livermore, CA
• Sponsoring Organization: USDOE
• DOE Contract Number: W-7405-ENG-48
• OSTI ID: 15013997
• Report Number(s): UCRL-JRNL-202313
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 32; ISSN 0305-1048; ISSN NARHAD
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ALGORITHMS
GENES
MATRICES
PROMOTERS
TRANSCRIPTION
TRANSCRIPTION FACTORS