title: CREME: Cis-Regulatory Module Explorer for the human genome.
abstract: 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 data set 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.
authors.affiliation: International Computer Science Institute, 1947 Center Street, Berkeley, CA 94704, USA. roded@icsi.berkeley.edu
authors.forename: Roded
authors.initials: R
authors.lastname: Sharan
authors.forename: Asa
authors.initials: A
authors.lastname: Ben-Hur
authors.forename: Gabriela G
authors.initials: GG
authors.lastname: Loots
authors.forename: Ivan
authors.initials: I
authors.lastname: Ovcharenko
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D020407:Internet; D011401:Promoter Regions, Genetic; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors