Name
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. |
Year | DOI | Venue |
|---|---|---|
2004 | 10.1093/nar/gkh385 | NUCLEIC ACIDS RESEARCH |
Keywords | Field | DocType |
transcription factor,gene transcription,computational biology,transcription factors,human genome,transcription factor binding site,evolutionary conservation,binding sites,binding site,cis regulatory module,internet,gene expression regulation | Genome,Promoter,Gene,Transcription (biology),Biology,DNA binding site,Human genome,Genetics,Molecular biology,Cis-regulatory module,Transcription factor | Journal |
Volume | Issue | ISSN |
32 | Web Server issue | 0305-1048 |
Citations | PageRank | References |
20 | 2.19 | 9 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Roded Sharan | 1 | 2792 | 186.61 |
| Asa Ben-Hur | 2 | 1405 | 110.73 |
| Gabriela G Loots | 3 | 87 | 9.49 |
| Ivan Ovcharenko | 4 | 166 | 17.49 |