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CREME: Cis-Regulatory Module Explorer for the human genome.
Roded Sharan1, Asa Ben-Hur, Gabriela G Loots
1International Computer Science Institute, 1947 Center Street, Berkeley, CA 94704, USA. roded@icsi.berkeley.edu
Nucleic Acids Research
|June 25, 2004
Summary
This study introduces CREME, a web server for identifying cis-regulatory modules (CRMs) by analyzing transcription factor binding sites. CREME aids in understanding gene regulation by pinpointing co-occurring binding sites in promoter regions.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Gene transcription is primarily controlled by transcription factors binding to regulatory sequences.
- Eukaryotic genes are often co-regulated by multiple transcription factors binding to clustered sites forming cis-regulatory modules (CRMs).
Purpose of the Study:
- To present CREME, a novel web server designed for the identification and visualization of CRMs.
- To facilitate the study of co-regulated genes by analyzing their promoter regions.
Main Methods:
- CREME utilizes a comprehensive database of human transcription factor binding sites, annotated using position weight matrices and cross-species conservation (human, mouse, rat).
- A specialized search algorithm identifies combinations of transcription factor binding sites that frequently co-occur in close proximity within promoter regions of user-defined gene sets.
- Statistical scoring and graphical visualization are employed to report significant CRMs.
Main Results:
- The CREME web server successfully identifies and visualizes statistically significant cis-regulatory modules.
- The tool enables the discovery of combinations of transcription factor binding sites indicative of co-regulated genes.
Conclusions:
- CREME provides a valuable resource for researchers investigating gene regulation and identifying functional CRMs.
- The web server aids in deciphering complex regulatory networks by highlighting co-occurring transcription factor binding patterns.