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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

cisRED: a database system for genome-scale computational discovery of regulatory elements.

G Robertson¹, M Bilenky, K Lin

¹Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada. grobertson@bcgsc.ca

Nucleic Acids Research

|December 31, 2005

Summary

cisRED is a new database that identifies and ranks conserved regulatory elements using a computational system. This resource aids in understanding gene regulation across diverse genomes.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Identifying conserved regulatory elements is crucial for understanding gene regulation.
Existing tools face challenges with rapidly evolving genomic data and diverse target genomes.

Purpose of the Study:

To introduce cisRED, a database and computational system for identifying and ranking conserved regulatory elements.
To provide a scalable solution for diverse genomes using high-throughput predictive pipelines.

Main Methods:

Utilizing a genome-scale computational system to predict motifs in promoter regions.
Employing multiple discovery methods on vertebrate sequence sets.
Estimating motif significance using randomized sequence sets and statistical thresholds.
Identifying groups of similar motifs and co-occurring motif patterns.

Main Results:

Developed cisRED, a web-accessible database of conserved regulatory elements.
The system ranks motifs based on statistical significance.
Information on atomic motifs, motif groups, and patterns is available.
The database can be queried, downloaded, or installed locally.

Conclusions:

cisRED offers a robust platform for discovering and analyzing conserved regulatory elements.
The system supports diverse genomic research by integrating evolving data and tools.
This resource facilitates a deeper understanding of gene regulation mechanisms across species.