DiRE: identifying distant regulatory elements of co-expressed genes
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
Nucleic Acids Research
|May 20, 2008
Summary
DiRE predicts distant regulatory elements (REs) in eukaryotic genomes using gene co-expression and transcription factor binding site data. This tool identifies enhancers, repressors, and silencers outside of gene promoters for functional analysis.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Gene expression regulation involves proximal promoters and distant regulatory elements (REs).
- Identifying these REs, such as enhancers, is crucial for understanding gene regulation.
- Current methods often focus on promoter regions, potentially missing important distant elements.
Purpose of the Study:
- To develop a web server, DiRE, for predicting distant regulatory elements in higher eukaryotic genomes.
- To determine the chromosomal location and functional characteristics of these predicted REs.
- To identify function-specific REs and score transcription factor associations with biological functions.
Main Methods:
- Utilized the Enhancer Identification (EI) method.
- Integrated gene co-expression data, comparative genomics, and transcription factor binding site (TFBS) profiles.
- Developed TFBS-association signatures to discriminate regulatory functions.
- Searched the full gene locus to detect REs outside proximal promoter regions.
Main Results:
- Developed DiRE, a web server for predicting distant REs.
- DiRE can identify common REs for user-defined gene sets (e.g., co-expressed genes).
- The server predicts function-specific REs and scores TF associations with shared biological functions.
Conclusions:
- DiRE effectively predicts distant regulatory elements in higher eukaryotes.
- The tool aids in understanding gene regulation by identifying elements beyond proximal promoters.
- Integration with Array2BIO allows analysis starting from raw microarray data.
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