ArticleNucleic acids research2007
CoMoDis: composite motif discovery in mammalian genomes.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Evaluation of the NOD/SCID xenograft model for glucocorticoid-regulated gene expression in childhood B-cell precursor acute lymphoblastic leukemia.BMC genomics · 2011Article
- A Runx1-Smad6 rheostat controls Runx1 activity during embryonic hematopoiesis.Molecular and cellular biology · 2011Article
- Transcription factor site dependencies in human, mouse and rat genomes.BMC bioinformatics · 2009Article
- Integrating sequence, evolution and functional genomics in regulatory genomics.Genome biology · 2009Review
- MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs.Nucleic acids research · 2008Article
- DiRE: identifying distant regulatory elements of co-expressed genes.Nucleic acids research · 2008Article
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Authors and funding
2 authors.
Funding
Abstract
Specificity of mammalian gene regulatory regions is achieved to a large extent through the combinatorial binding of sets of transcription factors to distinct binding sites, discrete combinations of which are often referred to as regulatory modules. Identification and subsequent characterization of gene regulatory modules will be a key step in assembling transcriptional regulatory networks from gene expression profiling data, with the ultimate goal of unravelling the regulatory codes that govern gene expression in various cell types. Here we describe the new bioinformatics tool, Composite Motif Discovery (CoMoDis), which streamlines computational identification of novel regulatory modules starting from a single seed motif. Seed motifs represent binding sites conserved across mammalian species. CoMoDis facilitates novel motif discovery by automating the extraction of DNA sequences flanking seed motifs and streamlining downstream motif discovery using a variety of tools, including several that utilize phylogenetic conservation criteria. CoMoDis is available at http://hscl.cimr.cam.ac.uk/CoMoDis_portal.html.
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Registered trials
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