CoMoDis: Composite motif discovery in mammalian genomes

Ian J. Donaldson, Berthold Göttgens

    Research output: Contribution to journalArticlepeer-review

    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. © 2007 Oxford University Press.
    Original languageEnglish
    Article numbere1
    JournalNucleic acids research.
    Volume35
    Issue number1
    DOIs
    Publication statusPublished - Jan 2007

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