About the Mouse 4 Database
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The cisRED mouse v4 database holds ~223K conserved DNA sequence motifs (empirical p-value < 0.1) in promoter regions of ~17.5K target genes (Ensembl v47, NCBI m37, mm9).
The v4 motifs were generated by transforming the coordinates of the motifs in the mouse v3.1 database from the NCBI m35 genome build to the m37 genome build, using UCSC's web lift-over tool. In the conversion, 86 motifs (< 0.04% of the ~223k v3.1 motifs) were lost. At this point, we have not rerun the pattern discovery algorithm, so the v4 database contains no regulatory module predictions.
The v3.1 motifs were computationally discovered in comparative genomics sequence sets consisting of regions around the transcription start site (TSS) of a single, canonical transcript for each gene, and corresponding regions from other species. Input sequence sets were generated from genome sequence data for 38 vertebrate species (34 of which were mammalian), using data from Ensembl, ENCODE and low coverage read files. A typical input sequence set contained genome sequence data 16 vertebrate species. Search regions for motif discovery were -1.5Kb/+200b relative to a TSS, net of most types of repeats and of coding sequences, which were masked.
An overview of the pipeline and database is available in an NAR 2006 publication.
Access to this database is not available at db.cisred.org at this time.
Direct SQL queries can be run against the database cisred_Mmus_4 at db.cisred.org, with the username 'anonymous', and no password.