About the Mouse 3.1 Database
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The cisRED mouse v3.1 database holds ~223K conserved motifs for promoter regions of ~17.5K target genes (Ensembl v38, NCBI m35, mm7) after applying an empirical p-value threshold of 0.1. (In addition to searching this database, you can browse a list of all ~17.5K search regions, sorted alphabetically.)
The mouse v3.1 database is the mouse v3 database with the addition of motif annotations based on known FoxA1 binding sites taken from ORegAnno. The pattern discovery algorithm has not been re-run, so this database does not contain any modules involving these FoxA1 binding sites.
Motifs were discovered in 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 contained a total of 38 vertebrate species (34 of which are mammalian) whose genome data were taken from Ensembl, ENCODE and low coverage read files. A typical (mode) input sequence set contained 16 vertebrate species. Search regions 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. A manuscript that describes the methods currently used to identify conserved genomic elements is in preparation.
Direct SQL queries can be run against the database cisred_Mmus_3_1 at db.cisred.org, with the username 'anonymous', and no password.