cisRED: cis-regulatory element database

cisRED > Rat 1.1

Search by Symbol Search for any of the following: - Ensembl gene IDs (e.g. ENSRNOG00000000001) - gene symbols (e.g. NM_053347, Cd82) - cisRED motif IDs (e.g. craRnor1) - cisRED group IDs (e.g. crtRnor2602) - cisRED module IDs (e.g. crmRnor46) Search by Sequence Find motif sequences on either strand that contain an IUPAC query sequence, e.g. TAARNGCMT.	Browse All Regions View a list of all the search regions in this database, and the number of motifs found in each region. Browse by Location View a list of all the search regions in this database found in the specified genomic region. chr: from to Browse Groups & Modules Browse summary information about motif groups or modules in this database. Show

About the Rat 1.1 Database

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The cisRED rat v1.1 database holds ~115K conserved motifs for promoter regions of ~7K target genes (Ensembl v22, NCBI v3.1, rn3) after applying a p-value threshold of 0.25. (In addition to searching this database, you can browse a list of all ~7K search regions, sorted alphabetically.)

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 28 vertebrate species whose genome data were taken from Ensembl, ENCODE and low coverage read files. A typical (mode) input sequence set contained 6 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_Rnor_1_1 at db.cisred.org, with the username 'anonymous', and no password.