The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. A Nucleic Acids Research article describes the system architecture; please use this publication to cite cisRED. PubMed publications that cite cisRED are listed here.

cisRED makes three levels of information available for regulatory elements:

1. 'Atomic' motifs: These are conserved, over-represented, sequence sets, typically 6 to 12 bp long, that have been discovered in a 'search region' sequence set.
2. Groups of 'similar' motifs: These are identified either by a) annotating motifs with site sequences from TRANSFAC, JASPAR and ORegAnno databases (annotation-based groups), or by b) 'de novo' hierarchical clustering with the OPTICS algorithm ('de novo' groups).
3. Patterns of motif group labels that co-occur in many search regions: These putative regulatory modules are ranked using genome-scale statistical and functional properties. Motifs in highly ranked patterns are likely the most reliable predictions.

In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, we use a base set of probabilistic ab initio discovery tools, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes.

In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species.

You can access cisRED's data in three ways:

1. view predicted regulatory elements directly in cisRED's web user interface. From this interface, motifs can be viewed 'live' in the UCSC or Ensembl genome browsers.
2. download the data and SQL structure for each species' MySQL 4.x database, with a schema diagram and example SQL queries, from the Databases and Methods tab.
3. query the databases directly with SQL at db.cisred.org. Queries can be driven from command line or graphical clients (e.g. the MySQL QueryBrowser), or programmatically from Perl, Python, Java, Ruby, etc. The username is 'anonymous' and the password should be left blank.

cisRED human motifs are available as a native data type at the Ensembl genome browser.

cisRED is an ongoing project. Updates will be released frequently.