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TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes
BIOBASE GmbH Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany
*To whom correspondence should be addressed. Tel: +49 5331 8584 28; Fax: +49 5331 8584 70; Email: vma{at}biobase.de
Received September 15, 2005. Revised October 27, 2005. Accepted October 27, 2005.
The TRANSFAC® database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel® on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of MatchTM and PatchTM provides increased functionality for TRANSFAC®. The list of databases which are linked to the common GENE table of TRANSFAC® and TRANSCompel® has been extended by: Ensembl, UniGene, EntrezGene, HumanPSDTM and TRANSPROTM. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel® contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC®, in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC® 7.0 and TRANSCompel® 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.
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