TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes

TLDR

The authors introduced a new web interface with expanded search options and integrated Match and Patch tools, linked to additional databases such as Ensembl, UniGene, EntrezGene, HumanPSD, and TRANSPRO, incorporated standard gene names from HGNC, MGI, and RGD, automatically assigned protein domains via InterProScan, Pfam, SMART, and PROSITE, and added a dedicated evidence table to TRANSCompel. The updated TRANSFAC 7.0 and TRANSCompel 7.0 databases now include expanded transcription factor binding site data from Drosophila and Arabidopsis, and are publicly available at http://www.gene-regulation.com/pub/databases.html.

Abstract

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 Match and Patch 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, HumanPSD and TRANSPRO. 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.