TRANSFACRG and its module TRANSCompelRG: transcriptional gene regulation in eukaryotes

• Published in: Nucleic acids research Vol. 34; no. S1; p. D108
• Main Authors: Matys, V, Kel-Margoulis, O V, Fricke, E, Liebich, I, Land, S, Barre-Dirrie, A, Reuter, I, Chekmenev, D, Krull, M, Hornischer, K, Voss, N, Stegmaier, P, Lewicki-Potapov, B, Saxel, H, Kel, A E, Wingender, E
• Format: Journal Article
• Language: English
• Published: 01.01.2006
• Subjects: Arabidopsis; Drosophila
• ISSN: 0305-1048; 1362-4962

The TRANSFAC super( registered ) database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel super( registered ) on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match(TM) and Patch(TM) provides increased functionality for TRANSFAC super( registered ) . The list of databases which are linked to the common GENE table of TRANSFAC super( registered ) and TRANSCompel super( registered ) has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD(TM) and TRANSPRO(TM). 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 super( registered ) 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 super( registered ) , 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 super( registered ) 7.0 and TRANSCompel super( registered ) 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.