TRANSFAC registered : transcriptional regulation, from patterns to profiles

• Published in: Nucleic acids research Vol. 31; no. 1; pp. 374 - 378
• Main Authors: Matys, V, Fricke, E, Geffers, R, Goessling, E, Haubrock, M, Hehl, R, Hornischer, K, Karas, D, Kel, A E, Kel-Margoulis, O V, Kloos, D-U, Land, S, Lewicki-Potapov, B, Michael, H
• Format: Journal Article
• Language: English
• Published: 01.01.2003
• ISSN: 0305-1048

The TRANSFAC registered database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER registered database on anatomical structures and developmental stages. The functionality of Match, a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with Match Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC registered public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC registered Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER registered free download versions are available at http://www.biobase.de:8080/index.html.