TRANSFAC: transcriptional regulation, from patterns to profiles

Abstract

The TRANSFAC 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 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 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 Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER free download versions are available at http://www.biobase.de:8080/index.html.

Figure 1

Application of specific profiles provided by the Match™ program. Potential binding sites found by Match™ are boxed, name of the transcription factor and score for the match are given under the sequence. (A) The immune-specific profile (with modified cut-offs) is applied to find potential binding sites within the promoter sequence of the human IL-12 p40 gene (EMBL accession no. AY008847, positions 2101 to 2460). Known binding sites for transcription factors are shown in bold, the name of the transcription factor is given above the sequence. The transcription start site (TSS) is indicated by an arrow. (B) The muscle-specific profile (with modified cut-offs) is used to find potential binding sites in the 5′ region of the hypothetical gene, LocusLink ID LOC88523. This gene encodes a protein with unknown function, a corresponding EST is shown to be expressed in skeletal muscles. The sequence has been retrieved from RefSeq, the start of the first exon is shown according to RefSeq annotation.