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.
Subject(s)
Databases, Genetic , Gene Expression Regulation , Regulatory Sequences, Nucleic Acid , Transcription Factors/metabolism , Animals , Arabidopsis/genetics , Arabidopsis Proteins/chemistry , Arabidopsis Proteins/metabolism , Binding Sites , DNA/chemistry , DNA/metabolism , Drosophila Proteins/chemistry , Drosophila Proteins/metabolism , Drosophila melanogaster/genetics , Humans , Internet , Mice , Protein Structure, Tertiary , Rats , Systems Integration , Transcription Factors/chemistry , Transcription, Genetic , User-Computer InterfaceABSTRACT
P-Match is a new tool for identifying transcription factor (TF) binding sites in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match is closely interconnected with the TRANSFAC database. In particular, P-Match uses the matrix library as well as sets of aligned known TF-binding sites collected in TRANSFAC and therefore provides the possibility to search for a large variety of different TF binding sites. Using results of extensive tests of recognition accuracy, we selected three sets of optimized cut-off values that minimize either false negatives or false positives, or the sum of both errors. Comparison with the weight matrix approaches such as Matchtrade mark tool shows that P-Match generally provides superior recognition accuracy in the area of low false negative errors (high sensitivity). As familiar to the user of Matchtrade mark, P-Match also allows to save user-specific profiles that include selected subsets of matrices with corresponding TF-binding sites or user-defined cut-off values. Furthermore, a number of tissue-specific profiles are provided that were compiled by the TRANSFAC team. A public version of the P-Match tool is available at http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi.
