footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.
BACKGROUND
Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases.


RESULTS
FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value.


METHODS
Web site implemented in PHP,Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb.
Laboratory of Computational Biology, Department of Genetics and Plant Production, Estación Experimental de Aula Dei/CSIC, Av. Montañana 1005, Zaragoza (http://www.eead.csic.es/compbio) and Fundación ARAID, Paseo María Agustín 36, Zaragoza, Spain.
Alvaro
A
Sebastian
Bruno
B
Contreras-Moreira
D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D001412:Bacillus subtilis / Q000235:genetics; D001665:Binding Sites; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D048168:Escherichia coli K12 / Q000235:genetics; D005786:Gene Expression Regulation; D006801:Humans; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs / Q000235:genetics*; D011485:Protein Binding; D020543:Proteome / Q000032:analysis; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012984:Software; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
D020543:Proteome; D014157:Transcription Factors