PlnTFDB: an integrative plant transcription factor database

PlnTFDB is an integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. It also provides an access point to its daughter databases of a species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags (ESTs), domain architecture and scientific literature is provided for each family.We have created lists of putatively complete sets of transcription factors and other transcriptional regulators for five plant genomes. They are publicly available through http://plntfdb.bio.uni-potsdam.de webcite. Further data will be included in the future when the sequences of other plant genomes become available.Transcription factors (TFs) are proteins (trans-acting factors) that regulate gene expression levels by binding to specific DNA sequences (cis-acting elements) in the promoters of target genes, thereby enhancing or repressing their transcriptional rates. The identification and functional characterization of TFs is essential for the reconstruction of transcriptional regulatory networks, which govern major cellular pathways in the response to biotic (e.g. response against pathogens or symbiotic relationships) and abiotic (e.g. light, cold, salt content) stimuli, and intrinsic developmental processes (e.g. growth of organs). Two global types of TFs can be distinguished: basal or general, and regulatory or specific TFs. Basal TFs belong to the minimal set of proteins required for the initiation of transcription (e.g. TATA-box binding protein). Together with RNA polymerase they form the basal transcription apparatus, representing the core of each transcriptional pr