RIKEN Plant Transcription Factor Databases: in silico Analysis of Transcription Factor Classification and Prediction in 15 Plant Species

Plant productivity is affected by a wide range of growing and environmental conditions. Transcription factors (TFs) play central roles in the regulation of many biological processes, including plant development and responses to environmental stimuli, by activating or repressing gene expression. In the last decade, the availability of complete plant genome sequences has enabled scientists to identify TF sets from various plant species and compile a number of species-specific TF databases. Although such databases are useful, the need for specific details such as expression profiles and cis-element sequences has increased in recent years. Our group has constructed the SoybeanTFDB (http://soybeantfdb.psc.riken.jp/), LegumeTFDB (http://legumetfdb.psc.riken.jp/), GramineaeTFDB (http://gramineaetfdb.psc.riken.jp/), and TreeTFDB (http://treetfdb.bmep.riken.jp/) during the last 3 years, focusing on economically important legumes, grass, and tree crops. Collectively, these databases contain predicted TF sets from 15 species, enabling convenient comparative and functional genomic analyses of crop TFs. These databases provide the following information: sequence features, domain alignments, GO assignment, promoter regions and predicted cis-regulatory motifs in the promoter regions, gene/protein expression data, and available FL-cDNA(s) and gain-/loss-of-function mutant(s). With the newly designed and user-friendly interfaces, these TF databases will enable researchers to predict the functions of TFs as well as provide access to available genetic resources for performing comparative and functional genomic studies of crop TFs, either individually or at whole-family level, in a comprehensive and convenient manner.