A platform for functional prediction and comparative analyses of transcription factors of legumes and beyond

Abstract

Sequence-specific DNA-binding transcription factors (TFs) are key molecular switches that control many of the biological processes in a cell or organism. Recent completion of the genomic sequences of soybean (Glycine max), Locus japonicus and Medicago truncatula has enabled us to carry out large-scale data mining to identify and annotate regulatory TFs for functional and comparative genomics of the TF repertoires of these three major legumes in themselves or with those of other species. The identified TFs of each legume were grouped in 61 TF families, and these TFs all together were integrated into a so-called LegumeTFDB (http://legumetfdb.psc.riken.jp). Detailed annotations of TF genes can be accessed at LegumeTFDB. Moreover, we included hyperlinks to expression data of a number of soybean TF genes, generated by high-throughput microarray analyses to facilitate functional prediction. LegumeTFDB enables the search for all types of known abiotic stress responsive motifs as well as cis-motifs provided by the PLACE database in promoter region of each of the TFs. Integration of expression analysis, comparative sequence analysis and cis-motif and GO annotations provided through this study would aid in systematic functional prediction of the legume TFs. LegumeTFDB provides an important user-friendly public resource for comparative genomics and understanding of transcriptional regulation in three important legumes and beyond. © 2010 Landes Bioscience.