Welcome to PvTFDB
Phaseolus vulgaris is a herbaceous annual plant grown globally for its eatable dry seed called as beans or green beans for unripe fruit. Its leaf has vegetable properties whereas the straw is used as fodder. It is a member of the legume family Fabaceae, well known for its nitrogen-fixing bacteria properties. Phaseolus vulgaris is a highly variable climber species with a long history of cultivation. Phaseolus vulgaris is one of the most significant food legume in the biosphere. Although this crop is an essential crop to both the developed and developing world as a resources of dietary protein source. It delivers 15% of the protein and 30% of the caloric necessity to the world's population, and symbolises 50% of the grain legumes used worldwide.
The recently published Common bean's genome sequence data (Jeremy, S, et al. 2014) given us an opportunity to develop a comprehensive transcription factors (TF) database, called Phaseolus vulgaris Transcription Factors Database (PvTFDB) using various computational methods. PvTFDB is the first online comprehensive TF database developed for the legume crop Phaseolus vulgaris L. (Common Bean). This database contains a set of 2370 predicted TFs (Gene models) and classifies them into 49 TF families. In addition, this databse provides comprehensive information at both family and gene level. At family level, this database provides description about the family, list of predicted TFs, phylogenetic tree for entire TF family and tissue specific RNA-Seq based gene expression in the form of heatmap for entire TF family. At gene level, this database provides physical location, sequences (Protein, CDS, Transcript, Genomic and 2kb Upstream sequences), functional annotation (by InterProScan), protein physical properties, mined SSRs along with their primers, mined Cis-elements from 2kb upstream sequences, orthologs in other legume crops along with their protein sequences and tissue specific RNA-Seq expression. This database also provides the researchers to download the entire data used to build the database freely.
The design of PvTFDB database schema follows the "Three-Level-Schema" architecture, is shown in Figure 1 and developed using open-source softwares, MySQL, Apache and PHP. The PvTFDB schema diagram is shown in Figure 2.
To use this database, please follow through the tutorial provided in "Tutorial" tab.
If you use this database, please cite us:Bhawna, VS Bonthala and Prasad G (2016). PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes. Database, Volume 2016, 1 January 2016, baw114. https://doi.org/10.1093/database/baw114