PlnTFDB: updated content and new features of the plant transcription factor database

Abstract

The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 families of TFs and TRs from 19 species ranging from unicellular red and green algae to angiosperms are included in PlnTFDB, representing >1.6 billion years of evolution of gene regulatory networks. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.

Figure 1.

Selecting the significance score threshold in newly created profile HMMs. The graphic shows the scores obtained for proteins in the V. carteri proteome when searched with the VARL HMM with an e-value cut-off of 10. Known members of the family in this species (TPs) are highlighted in green. The putative TN with the highest score is indicated by a purple arrow. The TP with the minimum score is highlighted by a green arrow. The significance score threshold (black line) is computed as the average between the minimum score for TPs (green line) and the maximum score for TNs (purple line). For this family, the selected threshold is −4.25 bits.

Figure 2.

Screenshot of a web page displaying details for a TF gene in PlnTFDB. (A) Every gene page in PlnTFDB displays basic information (including species name and gene family assignment) for a given TF or TR. If gene names had been assigned (only for A. thaliana and O. sativa ssp. japonica) they will be displayed as well. (B) The best hits (hhsearch, probability of being a TP ≥98%) to PDB protein 3D structures are visualized as static images, a link is provided to the embedded Java applet Jmol where basic operations on the 3D structure can be performed. (C) Links to orthologues in PlnTFDB are provided. (D) Users can query PlnTFDB through similarity searches (BLAST) using a protein or a nucleotide sequence as query. (E) Domain architecture is displayed with links to the original domain databases (Pfam or our local database, see section ‘Identification of protein domains and new domains models’). (F) Links to the protein and transcript sequences of the gene are provided.