PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

Abstract

With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.

Figure 1.

The flowchart for construction of PlantTFDB 4.0. Items marked with ‘(W)’ are web services. RBH means BLAST reciprocal best hit, and OG means orthologous group.

Figure 2.

Summary of TFs identified from 156 species with genome sequences. (A) Average number of TFs in different taxonomic lineages. (B) The origination stage of TF families. The number in the parentheses (e.g., Eudicots (95)) is the number of species used to date the origination stage for TF families according to the protocol described in (24).

Figure 3.

Workflow for parsing BLAST reciprocal best hits (RBHs) and inferring orthologous groups.

Figure 4.

Curation and projection of TF binding motifs. (A) Workflow for curation and projection of high-quality TF binding motifs derived from experiments. (B) The visualization of TF binding motifs in PlantTFDB.