PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool

Abstract

Background: Plants regulate intrinsic gene expression through transcription factors (TFs), transcriptional regulators (TRs), chromatin regulators (CRs), and the basal transcription machinery. An understanding of plant gene regulatory mechanisms at a systems level requires the identification of these regulatory elements on a genomic scale.

Results: Here, we present PlantTFcat, a high-performance web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences. The comprehensive prediction logics that are included in PlantTFcat are based on relationships between gene families and conserved domains from 108 published plant TF/TR/CR families. These prediction logics effectively distinguish TF/TR/CR families with common conserved domains. Our systematic performance evaluations indicate that PlantTFcat annotates known TF/TR/CR families with high coverage and sensitivity.

Conclusions: PlantTFcat provides an analysis tool to identify and categorize plant TF/TR/CR genes on a genomic scale. PlantTFcat is freely available to the public at http://plantgrn.noble.org/PlantTFcat/.

Figure 1

The data submission interface located under the “Analysis” tab of the PlantTFcat web server.

Figure 2

An example output page of PlantTFcat that includes search, sort, and batch download links.

Figure 3

Venn diagrams that show the differences in prediction results between PlantTFcat and BLAST-based methods. PlnTFDB represents the TF/TR dataset downloaded from PlnTFDB, PlantTFcat represents the PlantTFcat predictions, and BLAST represents the BLAST search predictions. (a) The results using the Arabidopsis thaliana gene models release 8 (TAIR8) as the test dataset. (b) The results using the Populus trichocarpa JGI gene models v1.1 as the test dataset.