PlantTFcat: An Online Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool

Plants undergoing developmental processes or responding to environmental changes typically alter the expression of many genes, which are controlled by transcription factors (TFs) and other transcriptional regulators (TRs) in local or global transcriptional regulatory networks. Understanding plant gene regulatory mechanisms at a systems level necessitates systematical identification and categorization of TFs and TRs on a genome scale.

We developed PlantTFcat, which is a high-performance TFs and TRs categorization and analysis tool, designed to identify and categorize these genes in genome-scale protein or nucleic acid sequences. The PlantTFcat’s prediction logic was built upon a comprehensive collection of manually compiled and curated conserved domain patterns found in almost all (118, to be specific) published plant TF and TR families up to date, and thus guarantees high quality prediction in terms of both accuracy and coverage.

The PlantTFcat consists of an intuitive web interface at the front-end and a sophisticate back-end module which employs InterProScan to search potential domains per TF/TR families in the user-submitted sequences. To enable high-throughput analysis capability, we customized InterProScan and adopted in-house BioGrid parallel computing platform. With these optimizations, PlantTFcat system is able to analyze the Arabidopsis genome in less than 10 minutes. When comparing with the 2,163 Arabidopsis TFs in the public plant transcription factor database, PlantTFDB V2.0, our predicted TFs and TRs cover 99.5% of genes at the match rate of 92.2%. In addition, the PlantTFcatreports 2,431 novel TR/TF gene candidates.

The PlantTFcat is publicly and freely available at http://plantgrn.noble.org/PlantTFcat/.