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

Xinbin Dai, Senjuti Sinharoy, Michael Udvardi and Patrick Xuechun Zhao*

  • * Corresponding author: Patrick X Zhao pzhao@noble.org

  • † Equal contributors

Author Affiliations

Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway 73401 Ardmore, OK, USA

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BMC Bioinformatics 2013, 14:321  doi:10.1186/1471-2105-14-321

Published: 12 November 2013

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/ webcite.

Keywords:
Transcription factor; Transcriptional regulator; Chromatin regulator; High-throughput prediction; Plant genome