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

BackgroundPlants 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.ResultsHere, 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.ConclusionsPlantTFcat 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/.

[1]  Jianlin Cheng,et al.  SoyDB: a knowledge database of soybean transcription factors , 2010, BMC Plant Biology.

[2]  Ken-ichiro Hayashi.  The interaction and integration of auxin signaling components. , 2012, Plant & cell physiology.

[3]  H. Hellmann,et al.  Arabidopsis thaliana BTB/ POZ‐MATH proteins interact with members of the ERF/AP2 transcription factor family , 2009, The FEBS journal.

[4]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[5]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[6]  Sarah A. Teichmann,et al.  DBD: a transcription factor prediction database , 2005, Nucleic Acids Res..

[7]  Maarten Koornneef,et al.  The Absence of Histone H2B Monoubiquitination in the Arabidopsis hub1 (rdo4) Mutant Reveals a Role for Chromatin Remodeling in Seed Dormancy[W][OA] , 2007, The Plant Cell Online.

[8]  C. Chothia,et al.  Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. , 2001, Journal of molecular biology.

[9]  Birgit Kersten,et al.  PlnTFDB: updated content and new features of the plant transcription factor database , 2009, Nucleic Acids Res..

[10]  Hank C Wu,et al.  A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula , 2008, Plant Methods.

[11]  BMC Bioinformatics , 2005 .

[12]  Alvaro J. González,et al.  The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses , 2011, Nature.

[13]  Amos Bairoch,et al.  PROSITE, a protein domain database for functional characterization and annotation , 2009, Nucleic Acids Res..

[14]  D. Leprince,et al.  The BTB/POZ domain: a new protein-protein interaction motif common to DNA- and actin-binding proteins. , 1995, Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research.

[15]  Peer Bork,et al.  SMART 7: recent updates to the protein domain annotation resource , 2011, Nucleic Acids Res..

[16]  J. A. Jarillo,et al.  Chromatin remodeling in plant development. , 2009, The International journal of developmental biology.