PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

By Jinpu Jin, He Zhang, Lei Kong, Ge Gao, Jingchu Luo. Nucleic Acids Res., 2013

879 citations recorded by the source corpus.

With the aim to provide a resource for functional and evolutionary study of plant transcription factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb.cbi.pku.edu.cn). After refining the TF classification pipeline, we systematically identified 129 288 TFs from 83 species, of which 67 species have genome sequences, covering main lineages of green plants. Besides the abundant annotation provided in the previous version, we generated more annotations for identified TFs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from UniProt, TAIR and NCBI GeneRIF, as well as references to provide clues for functional studies of TFs. To help identify evolutionary relationship among identified TFs, we assigned 69 450 TFs into 3924 orthologous groups, and constructed 9217 phylogenetic trees for TFs within the same families or same orthologous groups, respectively. In addition, we set up a TF prediction server in this version for users to identify TFs from their own sequences.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/defb77194bedfc4c2ec5dd8a636019cb2e275365

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Citations in the corpus

The WRKY Transcription Factor Family in Model Plants and Crops (2017, background): “…gene family is the 7th largest TF family in flowering plants following basic helix-loophelix (bHLH), myeloblastosis (MYB), Ethylene responsive factor (ERF), NAM (no apical meristem), ATAF1/2 and CUC2 (cup-shaped cotyledon) (NAC), basic leucine Zipper (bZIP), and C2H2 families (Jin et al., 2014).”
iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases. (2016, neutral): “Databases presenting these regulatory pr teins, especially TFs, have been developed, such as PlnTFDB (Pérez-Rodríguez et al., 2010) and PlantTFDB (Jin et al., 2013).”
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy (2015, methodology): “OrthoMCL was used here as it is the method by which all transcription factor families are currently classified [31].”
PLAZA 3.0: an access point for plant comparative genomics (2014, background): “The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB.”
Transcription Factors and Plants Response to Drought Stress: Current Understanding and Future Directions (2016, neutral): “%) potentially encode TFs (Franco-Zorrilla et al., 2014), which are categorized into diﬀerent gene families such as AREB, DREB, MYB, WRKY, NAC, and bZIP based on the distinct structure of their DNA-binding domain (Golldack et al., 2011; Jin et al., 2014).”
Evolution of Gene Duplication in Plants1[OPEN] (2016, background): “Another example illustrating the variation in plant gene family size is the large difference in the number of transcription factors, which can differ more than 10-fold among plant species (Jin et al., 2014).”
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants (2016, methodology): “Using our established TF prediction pipeline (16) and protein sequences downloaded from Joint Genome Institute and other plant genome sequencing and annotation projects (see http://planttfdb.”