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

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ID: 301047
2013
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Abstract
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.
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openalex_W2127968944 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Jinpu Jin, He Zhang, Lei Kong, Ge Gao, Jingchu Luo
Journal Nucleic Acids Research
Year 2013
DOI
10.1093/nar/gkt1016
URL
https://academic.oup.com/nar/article-pdf/42/D1/D1182/16949620/gkt1016.pdf
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