Computational identification of plant transcription factors and the construction of the PlantTFDB database

Methods Mol Biol. 2010:674:351-68. doi: 10.1007/978-1-60761-854-6_21.

Abstract

Transcription factors (TFs) play an important role in gene regulation. Computational identification and annotation of TFs at genome scale are the first step toward understanding the mechanism of gene expression and regulation. We started to construct the database of Arabidopsis TFs in 2005 and developed a pipeline for systematic identification of plant TFs from genomic and transcript sequences. In the following years, we built a database of plant TFs (PlantTFDB, http://planttfdb.cbi.pku.edu.cn ) which contains putative TFs identified from 22 species including five model organisms and 17 economically important plants with available EST sequences. To provide comprehensive information for the putative TFs, we made extensive annotation at both the family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of the TFs in other species. PlantTFDB has a simple interface to allow users to make text queries, or BLAST searches, and to download TF sequences for local analysis. We hope that PlantTFDB could provide the user community with a useful resource for studying the function and evolution of transcription factors.

MeSH terms

  • Binding Sites
  • Computational Biology / methods*
  • Databases, Protein*
  • Genome, Plant / genetics
  • Molecular Sequence Annotation
  • Plant Proteins / chemistry
  • Plant Proteins / classification
  • Plant Proteins / metabolism*
  • Plants / genetics
  • Plants / metabolism*
  • Sequence Homology, Amino Acid
  • Transcription Factors / chemistry
  • Transcription Factors / classification
  • Transcription Factors / metabolism*

Substances

  • Plant Proteins
  • Transcription Factors