TreeTFDB: An integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics

Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki, Lam Son Phan Tran

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Crop plants, whose productivity is affected by a wide range of growing and environmental conditions, are grown for economic purposes. Transcription factors (TFs) play central role in regulation of many biological processes, including plant development and responses to environmental stimuli, by activating or repressing spatiotemporal gene expression. Here, we describe the TreeTFDB (http://treetfdb.bmep.riken. jp/index.pl) that houses the TF repertoires of six economically important tree crop species: Jatropha curcas, papaya, cassava, poplar, castor bean and grapevine. Among these, the TF repertoire of J. curcas has not been reported by any other TF databases. In addition to their basic information, such as sequence and domain features, domain alignments, gene ontology assignment and sequence comparison, information on available full-length cDNAs, identity and positions of all types of known cis-motifs found in the promoter regions, gene expression data are provided. With its newly designed and friendly interface and its unique features, TreeTFDB will enable research community to predict the functions and provide access to available genetic resources for performing comparative and functional genomics of the crop TFs, either individually or at whole family level, in a comprehensive and convenient manner.

Original languageEnglish
Pages (from-to)151-162
Number of pages12
JournalDNA Research
Volume20
Issue number2
DOIs
Publication statusPublished - Apr 2013
Externally publishedYes

Keywords

  • Cis-Motif
  • Database
  • Expression
  • Transcription factor
  • Tree crops

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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