LegumeTFDB: An integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors

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

Research output: Contribution to journalArticle

55 Citations (Scopus)

Abstract

We have established a database named LegumeTFDB to provide access to transcription factor (TF) repertoires of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula. LegumeTFDB integrates unique information for each TF gene and family, including sequence features, gene promoters, domain alignments, gene ontology (GO) assignment and sequence comparison data derived from comparative analysis with TFs found within legumes, in Arabidopsis, rice and poplar as well as with proteins in NCBI nr and UniProt. We also analyzed the promoter regions for all of the TFs to identify all types of cis-motifs provided by the PLACE database. Additionally, we supply hyperlinks to make available expression data of 2411 soybean TF genes. LegumeTFDB provides an important user-friendly public resource for comparative genomics and understanding of transcriptional regulation in agriculturally important legumes.

Original languageEnglish
Article numberbtp645
Pages (from-to)290-291
Number of pages2
JournalBioinformatics
Volume26
Issue number2
DOIs
Publication statusPublished - 2010
Externally publishedYes

Fingerprint

Medicago truncatula
Glycine Max
Transcription factors
Transcription Factor
Soybeans
Fabaceae
Glycine
Amino acids
Transcription Factors
Soybean
Genes
Databases
Gene
Promoter
Arabidopsis
Sequence Comparison
Transcriptional Regulation
Gene Ontology
Comparative Genomics
Genomics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K., & Tran, L. S. P. (2010). LegumeTFDB: An integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors. Bioinformatics, 26(2), 290-291. [btp645]. https://doi.org/10.1093/bioinformatics/btp645

LegumeTFDB : An integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors. / Mochida, Keiichi; Yoshida, Takuhiro; Sakurai, Tetsuya; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo; Tran, Lam Son Phan.

In: Bioinformatics, Vol. 26, No. 2, btp645, 2010, p. 290-291.

Research output: Contribution to journalArticle

Mochida, K, Yoshida, T, Sakurai, T, Yamaguchi-Shinozaki, K, Shinozaki, K & Tran, LSP 2010, 'LegumeTFDB: An integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors', Bioinformatics, vol. 26, no. 2, btp645, pp. 290-291. https://doi.org/10.1093/bioinformatics/btp645
Mochida, Keiichi ; Yoshida, Takuhiro ; Sakurai, Tetsuya ; Yamaguchi-Shinozaki, Kazuko ; Shinozaki, Kazuo ; Tran, Lam Son Phan. / LegumeTFDB : An integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors. In: Bioinformatics. 2010 ; Vol. 26, No. 2. pp. 290-291.
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