Journal Article

LegumeTFDB: an integrative database of <i>Glycine max</i>, <i>Lotus japonicus</i> and <i>Medicago truncatula</i> transcription factors

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

in Bioinformatics

Volume 26, issue 2, pages 290-291
Published in print January 2010 | ISSN: 1367-4803
Published online November 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp645
LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors

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Summary: 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.

Availability: http://legumetfdb.psc.riken.jp/

Contact: tran@psc.riken.jp; mochida@psc.riken.jp

Supplementary information: Supplementary data available at Bioinformatics online.

Journal Article.  1301 words. 

Subjects: Bioinformatics and Computational Biology

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