豆科 TFDB：大豆、绿豆和蒺藜苜蓿转录因子的综合数据库。

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

机构信息

Plant Science Center, Gene Discovery Research Group, RIKEN, Yokohama 230-0045 Japan.

出版信息

Bioinformatics. 2010 Jan 15;26(2):290-1. doi: 10.1093/bioinformatics/btp645. Epub 2009 Nov 17.

DOI:10.1093/bioinformatics/btp645

PMID:19933159

Abstract

UNLABELLED

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/.

SUPPLEMENTARY INFORMATION

Supplementary data available at Bioinformatics online.

摘要

未标注

我们建立了一个名为 LegumeTFDB 的数据库，提供了三种主要豆科植物（大豆、绿豆和紫花苜蓿）转录因子（TF）库的访问。LegumeTFDB 整合了每个 TF 基因和家族的独特信息，包括序列特征、基因启动子、结构域比对、基因本体（GO）分配和来自与豆科植物、拟南芥、水稻和杨树中的 TF 以及 NCBI nr 和 UniProt 中的蛋白质进行比较分析得出的序列比较数据。我们还分析了所有 TF 的启动子区域，以确定由 PLACE 数据库提供的所有类型的顺式基序。此外，我们提供了超链接，以提供 2411 个大豆 TF 基因的表达数据。LegumeTFDB 为比较基因组学和理解农业中重要豆科植物的转录调控提供了一个重要的用户友好型公共资源。