PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

被引：718

作者：

Jin, Jinpu ^{[1
,2
]}

Zhang, He ^{[1
,2
]}

Kong, Lei ^{[1
,2
]}

Gao, Ge ^{[1
,2
]}

Luo, Jingchu ^{[1
,2
]}

机构：

[1] Peking Univ, Coll Life Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China

[2] Peking Univ, Ctr Bioinformat, Beijing 100871, Peoples R China

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / D1期

基金：

中国国家自然科学基金;

关键词：

INTEGRATIVE DATABASE; GENOME SEQUENCE; ARABIDOPSIS; RESOURCE;

D O I：

10.1093/nar/gkt1016

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

With the aim to provide a resource for functional and evolutionary study of plant transcription factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb.cbi.pku.edu.cn). After refining the TF classification pipeline, we systematically identified 129 288 TFs from 83 species, of which 67 species have genome sequences, covering main lineages of green plants. Besides the abundant annotation provided in the previous version, we generated more annotations for identified TFs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from UniProt, TAIR and NCBI GeneRIF, as well as references to provide clues for functional studies of TFs. To help identify evolutionary relationship among identified TFs, we assigned 69 450 TFs into 3924 orthologous groups, and constructed 9217 phylogenetic trees for TFs within the same families or same orthologous groups, respectively. In addition, we set up a TF prediction server in this version for users to identify TFs from their own sequences.

引用

页码：D1182 / D1187

页数：6

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