Open AccessPlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information
Author(s) -
Hao Zeng,
Lijun Luo,
Weixiong Zhang,
Jie Zhou,
Zuofeng Li,
Hongyan Liu,
Tiansheng Zhu,
Xinbin Feng,
Yang Zhong
Publication year - 2007
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkl814
Subject(s) - biology , quantitative trait locus , candidate gene , expressed sequence tag , genetics , gene , arabidopsis , oryza sativa , locus (genetics) , family based qtl mapping , genome , arabidopsis thaliana , microarray analysis techniques , computational biology , gene mapping , gene expression , chromosome , mutant
We have designed and implemented a web-based database system, called PlantQTL-GE, to facilitate quantitatine traits locus (QTL) based candidate gene identification and gene function analysis. We collected a large number of genes, gene expression information in microarray data and expressed sequence tags (ESTs) and genetic markers from multiple sources of Oryza sativa and Arabidopsis thaliana. The system integrates these diverse data sources and has a uniform web interface for easy access. It supports QTL queries specifying QTL marker intervals or genomic loci, and displays, on rice or Arabidopsis genome, known genes, microarray data, ESTs and candidate genes and similar putative genes in the other plant. Candidate genes in QTL intervals are further annotated based on matching ESTs, microarray gene expression data and cis-elements in regulatory sequences. The system is freely available at http://www.scbit.org/qtl2gene/new/.