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Nucleic Acids Research Advance Access originally published online on November 16, 2006
Nucleic Acids Research 2007 35(Database issue):D879-D882; doi:10.1093/nar/gkl814
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Nucleic Acids Research, 2007, Vol. 35, Database issue D879-D882
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information

Huazong Zeng1,2, Lijun Luo2, Weixiong Zhang3, Jie Zhou1, Zuofeng Li1, Hongyan Liu2, Tiansheng Zhu2, Xiangqian Feng1 and Yang Zhong1,4,*

1 School of Life Sciences, Fudan University Shanghai, 200433, China 2 Shanghai Agro-Biological Gene Center, Shanghai 201106 China 3 Department of Computer Science and Engineering, Washington University in St Louis St Louis, MO 63130, USA 4 Shanghai Center for Bioinformation Technology, Shanghai 200235 China

*To whom correspondence should be addressed. Tel: +86 21 55664436; Fax: +86 21 65642468: Email: yangzhong{at}fudan.edu.cn

Received July 31, 2006. Revised October 3, 2006. Accepted October 4, 2006.

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/.


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