The Rice Oligonucleotide Array Database: an atlas of rice gene expression

Rice - Tập 5 Số 1 - 2012
Peijian Cao1, Ki‐Hong Jung2, Daeseok Choi3, Daehee Hwang3, Jun Zhu1, Pamela C. Ronald4
1Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
2Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea
3School of Interdisciplinary Bioscience and Bioengineering & Integrative Biosciences and Biotechnology, POSTECH, Pohang, 790-784, Korea
4Department of Plant Pathology and the Genome Center, University of California, Davis, 95616, USA

Tóm tắt

Abstract Background Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed. Results In this study, we developed the Rice Oligonucleotide Array Database (ROAD,http://www.ricearray.org) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD’s user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes. Conclusions The Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species.

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