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Nucleic Acids Res. 2015 Jul 1;43(W1):W122-7. doi: 10.1093/nar/gkv253. Epub 2015 Mar 26.

RiceNet v2: an improved network prioritization server for rice genes.

Author information

1
Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea.
2
The Joint Bioenergy Institute, Emeryville CA and Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA.
3
The Joint Bioenergy Institute, Emeryville CA and Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA insuklee@yonsei.ac.kr.
4
Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea insuklee@yonsei.ac.kr.

Abstract

Rice is the most important staple food crop and a model grass for studies of bioenergy crops. We previously published a genome-scale functional network server called RiceNet, constructed by integrating diverse genomics data and demonstrated the use of the network in genetic dissection of rice biotic stress responses and its usefulness for other grass species. Since the initial construction of the network, there has been a significant increase in the amount of publicly available rice genomics data. Here, we present an updated network prioritization server for Oryza sativa ssp. japonica, RiceNet v2 (http://www.inetbio.org/ricenet), which provides a network of 25 765 genes (70.1% of the coding genome) and 1 775 000 co-functional links. Ricenet v2 also provides two complementary methods for network prioritization based on: (i) network direct neighborhood and (ii) context-associated hubs. RiceNet v2 can use genes of the related subspecies O. sativa ssp. indica and the reference plant Arabidopsis for versatility in generating hypotheses. We demonstrate that RiceNet v2 effectively identifies candidate genes involved in rice root/shoot development and defense responses, demonstrating its usefulness for the grass research community.

PMID:
25813048
PMCID:
PMC4489288
DOI:
10.1093/nar/gkv253
[Indexed for MEDLINE]
Free PMC Article

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