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.
Bibliographical noteFunding Information:
National Research Foundation of Korea [2010-0017649, 2012M3A9B4028641, 2012M3A9C7050151] to I.L.; The Joint BioEnergy Institute, the Office of Science, Office of Biological and Environmental Research, U.S. Department of Energy [DE-AC02–05CH11231]; Department of Energy Systems Biology Knowledgebase [KBase] to P.C.R. Funding for open access charge: National Research Foundation of Korea [2010-0017649]. Conflict of interest statement. None declared.
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