title: RiceNet v2: an improved network prioritization server for rice genes.
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.
authors: Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea.
authors: Tak
authors: T
authors: Lee
authors: The Joint Bioenergy Institute, Emeryville CA and Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA.
authors: Taeyun
authors: T
authors: Oh
authors: Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea.
authors: Sunmo
authors: S
authors: Yang
authors: Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea.
authors: Junha
authors: J
authors: Shin
authors: Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea.
authors: Sohyun
authors: S
authors: Hwang
authors: Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea.
authors: Chan Yeong
authors: CY
authors: Kim
authors: Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea.
authors: Hyojin
authors: H
authors: Kim
authors: Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea.
authors: Hongseok
authors: H
authors: Shim
authors: Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea.
authors: Jung Eun
authors: JE
authors: Shim
authors: 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.
authors: Pamela C
authors: PC
authors: Ronald
authors: Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Korea insuklee@yonsei.ac.kr.
authors: Insuk
authors: I
authors: Lee
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D020407:Internet; D012275:Oryza / Q000235:genetics*; D012984:Software