ArticleNucleic acids research2015
RiceNet v2: an improved network prioritization server for rice genes.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it, 86 citations in OpenAlex.
- Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach.PloS one · 2019Pooled it
- Functional and regulatory complexity: challenges and prospects for understanding rice WRKY transcription factors.Journal of experimental botany · 2026Review
- AgroLD: a knowledge graph for the plant sciences.BMC genomic data · 2025Article
- Leaf Na+ effects and multi-trait GWAS point to salt exclusion as the key mechanism for reproductive stage salinity tolerance in rice.Annals of botany · 2025Article
- Genomic prediction with NetGP based on gene network and multi-omics data in plants.Plant biotechnology journal · 2025Article
- RiceProteomeDB (RPDB): a user-friendly database for proteomics data storage, retrieval, and analysis.Scientific reports · 2024Article
- Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- Photosynthesis in rice is increased by CRISPR/Cas9-mediated transformation of two truncated light-harvesting antenna.Frontiers in plant science · 2023Article
- An open source plant kinase chemogenomics set.Plant direct · 2022Article
- NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions.Database : the journal of biological databases and curation · 2022Article
- Integration of probabilistic functional networks without an external Gold Standard.BMC bioinformatics · 2022Article
- Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases.Methods in molecular biology (Clifton, N.J.) · 2022Review
- The Elite Alleles of OsSPL4 Regulate Grain Size and Increase Grain Yield in Rice.Rice (New York, N.Y.) · 2021Article
- Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement.Plants (Basel, Switzerland) · 2021Article
- Status and prospects of genome-wide association studies in plants.The plant genome · 2021Review
- Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management.Frontiers in plant science · 2021Review
- A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome.Bioinformatics (Oxford, England) · 2020Article
- HpeNet: Co-expression Network Database forFrontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.