ArticleNucleic acids research2014
WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Uncovering coordinated pathway interactions through gene co-differential expression in yeast.Nucleic acids research · 2026Article
- iTraNet: a web-based platform for integrated trans-omics network visualization and analysis.Bioinformatics advances · 2024Article
- Examining Sporadic Cancer Mutations Uncovers a Set of Genes Involved in Mitochondrial Maintenance.Genes · 2023Article
- Identifying accurate link predictors based on assortativity of complex networks.Scientific reports · 2022Article
- Article
- Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes.Biology direct · 2020Article
- Identifying Influencers in Social Networks.Entropy (Basel, Switzerland) · 2020Article
- BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome.Bioinformatics (Oxford, England) · 2020Article
- BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley,Frontiers in plant science · 2020Article
- WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans.Database : the journal of biological databases and curation · 2020Article
- EPIC: software toolkit for elution profile-based inference of protein complexes.Nature methods · 2019Article
- An integrative tissue-network approach to identify and test human disease genes.Nature biotechnology · 2018Article
- Functional Annotation ofBiomolecules · 2018Article
- Transcriptomic, Functional, and Network Analyses Reveal Novel Genes Involved in the Interaction BetweenFrontiers in cellular and infection microbiology · 2018Article
- Ras/MAPK Modifier Loci Revealed by eQTL inG3 (Bethesda, Md.) · 2017Article
- SoyNet: a database of co-functional networks for soybean Glycine max.Nucleic acids research · 2017Article
- From sequencing data to gene functions: co-functional network approaches.Animal cells and systems · 2017Review
- Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans.Cell reports · 2016Article
- PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants.Scientific reports · 2016Article
- A quantitative genome-wide RNAi screen in C. elegans for antifungal innate immunity genes.BMC biology · 2016Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
High-throughput experimental technologies gradually shift the paradigm of biological research from hypothesis-validation toward hypothesis-generation science. Translating diverse types of large-scale experimental data into testable hypotheses, however, remains a daunting task. We previously demonstrated that heterogeneous genomics data can be integrated into a single genome-scale gene network with high prediction power for ribonucleic acid interference (RNAi) phenotypes in Caenorhabditis elegans, a popular metazoan model in the study of developmental biology, neurobiology and genetics. Here, we present WormNet version 3 (v3), which is a new network-assisted hypothesis-generating server for C. elegans. WormNet v3 includes major updates to the base gene network, which substantially improved predictions of RNAi phenotypes. The server generates various gene network-based hypotheses using three complementary network methods: (i) a phenotype-centric approach to 'find new members for a pathway'; (ii) a gene-centric approach to 'infer functions from network neighbors' and (iii) a context-centric approach to 'find context-associated hub genes', which is a new method to identify key genes that mediate physiology within a specific context. For example, we demonstrated that the context-centric approach can be used to identify potential molecular targets of toxic chemicals. WormNet v3 is freely accessible at http://www.inetbio.org/wormnet.
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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.