ArticlePloS one2007
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae.
Article in PloS one, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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106 citing papers in PubMed, 190 citations in OpenAlex.
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- The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma.BMC genomics · 2020Article
- Construction, comparison and evolution of networks in life sciences and other disciplines.Journal of the Royal Society, Interface · 2020Article
- BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley,Frontiers in plant science · 2020Article
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- Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.BMC systems biology · 2018Article
- Reduced Expression ofThe Plant cell · 2018Article
- Identifying term relations cross different gene ontology categories.BMC bioinformatics · 2017Article
- Mitogen-activated protein kinases, Fus3 and Kss1, regulate chronological lifespan in yeast.Aging · 2017Article
- Revealing protein functions based on relationships of interacting proteins and GO terms.Journal of biomedical semantics · 2017Article
- Combined GWAS and 'guilt by association'-based prioritization analysis identifies functional candidate genes for body size in sheep.Genetics, selection, evolution : GSE · 2017Article
- Predictability of Genetic Interactions from Functional Gene Modules.G3 (Bethesda, Md.) · 2017Article
- SoyNet: a database of co-functional networks for soybean Glycine max.Nucleic acids research · 2017Article
- The Roles of Puf6 and Loc1 in 60S Biogenesis Are Interdependent, and Both Are Required for Efficient Accommodation of Rpl43.The Journal of biological chemistry · 2016Article
- PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants.Scientific reports · 2016Article
- Algorithms for modeling global and context-specific functional relationship networks.Briefings in bioinformatics · 2016Article
- Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery.Briefings in bioinformatics · 2016Review
- Genomic Analysis of ATP Efflux in Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2015Article
46 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundProbabilistic functional gene networks are powerful theoretical frameworks for integrating heterogeneous functional genomics and proteomics data into objective models of cellular systems. Such networks provide syntheses of millions of discrete experimental observations, spanning DNA microarray experiments, physical protein interactions, genetic interactions, and comparative genomics; the resulting networks can then be easily applied to generate testable hypotheses regarding specific gene functions and associations. METHODOLOGY/PRINCIPAL
findingsWe report a significantly improved version (v. 2) of a probabilistic functional gene network of the baker's yeast, Saccharomyces cerevisiae. We describe our optimization methods and illustrate their effects in three major areas: the reduction of functional bias in network training reference sets, the application of a probabilistic model for calculating confidences in pair-wise protein physical or genetic interactions, and the introduction of simple thresholds that eliminate many false positive mRNA co-expression relationships. Using the network, we predict and experimentally verify the function of the yeast RNA binding protein Puf6 in 60S ribosomal subunit biogenesis. CONCLUSIONS/SIGNIFICANCE: YeastNet v. 2, constructed using these optimizations together with additional data, shows significant reduction in bias and improvements in precision and recall, in total covering 102,803 linkages among 5,483 yeast proteins (95% of the validated proteome). YeastNet is available from http://www.yeastnet.org.
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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.