ArticleNucleic acids research2014
YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae.
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 43 papers.
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Who cites it
43 citing papers in PubMed.
- Towards the construction of a virtual yeast.Nature · 2026Review
- Synthetic data enables human-grade microtubule analysis with foundation models for segmentation.PLoS computational biology · 2026Article
- Uncovering coordinated pathway interactions through gene co-differential expression in yeast.Nucleic acids research · 2026Article
- k- Strong Inference Algorithm: A Hybrid Information Theory Based Gene Network Inference Algorithm.Molecular biotechnology · 2024Article
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- PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains.BMC bioinformatics · 2021Article
- A functional genomic screen in Saccharomyces cerevisiae reveals divergent mechanisms of resistance to different alkylphosphocholine chemotherapeutic agents.G3 (Bethesda, Md.) · 2021Article
- Genetic dissection of complex traits using hierarchical biological knowledge.PLoS computational biology · 2021Article
- DeORFanizing Candida albicans Genes using Coexpression.mSphere · 2021Article
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- Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response.G3 (Bethesda, Md.) · 2020Article
- BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome.Bioinformatics (Oxford, England) · 2020Article
- Learning causal networks using inducible transcription factors and transcriptome-wide time series.Molecular systems biology · 2020Article
- Domain-mediated interactions for protein subfamily identification.Scientific reports · 2020Article
- YQFC: a web tool to compare quantitative biological features between two yeast gene lists.Database : the journal of biological databases and curation · 2020Article
- BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley,Frontiers in plant science · 2020Article
- Article
- Accurate prediction of protein-lncRNA interactions by diffusion and HeteSim features across heterogeneous network.BMC bioinformatics · 2018Article
- Using deep learning to model the hierarchical structure and function of a cell.Nature methods · 2018Article
Corrections and comments
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7 authors.
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Abstract
Saccharomyces cerevisiae, i.e. baker's yeast, is a widely studied model organism in eukaryote genetics because of its simple protocols for genetic manipulation and phenotype profiling. The high abundance of publicly available data that has been generated through diverse 'omics' approaches has led to the use of yeast for many systems biology studies, including large-scale gene network modeling to better understand the molecular basis of the cellular phenotype. We have previously developed a genome-scale gene network for yeast, YeastNet v2, which has been used for various genetics and systems biology studies. Here, we present an updated version, YeastNet v3 (available at http://www.inetbio.org/yeastnet/), that significantly improves the prediction of gene-phenotype associations. The extended genome in YeastNet v3 covers up to 5818 genes (∼99% of the coding genome) wired by 362 512 functional links. YeastNet v3 provides a new web interface to run the tools for network-guided hypothesis generations. YeastNet v3 also provides edge information for all data-specific networks (∼2 million functional links) as well as the integrated networks. Therefore, users can construct alternative versions of the integrated network by applying their own data integration algorithm to the same data-specific links.
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