title: YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae.
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.
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Hanhae
authors.initials: H
authors.lastname: Kim
authors.forename: Junha
authors.initials: J
authors.lastname: Shin
authors.forename: Eiru
authors.initials: E
authors.lastname: Kim
authors.forename: Hyojin
authors.initials: H
authors.lastname: Kim
authors.forename: Sohyun
authors.initials: S
authors.lastname: Hwang
authors.forename: Jung Eun
authors.initials: JE
authors.lastname: Shim
authors.forename: Insuk
authors.initials: I
authors.lastname: Lee
mesh_terms: D030541:Databases, Genetic; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D020407:Internet; D010641:Phenotype; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins