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YeastNet specifications

Information


Unique identifier OMICS_07445
Name YeastNet
Restrictions to use None
Version 3.0
Maintained Yes

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae

Publication for YeastNet

YeastNet citations

 (10)
library_books

InfAcrOnt: calculating cross ontology term similarities using information flow by a random walk

2018
BMC Genomics
PMCID: 5780854
PMID: 29363423
DOI: 10.1186/s12864-017-4338-6

[…] zymes by YeastCyc [] were obtained for yeast as PG, and corresponding 1750 random pairs were obtained as a NG. The WTGGN for calculating term pair similarity was built based on GO, GOA for yeast, and YeastNet []. After removing ‘IEA’ annotations, 1676 MF terms and 2655 BP terms are used to annotate 6332 yeast genes which generate 26,488 annotations were obtained. YeastNet [] is the latest and most […]

library_books

Taxonomically Restricted Genes with Essential Functions Frequently Play Roles in Chromosome Segregation in Caenorhabditis elegans and Saccharomyces cerevisiae

2017
PMCID: 5633384
PMID: 28839119
DOI: 10.1534/g3.117.300193

[…] n Wormnet (, ). Wormnet is a high-coverage network of functional linkages between genes that comprise coexpression, physical interactions, and genetic interactions among others; an analogous network (Yeastnet) exists for yeast (). We find that in Wormnet, many essential worm TRGs interact and have functional connections to genes that have well-characterized roles in chromosome segregation, includi […]

library_books

Erroneous energy generating cycles in published genome scale metabolic networks: Identification and removal

2017
PLoS Comput Biol
PMCID: 5413070
PMID: 28419089
DOI: 10.1371/journal.pcbi.1005494

[…] uire long computation times, GlobalFit resolved most solvable EGCs in under 10s, and all but one EGC within one minute (Supplementary ). The only calculation that required over one minute was for the yeastnet 7.6 model [], for which the CPLEX solver did not find an optimal solution within the set limit of 60 hours on 16 CPUs. The best set of changes found for this yeast model eliminated all EGCs b […]

library_books

Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms

2016
Sci Rep
PMCID: 5157009
PMID: 27976738
DOI: 10.1038/srep39237

[…] ply the summation of its weight in the original networks, which assumes equal importance of the input networks. It is seen that when inferring BP, information from BioGRID was most useful followed by YeastNet. On the other hand, when inferring CC, YeastNet was most useful followed by DRYGIN and BioGRID. Finally, when inferring MF, YeastNet was most useful followed by BioGRID. These results indicat […]

library_books

Genomic Analysis of ATP Efflux in Saccharomyces cerevisiae

2015
PMCID: 4704715
PMID: 26585826
DOI: 10.1534/g3.115.023267

[…] lationships within these groups, we generated interaction networks for each. This reveals additional relationships between genes that were not captured by GO analysis. Networks were constructed using YeastNet, a probabilistic functional gene network for yeast that incorporates experimental observations from DNA microarrays, physical protein interactions, genetic interactions, literature, and compa […]

library_books

Associations of SNPs located at candidate genes to bovine growth traits, prioritized with an interaction networks construction approach

2015
BMC Genet
PMCID: 4511253
PMID: 26198337
DOI: 10.1186/s12863-015-0247-3

[…] networks for each of these organisms were downloaded from the FunctionalNet server (http://www.functionalnet.org/): HumanNet v.1 [], MouseNet v.1 [], WormNet v.2 [], AraNet v.1 [], RiceNet v.1 [] and YeastNet v.2 []. From each of these functional networks, a B. taurus network was derived using an interologous approach [], and the value previously associated with each of these interactions served a […]

Citations

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YeastNet institution(s)
Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea

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