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DRYGIN: a database of quantitative genetic interaction networks in yeast
2009
Nucleic Acids Research
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To facilitate access to this resource, which will ultimately represent a complete genetic interaction network for a eukaryotic cell, we developed DRYGIN (Data Repository of Yeast Genetic Interactions)- ...
a web database system that aims at providing a central platform for yeast genetic network analysis and visualization. ...
Brost, Bilal Sheikh and other anonymous users of DRYGIN beta version for testing and suggestions, and Chris S.H. Tan for naming the database. Conflict of interest statement. None declared. ...
doi:10.1093/nar/gkp820
pmid:19880385
pmcid:PMC2808960
fatcat:jrd5dffhtver7h422serxhal4q
The Amidation Step of Diphthamide Biosynthesis in Yeast Requires DPH6, a Gene Identified through Mining the DPH1-DPH5 Interaction Network
2013
PLoS Genetics
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Here we mine the genetic interaction landscapes of DPH1-DPH5 to identify a candidate gene for the elusive amidase (YLR143w/DPH6) and confirm involvement of a second gene (YBR246w/ DPH7) in the amidation ...
The latter conclusion is based on our observation that dph7 mutants show drastically upregulated interaction between Dph5 and eEF2, indicating that their association is kept in check by Dph7. ...
Charles Boone and Michael Costanzo for their advice and assistance in SGA data analysis. In addition we thank Dr. ...
doi:10.1371/journal.pgen.1003334
pmid:23468660
pmcid:PMC3585130
fatcat:4yocq6cyy5azlkn3szhmqluoqa
Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis
2011
BMC Systems Biology
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evaluation among these quantitative maps of genetic interactions in yeast. ...
into the functional wiring diagrams of genetic interaction networks on a global scale. ...
Cosmin Saveanu for providing us with the quantitative SGA and GIM datasets, respectively. The work was supported by the Academy of Finland (grants 120 569, 133 227 and 140 880). ...
doi:10.1186/1752-0509-5-45
pmid:21435228
pmcid:PMC3079637
fatcat:m5b5w4aeczajrpsipk2dg4dchq
A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization
2012
BioData Mining
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In particular, it could improve drawing of large-scale networks of yeast genetic interactions and human physical interactions. ...
Using a wide variety of real life biological networks, we carried out a systematic evaluation of the method in comparison with other layout algorithms in Cytoscape. ...
The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. ...
doi:10.1186/1756-0381-5-2
pmid:22448851
pmcid:PMC3342218
fatcat:md7boc6imzge5is3ky2hrpz3xi
Characterization and Prediction of Haploinsufficiency Using Systems-Level Gene Properties in Yeast
2013
G3: Genes, Genomes, Genetics
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We compared the haploinsufficiency profiles against 23 gene properties and found that genes with (i) higher level of connectivity (degree) in a protein-protein interaction network, (ii) higher genetic ...
Using a similar approach we identified significant relationships between haploinsufficiency and two gene properties in Schizosaccharomyces pombe, relationships that hold despite the lack of conserved HI ...
ACKNOWLEDGEMENTS We would like to thank Ryan Ames, who provided assistance in calculating betweenness from protein and genetic interaction data, and Valerie Wood for providing S. cerevisiae and Sz. pombe ...
doi:10.1534/g3.113.008144
pmid:24048642
pmcid:PMC3815059
fatcat:yalusgnrvjc3fb3rbplptuaxji
Active learning of causal Bayesian networks using ontologies: A case study
2013
The 2013 International Joint Conference on Neural Networks (IJCNN)
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Due to its high impact in various applications involving reasoning tasks, machine learning researchers have proposed a number of techniques to learn Causal Bayesian Networks. ...
Within the last years, probabilistic causality has become a very active research topic in artificial intelligence and statistics communities. ...
Most of these scientific databases such as, Data Repository of Yeast Genetic Interactions (DRYGIN) 3 [25] , enable a convenient access to genes in terms of the biological pathways in which they intervene ...
doi:10.1109/ijcnn.2013.6706815
dblp:conf/ijcnn/MessaoudLA13
fatcat:ih2ji77ijrch7fz577m6tmix2q
A gene ontology inferred from molecular networks
2012
Nature Biotechnology
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M.S. and N.J.K. performed the quantitative genetic interaction profiling and interpreted the data. R.B. and J.M.C. investigated and curated the new ontology terms and relations. ...
We obtained four yeast networks from public databases, corresponding to physical protein-protein interactions (BioGRID 54 ), synthetic-lethal and epistatic genetic interactions (DRYGIN database 14 ; http ...
(c) Network density of general terms of size k ≥ k 0 in the YeastNet (blue bars) in comparison to a random network in which interactions falling within specific terms of size k < k 0 are preserved and ...
doi:10.1038/nbt.2463
pmid:23242164
pmcid:PMC3654867
fatcat:lshvmdsosvek5p2jptkpqr5yui
Assembling global maps of cellular function through integrative analysis of physical and genetic networks
2011
Nature Protocols
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by filtering and basic network visualization. next, panGIa is used to infer a set of modules and their functional inter-relationships. this module map is visualized in a number of intuitive ways, and ...
and genetic interaction alignment) is a plug-in for the bioinformatics platform cytoscape, designed to integrate physical and genetic interactions into hierarchical module maps. panGIa identifies 'modules ...
However, any single network (either physical or genetic) must consist of a single type of interactions (i.e., either all quantitative interactions or all non-quantitative interactions). 8| Click on the ...
doi:10.1038/nprot.2011.368
pmid:21886098
pmcid:PMC3383003
fatcat:xv5ntj7ilbgwdk3qciog3keb7a
Building a KATalogue of acetyllysine targeting and function
2015
Briefings in Functional Genomics
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The Saccharomyces cerevisiae model system provides such a toolkit in the context of both tried and true genetic techniques and cutting-edge proteomic and cell imaging methods. ...
While these enzymes are best characterized as histone modifiers and regulators of gene transcription, work in a number of systems highlights that acetylation is a pervasive modification and suggests a ...
K.B. is a Canada Research Chair in Functional and Chemical Biology. We thank Michael Kennedy for critical reading and suggestions. ...
doi:10.1093/bfgp/elv045
pmid:26512033
pmcid:PMC4803063
fatcat:wv2tjuu3pzdtzlqbsxbsxgdco4
Genome-Wide Scoring of Positive and Negative Epistasis through Decomposition of Quantitative Genetic Interaction Fitness Matrices
2010
PLoS ONE
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In general, the modeling framework, enabling accurate identification and classification of genetic interactions, provides a solid basis for completing and mining the genetic interaction networks in yeast ...
To address these questions, we introduce here a computational approach for improving the quantitative discrimination power encoded in the genetic interaction screening data. ...
Acknowledgments The authors thank Charlie Boone and Cosmin Saveanu for providing us with the quantitative SGA and GIM datasets, respectively, and Chad Myers for his valuable comments on the manuscript. ...
doi:10.1371/journal.pone.0011611
pmid:20657656
pmcid:PMC2904709
fatcat:4bguqhhz4jg4rb6jbldo7wnr74
Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae
2016
BMC Biology
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Therefore, the function of lncRNAs could be illuminated through systematic analysis of their synthetic genetic interactions (GIs). ...
Conclusions: Overall, our work proposes that systematic application of this genetic approach could determine the functional significance of individual lncRNAs in yeast and other complex organisms. ...
Availability of data and material All data generated or analysed during this study are included in this published article and its additional files. ...
doi:10.1186/s12915-016-0325-7
pmid:27927215
pmcid:PMC5142380
fatcat:jnnxijou2valvlwdsdo4jmiy74
Measuring similarity between gene interaction profiles
2019
BMC Bioinformatics
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We re-analyzed well-studied data on yeast genetic interactions, constructed four genetic networks using four different similarity measures, and detected gene modules in each network using the same algorithm ...
Conclusions: The discovery of molecular modules in genetic networks is sensitive to the way of measuring similarity between profiles of gene interactions in a cell. ...
A.Baryshnikova for the discussions of the yeast dataset, to Dr. R.Krumlauf and Dr. A. Sanchez Alvarado for support of this work, and to the reviewers for constructive suggestions. ...
doi:10.1186/s12859-019-3024-x
fatcat:rnwls6l4wvdadcfft45gwdxjku
Between compensatory mutations and synthetic lethals: genetic mutations, a new challenge for tomorrow's medicine
2014
Science Postprint
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Between compensatory mutations and synthetic lethals: genetic mutations, a new challenge for tomorrow's medicine. ...
of 6,000 deletions [78] in the 6,000 predicted genes of the yeast genome, opening up new horizons for global analysis of SL genetic interactions, called a synthetic genetic array (SGA). ...
WT: Wild Type RNA
[81], chromosome segregation [82], S. cerevisiae budding [83], and many others were compiled in the DRYGIN database [84]. ...
doi:10.14340/spp.2014.10r0002
fatcat:xnk2pgueirhmdf27poktm7z3ia
SCS3 and YFT2 Link Transcription of Phospholipid Biosynthetic Genes to ER Stress and the UPR
2012
PLoS Genetics
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genes in a human embryonic kidney cell line promotes LD formation, and expression of human FIT2 in yeast rescues the inositol auxotrophy and chemical and genetic phenotypes of strains lacking SCS3. ...
To better understand the function of SCS3 and YFT2, we investigated the chemical sensitivities of strains deleted for either or both genes and identified synthetic genetic interactions against the viable ...
Snapp and members of the Einstein yeast group for their insight and discussion during the course of this research. ...
doi:10.1371/journal.pgen.1002890
pmid:22927826
pmcid:PMC3426550
fatcat:usfnifae2bf2tmfga4ip3ukzce
A Functional Link Between Bir1 and the Saccharomyces cerevisiae Ctf19 Kinetochore Complex Revealed Through Quantitative Fitness Analysis
2017
G3: Genes, Genomes, Genetics
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Here, we report a genome-wide genetic interaction screen in Saccharomyces cerevisiae using the bir1-17 mutant, identifying through quantitative fitness analysis deletion mutations that act as enhancers ...
chl4∆ in combination with bir1-17, neither gene knockout showed any genetic interaction with either ipl1-321 or sli15-3 Our data therefore imply a specific functional connection between the Ctf19 complex ...
ACKNOWLEDGMENTS We thank Georjana Barnes for providing the nbl1-6 mutant, and Charlie Boone for providing yeast strains. ...
doi:10.1534/g3.117.300089
pmid:28754723
pmcid:PMC5592945
fatcat:nfy7ekg7gzfsjo3xbnyfraevka
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