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DRYGIN: a database of quantitative genetic interaction networks in yeast

Judice L. Y. Koh, Huiming Ding, Michael Costanzo, Anastasia Baryshnikova, Kiana Toufighi, Gary D. Bader, Chad L. Myers, Brenda J. Andrews, Charles Boone
2009 Nucleic Acids Research  
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

Shanow Uthman, Christian Bär, Viktor Scheidt, Shihui Liu, Sara ten Have, Flaviano Giorgini, Michael J. R. Stark, Raffael Schaffrath, Gregers Rom. Andersen
2013 PLoS Genetics  
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

Rolf O Lindén, Ville-Pekka Eronen, Tero Aittokallio
2011 BMC Systems Biology  
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

Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli S Nevalainen, Tero Aittokallio
2012 BioData Mining  
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

Matthew Norris, Simon Lovell, Daniela Delneri
2013 G3: Genes, Genomes, Genetics  
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

Montassar Ben Messaoud, Philippe Leray, Nahla Ben Amor
2013 The 2013 International Joint Conference on Neural Networks (IJCNN)  
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

Janusz Dutkowski, Michael Kramer, Michal A Surma, Rama Balakrishnan, J Michael Cherry, Nevan J Krogan, Trey Ideker
2012 Nature Biotechnology  
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

Rohith Srivas, Gregory Hannum, Johannes Ruscheinski, Keiichoro Ono, Peng-Liang Wang, Michael Smoot, Trey Ideker
2011 Nature Protocols  
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

Michael Downey, Kristin Baetz
2015 Briefings in Functional Genomics  
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

Ville-Pekka Eronen, Rolf O. Lindén, Anna Lindroos, Mirella Kanerva, Tero Aittokallio, Jürg Bähler
2010 PLoS ONE  
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

Dimitris Kyriakou, Emmanouil Stavrou, Panayiota Demosthenous, Georgia Angelidou, Bryan-Joseph San Luis, Charles Boone, Vasilis J. Promponas, Antonis Kirmizis
2016 BMC Biology  
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

Joëlle Barido-Sottani, Samuel D. Chapman, Evsey Kosman, Arcady R. Mushegian
2019 BMC Bioinformatics  
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

Anne Vanet, Claude Bazin, Rmi Coupaye, Sandrine Middendorp
2014 Science Postprint  
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

Robyn D. Moir, David A. Gross, David L. Silver, Ian M. Willis, Kaveh Ashrafi
2012 PLoS Genetics  
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

Vasso Makrantoni, Adam Ciesiolka, Conor Lawless, Josefin Fernius, Adele Marston, David Lydall, Michael J. R. Stark
2017 G3: Genes, Genomes, Genetics  
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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