scholarly journals Automated identification of pathways from quantitative genetic interaction data

2010 ◽  
Vol 6 (1) ◽  
pp. 379 ◽  
Author(s):  
Alexis Battle ◽  
Martin C Jonikas ◽  
Peter Walter ◽  
Jonathan S Weissman ◽  
Daphne Koller
Keyword(s):  
Genetic Interaction ◽  
Interaction Data ◽  
Automated Identification ◽  
Quantitative Genetic ◽  
Genetic Interaction Data

scholarly journals Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

2008 ◽  
Vol 4 (4) ◽  
pp. e1000065 ◽  
Author(s):  
Sourav Bandyopadhyay ◽  
Ryan Kelley ◽  
Nevan J. Krogan ◽  
Trey Ideker
Keyword(s):  
Genetic Interaction ◽  
Protein Complexes ◽  
Interaction Data ◽  
Quantitative Genetic ◽  
Genetic Interaction Data

scholarly journals MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action

2017 ◽  
Vol 34 (7) ◽  
pp. 1251-1252 ◽  
Author(s):  
Justin Nelson ◽  
Scott W Simpkins ◽  
Hamid Safizadeh ◽  
Sheena C Li ◽  
Jeff S Piotrowski ◽  
...  
Keyword(s):  
Genetic Interaction ◽  
Data Repository ◽  
Interaction Data ◽  
Chemical Genetic ◽  
Web Resource ◽  
Modes Of Action ◽  
Genetic Interaction Data

scholarly journals Maximal Extraction of Biological Information from Genetic Interaction Data

2009 ◽  
Vol 5 (4) ◽  
pp. e1000347 ◽  
Author(s):  
Gregory W. Carter ◽  
David J. Galas ◽  
Timothy Galitski
Keyword(s):  
Genetic Interaction ◽  
Biological Information ◽  
Interaction Data ◽  
Genetic Interaction Data

scholarly journals Porting and using PanGIA for Cytoscape 3: challenges and solutions

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 150 ◽  
Author(s):  
David Welker ◽  
Barry Demchak
Keyword(s):  
Data Model ◽  
Genetic Interaction ◽  
Third Party ◽  
Physical Interaction ◽  
Interaction Data ◽  
Scientific Analysis ◽  
Genetic Interaction Data

Much of the biologically significant functionality in Cytoscape is contained within third-party add-ons, called plugins in Cytoscape 2 and apps in Cytoscape 3. In the transition from Cytoscape 2 to Cystoscape 3, some of the underlying assumptions upon which plugins relied changed, requiring a significant porting effort for plugins to work as Cytoscape 3 apps. PanGIA is a Cytoscape add-on (http://apps.cytoscape.org/apps/pangia) designed to analyze and visualize genetic interaction data in light of physical interaction data. In order to convert the PanGIA plugin to an app, various challenges, including those related to a transformed data model, concurrency, and randomization had to be overcome. In the process, the ability to control randomization was added to the GUI, a feature which was not only integral to the porting process, but which also ensures more easily reproducible scientific analysis for PanGIA users. Most authors of Cytoscape 2 plugins will face similar challenges porting their software to work with Cytoscape 3, and this paper gives details of how the PanGIA port addressed them.

scholarly journals TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Erik M. Lehmkuhl ◽  
Suvithanandhini Loganathan ◽  
Eric Alsop ◽  
Alexander D. Blythe ◽  
Tina Kovalik ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Rna Binding ◽  
Genetic Interaction ◽  
Neuromuscular Synapse ◽  
Pentose Phosphate ◽  
Interaction Data ◽  
Specific Effects ◽  
Genetic Interaction Data ◽  
Lateral Sclerosis ◽  
Ribosome Association

AbstractAmyotrophic lateral sclerosis (ALS) is a genetically heterogeneous neurodegenerative disease in which 97% of patients exhibit cytoplasmic aggregates containing the RNA binding protein TDP-43. Using tagged ribosome affinity purifications in Drosophila models of TDP-43 proteinopathy, we identified TDP-43 dependent translational alterations in motor neurons impacting the spliceosome, pentose phosphate and oxidative phosphorylation pathways. A subset of the mRNAs with altered ribosome association are also enriched in TDP-43 complexes suggesting that they may be direct targets. Among these, dlp mRNA, which encodes the glypican Dally like protein (Dlp)/GPC6, a wingless (Wg/Wnt) signaling regulator is insolubilized both in flies and patient tissues with TDP-43 pathology. While Dlp/GPC6 forms puncta in the Drosophila neuropil and ALS spinal cords, it is reduced at the neuromuscular synapse in flies suggesting compartment specific effects of TDP-43 proteinopathy. These findings together with genetic interaction data show that Dlp/GPC6 is a novel, physiologically relevant target of TDP-43 proteinopathy.

scholarly journals Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data

2011 ◽  
Vol 7 (5) ◽  
pp. e1002048 ◽  
Author(s):  
Hilary Phenix ◽  
Katy Morin ◽  
Cory Batenchuk ◽  
Jacob Parker ◽  
Vida Abedi ◽  
...  
Keyword(s):  
Genetic Interaction ◽  
Interaction Data ◽  
Epistasis Analysis ◽  
Pathway Inference ◽  
Genetic Interaction Data
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