Differential analysis of high-throughput quantitative 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.

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High-Throughput Quantitative Genetic Interaction Mapping in the Fission YeastSchizosaccharomyces pombe

Cold Spring Harbor Protocols ◽

10.1101/pdb.top079905 ◽

2017 ◽

Vol 2018 (2) ◽

pp. pdb.top079905 ◽

Cited By ~ 2

Author(s):

Assen Roguev ◽

Colm J. Ryan ◽

Edgar Hartsuiker ◽

Nevan J. Krogan

Keyword(s):

High Throughput ◽

Genetic Interaction ◽

Quantitative Genetic

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Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data

BMC Systems Biology ◽

10.1186/s12918-017-0454-9 ◽

2017 ◽

Vol 11 (S4) ◽

Cited By ~ 9

Author(s):

Changhe Fu ◽

Su Deng ◽

Guangxu Jin ◽

Xinxin Wang ◽

Zu-Guo Yu

Keyword(s):

Bayesian Network ◽

Network Model ◽

Protein Interaction ◽

Genetic Interaction ◽

Interaction Data ◽

Bayesian Network Model ◽

Genetic Interaction Data

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

Acta Neuropathologica Communications ◽

10.1186/s40478-021-01148-z ◽

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.

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