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IntAct App: a Cytoscape application for molecular interaction network visualization and analysis

SUMMARY: IntAct App is a Cytoscape 3 application that grants in-depth access to IntAct’s molecular interaction data. It build networks where nodes are interacting molecules (mainly proteins, but also genes, RNA, chemicals…) and edges represent evidence of interaction. Users can query a network by pr...

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Detalles Bibliográficos
Autores principales: Ragueneau, Eliot, Shrivastava, Anjali, Morris, John H, del-Toro, Noemi, Hermjakob, Henning, Porras, Pablo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8545338/
https://www.ncbi.nlm.nih.gov/pubmed/33961020
http://dx.doi.org/10.1093/bioinformatics/btab319
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author Ragueneau, Eliot
Shrivastava, Anjali
Morris, John H
del-Toro, Noemi
Hermjakob, Henning
Porras, Pablo
author_facet Ragueneau, Eliot
Shrivastava, Anjali
Morris, John H
del-Toro, Noemi
Hermjakob, Henning
Porras, Pablo
author_sort Ragueneau, Eliot
collection PubMed
description SUMMARY: IntAct App is a Cytoscape 3 application that grants in-depth access to IntAct’s molecular interaction data. It build networks where nodes are interacting molecules (mainly proteins, but also genes, RNA, chemicals…) and edges represent evidence of interaction. Users can query a network by providing its molecules, identified by different fields and optionally include all their interacting partners in the resulting network. The app offers three visualizations: one only displaying interactions, another representing every evidence and the last one emphasizing evidence where mutated versions of proteins were used. Users can also filter networks and click on nodes and edges to access all their related details. Finally, the application supports automation of its main features via Cytoscape commands. AVAILABILITY AND IMPLEMENTATION: Implementation available at https://apps.cytoscape.org/apps/intactapp, while the source code is available at https://github.com/EBI-IntAct/IntactApp.
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spelling pubmed-85453382021-10-26 IntAct App: a Cytoscape application for molecular interaction network visualization and analysis Ragueneau, Eliot Shrivastava, Anjali Morris, John H del-Toro, Noemi Hermjakob, Henning Porras, Pablo Bioinformatics Applications Notes SUMMARY: IntAct App is a Cytoscape 3 application that grants in-depth access to IntAct’s molecular interaction data. It build networks where nodes are interacting molecules (mainly proteins, but also genes, RNA, chemicals…) and edges represent evidence of interaction. Users can query a network by providing its molecules, identified by different fields and optionally include all their interacting partners in the resulting network. The app offers three visualizations: one only displaying interactions, another representing every evidence and the last one emphasizing evidence where mutated versions of proteins were used. Users can also filter networks and click on nodes and edges to access all their related details. Finally, the application supports automation of its main features via Cytoscape commands. AVAILABILITY AND IMPLEMENTATION: Implementation available at https://apps.cytoscape.org/apps/intactapp, while the source code is available at https://github.com/EBI-IntAct/IntactApp. Oxford University Press 2021-05-07 /pmc/articles/PMC8545338/ /pubmed/33961020 http://dx.doi.org/10.1093/bioinformatics/btab319 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Ragueneau, Eliot
Shrivastava, Anjali
Morris, John H
del-Toro, Noemi
Hermjakob, Henning
Porras, Pablo
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis
title IntAct App: a Cytoscape application for molecular interaction network visualization and analysis
title_full IntAct App: a Cytoscape application for molecular interaction network visualization and analysis
title_fullStr IntAct App: a Cytoscape application for molecular interaction network visualization and analysis
title_full_unstemmed IntAct App: a Cytoscape application for molecular interaction network visualization and analysis
title_short IntAct App: a Cytoscape application for molecular interaction network visualization and analysis
title_sort intact app: a cytoscape application for molecular interaction network visualization and analysis
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8545338/
https://www.ncbi.nlm.nih.gov/pubmed/33961020
http://dx.doi.org/10.1093/bioinformatics/btab319
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