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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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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. |
format | Online Article Text |
id | pubmed-8545338 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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