Summary: SIGNORApp is a Cytoscape 3 (3.8 and later) application that provides access to causal interactions annotated in the SIGNOR resource. The application builds networks that can be represented as weighted, signed, directed graphs, where nodes are interacting biological entities and edges represent causal interactions captured by expert curators from experiments reported in peer reviewed journals. Users can query the SIGNOR dataset with i) single or multiple entity name(s) or identifier(s) and optionally they may require to include in the output network their interacting partners; ii) browse pathways that are annotated in the SIGNOR resource; iii) extract the entire causal interactome. The app offers two visualizations modes: one only displaying entity interactions and a second emphasizing the post translational modifications occurring as a consequence of the interaction. In addition, users can click on nodes and edges to access entity and interaction annotations. Causal information is available for three model organisms: H. sapiens, M. musculus and R. norvegicus. Availability: SIGNORApp has been developed for Cytoscape 3 (3.8 and later) in the Java programming language. The latest source code and the plugin can be found at: https://github.com/SIGNORcysAPP/signor-app and https://apps.cytoscape.org/apps/signorapp, respectively.

SIGNORApp: a Cytoscape 3 application to access SIGNOR data / De Marinis, I; Lo Surdo, P; Cesareni, G; Perfetto, L. - In: BIOINFORMATICS. - ISSN 1367-4803. - 38:6(2022), pp. 1764-1766. [10.1093/bioinformatics/btab865]

SIGNORApp: a Cytoscape 3 application to access SIGNOR data

Lo Surdo P;Perfetto L
Ultimo
2022

Abstract

Summary: SIGNORApp is a Cytoscape 3 (3.8 and later) application that provides access to causal interactions annotated in the SIGNOR resource. The application builds networks that can be represented as weighted, signed, directed graphs, where nodes are interacting biological entities and edges represent causal interactions captured by expert curators from experiments reported in peer reviewed journals. Users can query the SIGNOR dataset with i) single or multiple entity name(s) or identifier(s) and optionally they may require to include in the output network their interacting partners; ii) browse pathways that are annotated in the SIGNOR resource; iii) extract the entire causal interactome. The app offers two visualizations modes: one only displaying entity interactions and a second emphasizing the post translational modifications occurring as a consequence of the interaction. In addition, users can click on nodes and edges to access entity and interaction annotations. Causal information is available for three model organisms: H. sapiens, M. musculus and R. norvegicus. Availability: SIGNORApp has been developed for Cytoscape 3 (3.8 and later) in the Java programming language. The latest source code and the plugin can be found at: https://github.com/SIGNORcysAPP/signor-app and https://apps.cytoscape.org/apps/signorapp, respectively.
2022
networks; Cytoscape;SIGNOR;post-translational modifications(PTMs); Phosphoproteomic studies
01 Pubblicazione su rivista::01a Articolo in rivista
SIGNORApp: a Cytoscape 3 application to access SIGNOR data / De Marinis, I; Lo Surdo, P; Cesareni, G; Perfetto, L. - In: BIOINFORMATICS. - ISSN 1367-4803. - 38:6(2022), pp. 1764-1766. [10.1093/bioinformatics/btab865]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/1660183
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