TY - JOUR

T1 - Cytoscape stringApp 2.0

T2 - Analysis and Visualization of Heterogeneous Biological Networks

AU - Doncheva, Nadezhda T.

AU - Morris, John H.

AU - Holze, Henrietta

AU - Kirsch, Rebecca

AU - Nastou, Katerina C.

AU - Cuesta-Astroz, Yesid

AU - Rattei, Thomas

AU - Szklarczyk, Damian

AU - Von Mering, Christian

AU - Jensen, Lars J.

N1 - Publisher Copyright: © 2022 The Authors. Published by American Chemical Society.

PY - 2022

Y1 - 2022

N2 - Biological networks are often used to represent complex biological systems, which can contain several types of entities. Analysis and visualization of such networks is supported by the Cytoscape software tool and its many apps. While earlier versions of stringApp focused on providing intraspecies protein-protein interactions from the STRING database, the new stringApp 2.0 greatly improves the support for heterogeneous networks. Here, we highlight new functionality that makes it possible to create networks that contain proteins and interactions from STRING as well as other biological entities and associations from other sources. We exemplify this by complementing a published SARS-CoV-2 interactome with interactions from STRING. We have also extended stringApp with new data and query functionality for protein-protein interactions between eukaryotic parasites and their hosts. We show how this can be used to retrieve and visualize a cross-species network for a malaria parasite, its host, and its vector. Finally, the latest stringApp version has an improved user interface, allows retrieval of both functional associations and physical interactions, and supports group-wise enrichment analysis of different parts of a network to aid biological interpretation. stringApp is freely available at https://apps.cytoscape.org/apps/stringapp.

AB - Biological networks are often used to represent complex biological systems, which can contain several types of entities. Analysis and visualization of such networks is supported by the Cytoscape software tool and its many apps. While earlier versions of stringApp focused on providing intraspecies protein-protein interactions from the STRING database, the new stringApp 2.0 greatly improves the support for heterogeneous networks. Here, we highlight new functionality that makes it possible to create networks that contain proteins and interactions from STRING as well as other biological entities and associations from other sources. We exemplify this by complementing a published SARS-CoV-2 interactome with interactions from STRING. We have also extended stringApp with new data and query functionality for protein-protein interactions between eukaryotic parasites and their hosts. We show how this can be used to retrieve and visualize a cross-species network for a malaria parasite, its host, and its vector. Finally, the latest stringApp version has an improved user interface, allows retrieval of both functional associations and physical interactions, and supports group-wise enrichment analysis of different parts of a network to aid biological interpretation. stringApp is freely available at https://apps.cytoscape.org/apps/stringapp.

KW - cross-species interactions

KW - Cytoscape

KW - enrichment analysis

KW - heterogeneous networks

KW - host-parasite

KW - omics data

KW - STRING

KW - stringApp

KW - virus-host

U2 - 10.1021/acs.jproteome.2c00651

DO - 10.1021/acs.jproteome.2c00651

M3 - Journal article

C2 - 36512705

AN - SCOPUS:85144100215

VL - 22

SP - 637

EP - 646

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 2

ER -