2019 February 01; 18(2): 623–632. | Nadezhda T. Doncheva*,†,‡,§, John H. Morris†, Jan Gorodkin§,‡, Lars J. Jensen*†,‡
The article introduces stringApp, a Cytoscape app designed to integrate the STRING database with Cytoscape for network analysis and visualization of proteomics data. STRING provides protein networks for over 2000 organisms, including physical interactions and functional associations, while Cytoscape is better suited for handling large networks and offers more flexibility in data import and visualization. stringApp facilitates the import of STRING networks into Cytoscape, retains the appearance and features of STRING, and integrates data from associated databases. The app supports various types of queries, including protein lists, chemical compounds, diseases, and PubMed queries, and retrieves additional information such as small molecule interactions, subcellular localization, tissue expression, and drug target data. The article demonstrates how stringApp can be used to analyze and visualize a phosphoproteomics dataset from ovarian cancer, highlighting the network's structure, functional enrichment, and disease associations. The app is freely available from the Cytoscape app store and can be used for a wide range of high-throughput data types, including transcriptomics, phenotypic screens, and mutation data.The article introduces stringApp, a Cytoscape app designed to integrate the STRING database with Cytoscape for network analysis and visualization of proteomics data. STRING provides protein networks for over 2000 organisms, including physical interactions and functional associations, while Cytoscape is better suited for handling large networks and offers more flexibility in data import and visualization. stringApp facilitates the import of STRING networks into Cytoscape, retains the appearance and features of STRING, and integrates data from associated databases. The app supports various types of queries, including protein lists, chemical compounds, diseases, and PubMed queries, and retrieves additional information such as small molecule interactions, subcellular localization, tissue expression, and drug target data. The article demonstrates how stringApp can be used to analyze and visualize a phosphoproteomics dataset from ovarian cancer, highlighting the network's structure, functional enrichment, and disease associations. The app is freely available from the Cytoscape app store and can be used for a wide range of high-throughput data types, including transcriptomics, phenotypic screens, and mutation data.