TY - JOUR
T1 - Cytoscape stringApp
T2 - Network analysis and visualization of proteomics data
AU - Doncheva, Nadezhda T
AU - Morris, John
AU - Gorodkin, Jan
AU - Jensen, Lars J.
N1 - This article is part of the Software Tools and Resources 2019 special issue
PY - 2019/2/1
Y1 - 2019/2/1
N2 - Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import and visualization of additional data. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics dataset, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.
AB - Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import and visualization of additional data. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics dataset, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.
KW - Cytoscape
KW - functional enrichment
KW - network analysis
KW - network visualization
KW - protein networks
KW - proteomics data
KW - STRING database
U2 - 10.1021/acs.jproteome.8b00702
DO - 10.1021/acs.jproteome.8b00702
M3 - Journal article
C2 - 30450911
SN - 1535-3893
VL - 18
SP - 623
EP - 632
JO - Journal of Proteome Research
JF - Journal of Proteome Research
IS - 2
ER -