Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

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 data set, all through the Cytoscape user interface. stringApp
is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.