PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks

Protein phosphorylation is an essential
post-translational modification
(PTM) regulating many biological processes at the cellular and multicellular
level. Continuous improvements in phosphoproteomics technology allow
the analysis of this PTM in an expanding biological content, yet up
until now proteome data visualization tools are still very gene centric,
hampering the ability to comprehensively map and study PTM dynamics.
Here we present PhosphoPath, a Cytoscape app designed for the visualization
and analysis of quantitative proteome and phosphoproteome data sets.
PhosphoPath brings knowledge into the biological network by importing
publically available data and enables PTM site-specific visualization
of information from quantitative time series. To showcase PhosphoPath
performance we use a quantitative proteomics data set comparing patient-derived
melanoma cell lines grown in either conventional cell culture or xenografts.