76 A Practical Guide to Cancer Systems Biology
PhosphoPath^6 is a Cytoscape app designed for the visualization of protein-
protein interactions and site-specific kinase-substrate interactions with
quantitative information for multiple conditions or time points. SELPHI^9 is a
web-based server providing various functional analysis of phosphoproteomics
data, such as enrichment analysis and correlation analysis.
In this chapter, we will demonstrate how to utilize DynaPho^10 to
unveil the biological information behind the phosphoproteomics data.
DynaPho is an integrative and web-based platform for analysis of large-
scale phosphoproteomics data, especially time-course or multiple-condition
experiments. DynaPho aims to provide the analysis of phosphoproteomics
data readily available to the non-bioinformatics experts. Various func-
tional analysis methods have been implemented in DynaPho, including
phosphorylation profile clustering, temporal function enrichment analysis,
kinase activity analysis, dynamic network analysis, and kinase/phosphatase-
phosphosite association analysis. These methods have been comprehensively
used in phosphoproteomics research as well as improved and extended for
the investigation of time-series and multiple-condition data. In addition,
DynaPho can record all analysis results with different parameter settings
for a dataset. When a user uploads a phosphoproteomics dataset, a
unique accession number is assigned to it and the user can retrieve their
previous analysis results and resubmit an analysis with different parameter
settings via this accession number. Through these different analysis results,
users can interpret their data and generate a hypothesis for further
studies.
Materials
Equipment requirements
DynaPho is accessed via the web interface and data analysis is performed
on a dedicated web server. Thus, a standard computer with a modern web
browser that supports JavaScript and HTML5 is required for the interaction
of DynaPho interface.
Input data
After the processes of the peptide identification, quantification, and phos-
phosite estimation by other MS analysis softwares, such as MaxQuant,^11
users can extract the required information from the output files of these