A Practical Guide to Cancer Systems Biology

82 A Practical Guide to Cancer Systems Biology

Construction of function profile

Gene set overrepresentation analysis is commonly used for the interpretation
of proteomics and phosphoproteomics data. To reveal the dynamics of
biological processes, DynaPho integrates the overrepresented gene set of
all time point or conditions into a functional profile. In this analysis,
DynaPho only considers the gene sets from biological process category of
Gene Ontology (GO).

1. Click on “Function Enrichment” on the header.


2. Set a criterion for defining the proteins with differential change on
   phosphorylation.


3. Specify the parameters for function enrichment analysis. Select a back-
   ground set and define ap-value cutoff.


4. Click on “Submit” to get to the result page.


5. Inspect function enrichment analysis results. For each time point or
   condition, the overrepresented GO terms are tabularized and graphed
   as an enrichment map, respectively (Fig. 6). The different GO terms and
   theiroverlapcanbeviewedinaninteractivenetwork.Thenodesizeis
   proportion to the number of members of the GO term, and the node color
   denotes enrichment significance. The GO terms with similar semantic
   meanings will tend to be connected and form a cluster. The complexity
   of the graph can be reduced by filtering edges based on the overlap score.


6. Inspect function profiles. DynaPho compiles the enrichment analysis
   results of all time points or conditions into a function profile and presents
   them as a heatmap. Hit the tab of “Function profile” to view the function
   profile (Fig. 7). The hierarchical cluster will be performed by enriched GO
   terms, and the GO terms with similar function profiles will be clustered
   together.

Construction of dynamic interaction networks

Protein–protein interaction network (PIN) can provide insights into signaling
cascade. This analysis will generate PIN for each time point or condition,
and user can compare the PINs among different time points or conditions to
indicate the important interactions and pathways.

1. Click on “Dynamic Network” on the header.


2. Set a criterion for defining the proteins with differential change on phospho-
   rylation. These proteins are used as seeds to construct the network.