78 A Practical Guide to Cancer Systems Biology
Figure 2. Submit data to DynaPho. The interface for (a) data selection and (b) data
preview and attribution edition.
- As the process is completed, the page will be directed to “Data
Summary”. In this page, DynaPho shows the distribution of phospho-
rylation residues by a pie chart and the distribution of phosphorylation
ratios by a histogram. In addition, users can view their data and plot the
profile of interested phosphosites (Fig. 3).
Clustering of phosphorylation profiles
The phosphosites with similar phosphorylation profiles might be involved
in the same biological process or regulated by the same kinase family. To
investigate the possible biological processes or regulators within the phospho-
proteomics, the phosphosites will be grouped based on their phosphorylation
profiles, and then the GO overrepresentation analysis and motif enrichment
analysis will be performed on each group.
- Click on “Profile Clustering” on the header.
- Specify the method for missing value imputation (Fig. 4(a)). Because
missing value is not allowed in clustering analysis, the phosphosites with