88 A Practical Guide to Cancer Systems Biology
Figure 11. Visualization of kinase/phosphatase–phosphosite association network.phosphosite, the correlation value and the correspondingp-value are both
considered. DynaPho requires a minimum number of three time points;
however, users can set their data to only phosphosites that appear in a
minimum number of time points via the parameter “Minimum samples”,
to be greater than required value. DynaPho provides two methods
to calculate the correlation values: Spearman and Pearson correlation
coefficients. The Spearman correlation is used by default.- Click on “Submit” to get to the result page.
- Inspect kinase/phosphatase–phosphosite association network. The
associations can be viewed in an interactive network (Fig. 11). The node
color represents protein type, including kinase, phosphatase, and sub-
strate. The edge color denotes the correlation type: positive (red) or
negative (blue) correlation. The complexity of the graph can be reduce
by filtering edges based on the correlation score.
Summary
DynaPho is a computational tool created with the aim of facilitating various
analyses methods in a user-friendly and user-tailored way. In addition,