Here, we will focus on a network module encompassing pathways involved in
cell cycle control, apoptosis and protein degradation processes.
Modularity methods can be reviewed in the SARS CoV pathways analysis section in this web site.
First, we can have a look at the pathway/gene network graph. We can identify as key players Ub-ligases, P53 and its modulators, cyclin-dependent kinases, RUNX3 and NF-kB.
Next, observe how pathways in this module score in this aggregation scatter plot.
And how pathways in this module score in the volcano enrichment plot.
Aggregation and enrichment scores are ranked in the bar chart below.
We can also visualize GSEA Enrichment plots for some representative pathways.
For full reference, see “Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles.” and “ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization.“.
By using Reactome pathways hierarchies, we can identify additional biological roles to be played with associations of pathways in this module with same and higher level pathways.
This hierarchical association with different level pathways can also be visualized in a tree map, where parent pathways in headings embrace their child partners, sized and colored by their respective scores as described in the legend.