In this section we will focus on pathways associated to calcium channels. This interaction module has been resolved by modularity analysis in the SARS CoV pathways analysis page in this web site.
First, we can have a look at the pathway/gene network graph. Although some calcium channels subunits in this module are associated to two generic pathways related to membrane potential, they also point to NCAM and LGI-ADAM interaction pathways, both related to neurite outgrowth and nerve development.
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.