I would like to get the pairs of coexpressed/coregulated genes that belong to the same KEGG pathways. However, I am not sure if I should use all the pairs shown in KEGG or if I should filter out some of them first.
So, I managed to retrieve all the KEGG pathways and edges using the graphite R package, but I don't know if all of the edges are valid and reliable, since there are many interaction types and I don't know all of them. These are the types:
- Process(expression) .Process(missing interaction)
- Process(indirect effect)
- Process(state change)
And according to the KEGG documentation (https://www.genome.jp/kegg/document/help_pathway.html) there are only two types for gene expression relations: expression and repression. Since I only want to get the genes in the pathway, should I only use these two? Or also use the rest of them (like "Process(methylation)", etc) ?
Then, what are the following: "Process(missing)" or "Process(missing interaction)" or "Process"?