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2 hours ago by

Hello all,

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(indirect)
  • Binding
  • Process(missing)
  • Process(inhibition)
  • Process(phosphorylation)
  • Process(activation)
  • Process(expression) .Process(missing interaction)
  • Process(indirect effect)
  • Process(binding/association)
  • Process(ubiquitination)
  • Process(dephosphorylation)
  • Process(dissociation)
  • Process(methylation)
  • Process(repression)
  • Process
  • Process(glycosylation)
  • Process(state change)

And according to the KEGG documentation (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"?



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