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How to follow the flow of a cell signaling network?

I have a large igraph as follows:

IGRAPH f3064a8 DN-- 4482 17489 -- 
+ attr: name (v/c), id (v/c), symbol (v/c), description (v/c), pathway (v/c), activationSignal (e/c), status (e/c)

After that, I want to subgraph a query with genes of interest in order to know which pathways are active. A single node in g might participate in multiple pathways, but V(g)$description displays the "function" of the gene (i.e. TF, Receptor, Protein...). Based on that info, what I do not know is what's the best approach?

  1. Subgraph specifically the genes of interest and based on that obtain the V(g)$pathway (pathways) flow. This means, the pathways containing just the genes of interest.
  2. Subgraph the neighborhood of the genes of interest (order = 1) and based on that obtain the V(g)$pathway[grepl('Receptor', V(g)$description)] (receptors for pathways) flow. This means, obtain the neighbor receptors which activate pathways.

Any help is much appreciated!

igraph r signaling
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written by Spacebio Spacebio

If you want to determine if a group of genes represents a specific complex or process why not use GO term enrichment analysis? What do your edges represent in this graph?

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written by ejm32 ejm32

I created a cell signaling network enclosing 80 pathways. The group of genes representing a complex process is determined already. What I want to know is what is better, if determine the pathways by the edges interactions or the nodes comprised by that group of genes?

• 1 views • link
written by Spacebio Spacebio

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