Question: How to follow the flow of a cell signaling network?
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gravatar for Spacebio
10 months ago by
Spacebio180
Spacebio180 wrote:

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 signaling R • 181 views
ADD COMMENTlink written 10 months ago by Spacebio180

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?

ADD REPLYlink written 10 months ago by ejm32430

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?

ADD REPLYlink written 10 months ago by Spacebio180
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