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I am working on big networks of genes. I want to locate KEGG/Reactome pathways in my network. I have already tried cytoKegg and ReactomeFI (Plugins of Cytoscape), they only give me a list of Pathways with the genes in it. But I want to visually see the grouped genes from my network which belong to one pathway in either KEGG or Reactome.

My network file looks like this

ADAM17 NOTCH1 ->
ADAM17 TNF ->
ADAM17 TRAF6 ->
ADRB2 GNAI1 ->
ADRB2 GNAI2 ->
AJUBA CDH1 <-
AJUBA CTNNB1 <-
AJUBA LATS2 -|
AMOTL2 LATS2 ->
AMPH EGF ->

I would like to see the genes in a pathway in KEGG or Reactome from my network to be either grouped together or colored. Is there any tool that does this?

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  • $\begingroup$ How is stored your network of genes? (Or where are you working with it, you seem to be using Cytoscape but just to be sure). When do you say watch the pathways visually, do you want to get them highlighted with some color, or just focus on them, or group them aside from the main node of your network? Could you edit the question to add these details? Thanks $\endgroup$ – llrs Feb 8 '18 at 12:55
  • $\begingroup$ Exactly either of these, grouped or colored! $\endgroup$ – Saad Feb 8 '18 at 13:02
  • $\begingroup$ You forget to answer if you are working in Cytoscape :D. And could you add please what strategies have you looked for to find a solution? To prevent proposing the same (not-optimal) solution $\endgroup$ – llrs Feb 8 '18 at 13:05
  • $\begingroup$ I did not find any tool that could do this in R so yes I tried a few plugins from Cytoscape. But I am not confined to use cytoscape. Like I mentioned above I did try a few tools from R like KEGG itself and Pathview and plugins from Cytoscape and tried to even manually find the pathways but it gets tedious once the network starts growing. $\endgroup$ – Saad Feb 8 '18 at 13:09
  • $\begingroup$ How big is your network 1000 genes? Did you try pathview package of Bioconductor? I'm sure that in Cytoscape you can select a genes from a list and highlight them, but as I can't point to the options I'll abstain to post an answer $\endgroup$ – llrs Feb 8 '18 at 13:15

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