Locate Kegg Pathways from my network

Question

[saamar.rajput]

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?

Answer 1

[Jean-Karim Heriche]

You can do this in Cytoscape. Create a mapping file in which you assign to each node the pathway it belongs to. Upload this file into Cytoscape as a table using node names/IDs as keys. This will make another column in the node table associating the pathway as an extra node attribute. Once you have this pathway attribute, use discrete mapping to this node attribute. In the style control panel, click on the little triangle next to 'Fill Color' to expand the selector, then select a column, select discrete mapping as mapping type then select a colour for each category of nodes.

EDIT: I offered a Cytoscape solution because Cytoscape was mentioned but this can also be done in R with the igraph package simply by creating a vector of node colours and using it like this:

plot.igraph(myGraph, vertex.color = V(myGraph)$colour)