visualize overlapping nodes in Cytoscape

Question

[TriS]

Hi all

I am using cytoscape to evaluate the overlaps between multiple PPi networks.

After importing the networks from a txt file I used the "merge" tool using the "union" option to create the merged network. This part works well but ideally I would like to color differently each network and highlight the overlapping nodes with different colors/shapes, but I can't seem to find the way to do it. I tried to google the various "visualize/color overlapping nodes", someone suggested a plugin here but I can't find any indications that this was actually done.

Any suggestions/workarounds?

Thanks :)

Answer 1

[Jean-Karim Heriche]

Create a mapping file in which you assign to each node the category it belongs to (i.e. network 1, network 2 or shared). 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 category as an extra node attribute. Then in the style tab, assign a color to each category using the discrete color mapping option of the node color.

[TriS]

Jean, thanks for the reply. I was able to create the mapping file and it looks like this:

11214      8727     unique      11214_8727
11214      7067     unique      11214_7067
27034      84129     shared      27034_84129
196528      8900     unique      196528_8900
57492      6921     shared      57492_6921
10006      5296     unique      10006_5296
351      5067     unique      351_5067
57584      7730     shared      57584_7730
88      8850     unique      88_8850
196528      6602     unique      196528_6602

columns 1 and 2 are the genes, col 3 is the interaction (unique or shared) and the last one should be the key made by concatenating the two node/gene names.

however, I can't find the way to pass those info to Cytoscape. what I did was: 1) import this file as network, use column 3 as interaction type, 2) import the same file as table and use as key column 1. in "where to import data" I select "to selected networks only", I pick my network, then I "import data as" "Node Table Column" but it tells me "types of keys selected for tables are not matching". if I use the 4th column as key it adds three empty columns to the Node Table, probably because it doesn't really match the keys...I think that the problem are the keys but I can't seem to be able to fix it...even if I use the IDs in the first col as key, it still doesn't give me the column with the "unique" "shared" values

[Jean-Karim Heriche]

Your question was about showing shared nodes but if you select column 3 as interaction type, it means you're interested in shared edges. Could you then clarify ?

Assuming, you're still interested in showing shared nodes and assuming you already have your networks merged in cytoscape, my suggestion was a way to add the unique/shared attribute to the nodes. The mapping file I suggested is of the form

Gene ID     category
8727     unique
84129     shared

which you upload with File > Import > Table > File then in the menu select gene ID as key column for network and import data as node table columns. This adds a column category with unique/shared associated with each node, not with an edge as in your table above. In the control panel, select the style tab and the node style tab then Fill color; in column, select "category" (or whatever you've called the new attribute), and select discrete mapping and assign a color to each category.

If you're interested in shared edges, you could go about it the same way selecting the edge style tab and mapping colors using the interaction type.

[TriS]

Jean, yes, I wanted to see the common nodes. the data I have are organized in paired nodes, retrieved from interactome data and they look like the first two columns of my data above. it seems I created and imported the mapping file in the wrong way, I'll follow your latest directions...I'm omw to a meeting now, I'll work on it as soon as I'm back. thanks for the suggestions, I'll post the updates!

[TriS]

---EDITED----

now it is working

alright...it's still not really working...so,

I'm not sure what happened but I re-did it from scratch and this time it worked...thanks for the help!!

Answer 2

[ammasachu]

Hi,

I am trying the same with data of three Groups. Eventually i want to merge network and visualize common nodes present in two networks (each color for the combination of two groups) and another color for common nodes in all three groups. I have a few doubts in this regard,

in order to create the mapping file how did you find the unique and shared gene list as shown above? Have you taken the common genes from the input text file suing some script or identified with the help of cytoscape? How can I create the mapping file for three groups(like shared in Group1 and 2 , Group2 and 3, Group1 and 3 && in all three )?

Thank you for any reply.

Aswathy

[Benn]

This is not an answer but a new question. Please open a new question instead of asking a question here as answer.

[barlu1432]

Hi Aswathy, did you manage to get the way to solve the problem? I am having the same issue. Thanks