Coloring nodes using Cytoscape based on gene to pathway annotation information

Question

[ishengomae]

Hi,

I want to overlay pathway information to genes, mapped onto Biogrid database accessible via Cytoscape and visualize using Cytoscape.

Basically I have about 200 overexpressed genes and I have obtained information about which pathways they map.

According to various answers here it seems I have to prepare two files -- the overexpressed gene list file and the tab delimited attribute file( gene plus associated pathway) and import it into Cytoscape. The attribute file should like so considering one gene may map to multiple pathways

gene1     pathway1
gene2     pathway2
gene1     pathway3
..
..
..

I'm using Cytoscape 3.2.1 which is the newest version. How do I overlay the pathway information to my genes on the network? I want to color code pathway information in such a way that different pathway will have different color. Is this possible to do with Cytoscape? My aim is to actually see how gene-to-pathway information is structured on the network. I'm a beginning user in Cytoscape and what is particularly confusing me right now is that I don't see Import Attribute function that should at least help me learn by doing? What can I do?

Thanks for your help. Look forward.

Answer 1

[AndreiR]

Hello,

As far as I understand, you need to build/import a pathway that comprises all your genes. One way you can do that is by merging different pathways.

After that you should import both files. Important that they have some common identifier (for the pathway, overexpressed genes and pathway association, i.e. gene name).

Then you can set node shape/color/size/border color to each of your attributes. For example you can set red to overexpressed and set border color for each of your pathways.

Maybe this tutorial help you: http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3.1-part2