Visualize pathways from MSigDB

[Chinh Doan]

Hi all,

I have some pathways of interested from MSigDB and gene expression matrix between two conditions. Could I use cytoscape to make a network that color the genes in the pathways by it expression? A plot with pathways name in the center connect with its gene surrounding. Currently I use igraph package but it is hard to use, just want to try if there is a better way. Thank you so much!

Chris

[Alex Pico]

Hi Chris,

Sure thing. This is one of the more common uses of Cytoscape. I'd start with the Differential Gene Expression Network Analysis tutorial here: https://tutorials.cytoscape.org/.

For your case, you'll need to turn the MSigDB info into a table format called .sif (simple interaction format):

pathway name | member | gene A

pathway name | member | gene B

Cytoscape can read this file and generate the network. Then the rest of the work is just like the tutorial... import your data and play with visual styles.

 - Alex

[Chinh Doan]

Hi Alex,

Thanks for a quick reply! The expression level is just slightly different between 2 conditions. I use limma to get logFC with the range about -0.06-0.06. There are arrows to the right and go down which I find quite hard to navigate through the tutorial. I can prepare the .sif file but am not sure where to upload it along with the logFC of each gene. 

Best,

Chris

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[Alex Pico]

The tutorials are composed of modules. You navigate down within each module and to the right to go to the next module. You can also press ‘o’ at anytime to get an overview. The first module contains the info you are looking for: https://cytoscape.org/cytoscape-tutorials/protocols/differentially-expressed-genes/#/ex1-up-data-integration2

- Alex

[Chinh Doan]

I see. Thanks Alex! Have a nice day.

Best,

Chris

On Thu, Apr 25, 2024 at 5:04 PM 'Alex Pico' via cytoscape-helpdesk <cytoscape...@googlegroups.com> wrote:

The tutorials are composed of modules. You navigate down within each module and to the right to go to the next module. You can also press ‘o’ at anytime to get an overview. The first module contains the info you are looking for:  https://cytoscape.org/cytoscape-tutorials/protocols/differentially-expressed-genes/#/ex1-up-data-integration2 

 - Alex

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