Hello!
I am new to the network analysis and, following the suggestions of some colleagues, I am using Cytoscape to perform it. I have some RNA-seq data (list of UP and DOWN DEGs) which I first used to generate on STRING a scoring file (.txt file) to use as input into Cytoscape. Together with it, I have also used as input an expression file in order to colour the DEGs in the network map accordingly to their logFC value.
At this stage, Cytoscape generates me a full network map as expected. However, I am wondering how I can obtain single pathway network maps. For example, showing only the network map for MYC pathway or whatever other enriched pathways according to my input DEGs.
I hope I was clear enough and thank you in advance for the help!
There are a couple of ways to approach what you want to do. First, you need to realize that the differentially expressed genes might belong to multiple pathways, and that taken all of your genes together, they might not completely cover any of those pathways. So, typically, what researchers will do is to perform some kind of pathway enrichment analysis on the data set. That will give you the set of pathways that your genes seem to be more involved with. Then, you could load those pathways (or any pathway of particular) from WikiPathways or Reactome or any other pathway resource -- that will give you a set of figures for each pathway. Finally, you can load the log2FC for the genes to color each pathway.
Alternatively, you can use the stringApp in Cytoscape to create the network and use it's built-in enrichment tool (select just pathway resources in the filters) to find the pathways of interest. stringApp will give you some pie or doughnut plots to show the pathway enrichment on top of the PPI. You can still load pathway figures from wikipathways (via the wikipathways app) from there.
Thanks so much! It was very helpful :)