Entering edit mode
9.7 years ago
Samgoldman97
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0
Hi all,
I'm pretty new to all this so bear with me. I have a list of about 400 subnetworks with roughly five genes each. The subnetworks are all interconnected, so I have them in a text file not cytoscape. I was wondering if anyone could suggest a tool that would help me to find subnetworks enriched for GO terms and possibly output the results to a chart of some sort. I've looked at some of the posts on here relating to go enrichment tools, but I can't find any specifically talking about enrichment in multiple groups of genes. I'm guessing the answer is going to be a package in R.
I realize this question may be a little redundant, but really appreciate any help.
Thanks so much!
Could you tell us a little about the origin of your subnetworks, are they from protein-protein interaction data or some similar experiment? GO enrichment tools (Fisher test-based ones) aren't capable of controlling for differences in a gene (or gene-set)'s number of interactions.
The subnetworks are coming from a network that had both protein protein interaction data and regulatory data. I guess GO enrichment may have been the wrong thing to ask about. I just want to see if the genes in each subnetwork have any common biological process.