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2.2 years ago
mropri
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I have 528 proteins that I have in my gene set from the cerebrospinal fluid that we measured using from proteomics analysis. I have correlated a subset of these genes (97) with alzheimer's pathology and done a GO analysis against the full genome to see what pathways or molecular function these 97 genes are enriched for. My question is, is there a way or tool that lets me set the 528 proteins as the background genes that I can search the 97 proteins against and see what pathways and functions show up? I would appreciate any help or guidance in this.
Yes it is mostly possible for every tool. Which tool did you use ?
I used ENRICHR, but now looking at DAVID looks like I can set my own background protein set. Any tool that you use or might recommend?
If you are familiar with R, you could try clusterProfiler.
thank you will try that out
I usually use R with clusterProfiler and the enrichGO function. An online tool that I like to use and where you can set a background gene list is Metascape
will try clusterProfiler as both of you have recommended it, will also give Metascape a shot. Thank you