GO analysis where I can set by own set of genes to search against
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21 months ago
mropri ▴ 150

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.

Analysis GO • 830 views
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Yes it is mostly possible for every tool. Which tool did you use ?

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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?

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If you are familiar with R, you could try clusterProfiler.

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thank you will try that out

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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

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will try clusterProfiler as both of you have recommended it, will also give Metascape a shot. Thank you

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