GSEA: what does 'enriched' and TOP 'X' enriched process/pathways mean?
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3 months ago
Akash D ▴ 20

When considering Top 'X' enriched pathways of GO results. On what basis is the TOP 'X' say TOP 10/30 taken?

If I have obtained say 50 terms after taking enriched p adj. <0.05, on what basis i select the top 10 from the enriched 50 terms? Can i take 'counts/no of genes' to select top 10?

KEGG RNA-Seq GO • 462 views
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3 months ago

This is often done via ranking by the normalized enrichment score. Full results are usually supplied in a supplemental table.

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Are 'normalized enrichment score', 'Rich factor', 'P value' same thing? can you please brief a bit...

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I've never heard of rich factor, but no, p-values and normalized enrichment scores are not the same. Your title says GSEA, but your post says GO, so I'm not sure whether you're doing GO term enrichment analyses with a gene list or GSEA from actual differential expression results. There is a good summary of what these values mean in relation to GSEA here.

Can you clarify what you are actually doing and with what tools?

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Thank you. I will get back to basics.

I am trying to do GO term enrichment with my data. My data contains rice gene ids (DEGs) and i am using CARMO online tool for the analysis.

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Oh, I have not used that tool. Some tools spit out scores based on some combination of p-values, gene set size, and enrichment (like enrichr), and I assume that's what the rich factor is here. I can't find anything about that specific metric in their manual though.

People do rank by p-value (or -log10(p-value)) sometimes, which is rather questionable in terms of what a p-value actually means, but so long as you provide the full results, it's probably okay for trimming the list down to something that's easier to visualize and show.

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Thanks al lot for your insights. I am benefitted.

As per my knowledge ''Rich Factor" is nothing but the ratio of 'No. of genes (of any process X) found in your list/ Total no. of genes in that process X'.

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