Question: Question: Gene Ontology Enrichment using Constrained Genes as Reference Set; P-values = 1
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gravatar for rb14sp
19 months ago by
rb14sp40
rb14sp40 wrote:

I'm trying to do gene set enrichment analysis using the set of constrained genes from ExAC (pli >= 0.9 || mis-z >= 0.3) as a reference list (attached), as I did not look at missense in genes with mis-z < 0.3 or undefined and I did not look at PTVs in genes with pli < 0.9 or undefined in my analysis. That's 10328 genes. None of my earlier enrichments are significant.

There's a problem here though. If your reference list only includes 3 genes that map to a process and the expectation is to observe 0.16 genes then even if you see those 3 genes (18.38 fold enrichment) the p-value is still reported as 1. So I have a lot of greater than 2X fold enrichments, for example, but no significant p-values. In fact, virtually all my p-values are 1.

Is there a better way to go about doing this.I was using the service at http://geneontology.org/

Thanks, Robert

ADD COMMENTlink written 19 months ago by rb14sp40

Hi Robert,

1) We cannot see (or at least, I can't) the attached list

2) 3 is a really small number, and the lack of statistical significance for that comparison is expected. Enrichment analysis are more informative for Ontology terms containing relatively large numbers of genes

ADD REPLYlink written 19 months ago by Fabio Marroni2.1k
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