Question: the best combine score for enrichment analysis from Enrichr
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7 months ago by
Expert30
Expert30 wrote:

I have a qustion, what is the best combine score (adj p.value and z score) for enrichment analysis from Enrichr, exactly?

gene • 705 views
ADD COMMENTlink modified 7 months ago by Charles Warden6.5k • written 7 months ago by Expert30
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gravatar for Charles Warden
7 months ago by
Charles Warden6.5k
Duarte, CA
Charles Warden6.5k wrote:

I've found Enrichr to be useful, and I can say that the tables are scored by the combined score and there are a fair number of experiments that identify relevant categories among the top ~10 gene sets with at least one reference set (ChEA 2016, GO, KEGG, etc.).

I also see that Enrichr website lists two publications: Chen et al. 2013 and Kuleshov et al. 2016.

In terms of answering your question about how the combined score is calculated, Chen et al. 2013 describe the combined score is described as c = log(p) * z, where c = the combined score, p = Fisher exact test p-value, and z = z-score for deviation from expected rank. So, I think that is how the combined score is being calculated. In a downloaded table for the example differentially expressed gene list, I can replicate that calculation (if using the natural log for transforming the unadjusted p-value).

In terms of the z-score calculation, the In Enrichr: What is "Gene weight" or "levels of membership"? Biostar discussion helped me see this Help Center that describes calculation of the background for the z-score from a pre-defined table with random gene lists.

ADD COMMENTlink modified 7 months ago • written 7 months ago by Charles Warden6.5k
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