z-Score vs fold enrichment

Question

[jenny_keh]

Hi everyone,

I have performed a GO analysis of microarray data using both GO-Elite and David. I did it in both because some of the genes that are included in DAVID analysis do not appear in GO-Elite. And here comes the confusion! DAVID scores the results based on fold enrichment and GO-Elite based on z-score. What is the difference between these 2 if any?

Thank you in advance!

Best,
Jenny

Answer 1

[mark.ziemann]

Hi Jenny. I share your frustration. Keep in mind that some of these databases are more current than other and they will have a different set of array probes and gene ontologies to test against.

With David, you submit a list of genes and the algo looks for enrichments in the ontologies that can be tested with Fisher exact or hypergeometric test. GO-elite is a bit more sophisticated and in addition to Fisher test performs permutations to see how often these enrichments are observed by chance. I would suggest that Go-Elite is a better approach, but I would also suggest to compare it with GSEA (preranked) as the "real" enrichments will be consistent for both methods.

For fun, try submitting a set of random genes to David a few times and get a feel for false positives.