Sample gene set enrichment table using Disease Ontology:
Sample gene set enrichment table using Human Phenotype Ontology:
<aside> 💡 In all of the INRICH results file, results are first sorted by empirical p-value followed by number of genes in the overlap. Note that in the results table, overlap_size calculated by INRICH may be a bit smaller than the number of overlapping_genes. This is due to the fact that in target mode, size of the overlap will always be max. 1 for any given interval regardless of the number of individual genes within the interval matching the term. Secondly, in both target and gene modes, genes with overlapping coordinates are always counted as 1.
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<aside> 💡 Asterisk (*) next to bootstrapped p-values indicates that the p-values may be conservative. See INRICH manual: “The corrected significance values are based on looking at the distribution of the minimum nominal significance value over all sets that we'd expect to obtain by chance -- thus necessitating the two rounds of permutation that you'll see INRICH uses. This also means that if not enough permutations are used in the first round (controlled by the "-r" flag) then the corrected significance may be conservative.”
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