Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans.

These pathway-level results are highly significant, even though there is no functional enrichment when only focusing on top scoring genes.

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To account for the fact that some genes in sets are more conserved, we created null distributions that explicitly reflect the expected genomic background by randomly sampling from the group of genes that are part of at least one gene set. As we are essentially interested in finding gene sets that show a global shift in selection scores and not those gene sets that include a single or a few extremely significant genes, we repeated the procedure after excluding in each set the highest scoring gene.

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