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Chunk #13 — Methods — Structure of gene expression variation among populations

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Patterns of cis regulatory variation in diverse human populations.
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To address the question of whether genes of specific functional classes tend to be among those exhibiting highest expression differentiation between populations (any pair of populations), we used the VST statistic as a determinant of expression differentiation and selected the top 5% of the probes which were significantly differentiated between any two populations. Using this cutoff, we computed a one-sided Fisher's exact probability to determine enrichment of Gene Ontology (GO) terms. The GO p-values were for all pairwise comparisons were combined using Fishers combined probability, to identify those functional categories that across all pairs of populations are consistently among the most diverged between pairs of populations. To address the question of whether genes of specific functions exhibit significant population-specific expression differentiation, we used the VST score and selected the top 5% of the probes which were significantly differentiated between any two populations. Using this cutoff, we computed a one-sided Fisher's exact probability to determine enrichment of GO terms in the top 5% of probes. For a single population, such as CEU, all GO term p-values from pairwise population comparisons with