Table 3 Statistical summary for gene set enrichment analysis of the histaminergic genes of interest

Gene set	Up P-value	Up q-value	Effect size g	Mixed P-value	Mixed q-value	Effect size g	Number of genes	Up active prop	Mixed active prop
Hypothesis-driven gene set	0.001	0.010	0.84 (0.19, 1.5)	0.006	0.024	0.73 (0.08, 1.38)	4	0.50	0.50
GO: histamine receptor activity	0.015	0.036	0.68 (0.03, 1.33)	0.096	0.193	0.42 (−0.22, 1.06)	3	0.33	0.33
GeneRIF: histaminergic	0.461	0.564	0.18 (−0.45, 0.82)	0.011	0.032	0.70 (0.05, 1.35)	5	0.20	0.60
GeneRIF: histamine	0.373	0.564	0.18 (−0.45, 0.82)	0.003	0.016	0.79 (0.13, 1.44)	41	0.15	0.34
GO: histamine secretion	0.452	0.564	0.18 (−0.45, 0.82)	0.976	0.976	0.01 (−0.62, 0.64)	6	0	0
GO: histamine production in inflammation	0.470	0.564	0.18 (−0.45, 0.82)	0.911	0.976	0.01 (−0.62, 0.64)	4	0	0

Abbreviation: GO, Gene Ontology.
Summary of results for the gene set enrichment tests of the histaminergic genes. The results are shown with the controls as the reference group. Therefore, the hypothesis of ‘Up’ refers to the gene set being increased in autism spectrum disorder (ASD) patients as compared with controls, whereas the hypothesis of ‘Mixed’ refers to the gene set including genes with extreme t-statistics in both directions. Thus, as the results indicate that several of the gene sets show altered expression in ASD, the active prop is the proportion of genes in the set contributing meaningfully to significance, defined as those with squared z-values greater than 2.

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