Table 1 Over-representation analysis of differentially expressed genes (DEG) upregulated upon antigen stimulation before and after vaccination using the Reactome pathway database

Over-represented pathways before vaccination	Combined score	Over-represented pathways after vaccination	Combined score
		Interleukin-21 Signaling	595.79
		Interleukin-1 Processing	465.40
Interleukin-10 Signaling	428.00
		Interleukin-35 Signaling	332.19
		Interleukin-10 Signaling	281.92
Regulation of IFNG Signaling	219.89
		Interleukin-1 Signaling	169.22
		Interleukin-1 Family Signaling	163.20
		Interleukin-23 Signaling	153.09
		OAS Antiviral Response	153.09
Interleukin-4 and Interleukin-13 Signaling	141.08
OAS Antiviral Response	131.14	Regulation of IFNG Signaling	137.34
		Interleukin-12 Family Signaling	135.54
		Interleukin-4 and Interleukin-13 Signaling	127.69
		Interleukin-27 Signaling	121.94
		DDX58/IFIH1-mediated Induction of Interferon-Alpha/Beta	115.30
Interleukin-35 Signaling	114.29	Signaling by CSF3 (G-CSF)	112.89
		TNFR1-induced NFkappaB Signaling Pathway	111.83
		Interleukin-18 Signaling	109.23
		Regulation of TNFR1 Signaling	103.27
Signaling by CSF3 (G-CSF)	87.79
Antiviral Mechanism by IFN-stimulated Genes	61.83
Interferon Gamma Signaling	60.72
Interleukin−12 Family Signaling	57.94

Representative immune-relevant pathways in contrasts comparing unstimulated vs. antigen-stimulated samples pre- and post-vaccination are listed ranked by their combined scores. DEG with an adjusted p value (padj) ≤0.01 were included in the analysis. Over-representation was assessed using a one-sided Fisher’s exact test, with Benjamini-Hochberg correction for multiple comparisons. The combined score is defined as the z-score of the observed and expected means of the DEG and pathways overlap. Only pathways with padj ≤0.01 and a combined score ≥50 (pre-vaccination) and ≥100 (post-vaccination) were deemed significant.
Pathways that were over-represented in both pre- and post-vaccination comparisons are presented in italics.

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