Table 3.

KEGG pathways identified for the downregulated genes in the high-RFI group with an FDR q-value < 0.01 from the output of the GSEA in the Holsteins

	Name	FDR q-value	Core enrichment gene
1	Primary immunodeficiency	~0	CD3D, IL7R, PTPRC, JAK3, ZAP70, CD3E, LCK, ADA, CD8A, BTK, TAP1, UNG, RFX5, CD4
2	Natural killer cell mediated cytotoxicity	~0	NFATC2, TNFRSF10D, NCR3, ICAM1, RAC2, ZAP70, PIK3CG, GRB2, LCK, NFAT5, PTK2B, LCP2, PRF1, ITGAL, TYROBP, PIK3CD, SH2D1A, TNF, VAV1, TNFSF10, PLCG2, ITGB2, PAK1, PIK3R5, KRAS, PRKCA, FASLG, SYK, LAT, CD48, IFNGR1, PIK3CA, FCER1G, KLRK1, RAF1, PTPN11, FAS, IFNAR1, PTPN6, HRAS, SOS2, PRKCB
3	T cell receptor signaling pathway	~0	CD3D, NFATC2, JUN, PTPRC, ITK, CD3G, ZAP70, CD3E, PRKCQ, PIK3CG, GRB2, LCK, NFAT5, CD8A, RASGRP1, LCP2, TEC, CARD11, PIK3CD, TNF, VAV1, NFKBIA, PAK1, PIK3R5, KRAS, MAPK9, CD4, PDK1
4	Leukocyte transendothelial migration	0.002	GNAI1, NCF1, RAPGEF4, OCLN, ITK, CLDN2, ICAM1, RAC2, CLDN1, NCF4, PIK3CG, CDH5, CXCL12, EZR, PTK2B, ITGAM, CLDN4, CYBB, ITGAL, NCF2, PIK3CD, VAV1, CLDN15, PLCG2, ITGB2, PIK3R5, PRKCA, MYL12B, ARHGAP35, F11R, ROCK2, RAP1A, ITGB1, ITGA4, PIK3CA, CXCR4, MSN, CTNNB1
5	Chemokine signaling pathway	0.002	CXCR6, GNAI1, CCR2, NCF1, ITK, CXCL9, DOCK2, CCL14, PLCB2, RAC2, JAK3, HCK, PIK3CG, GRB2, CX3CR1, CXCL12, ADCY7, ELMO1, PTK2B, GRK5, CCR5, WAS, ARRB1, PIK3CD, ADRBK2, VAV1, LYN, NFKBIA, PAK1, PIK3R5, KRAS, GNB4, GNG2, PRKX, FGR, STAT3, ROCK2, GNB5, RAP1A, PLCB1, STAT1, IKBKG, AKT3, CHUK, PIK3CA, CXCR4, GNG10, PRKACB
6	FC gamma R mediated phagocytosis	0.008	NCF1, SCIN, PTPRC, DOCK2, RAC2, HCK, ARPC1B, MYO10, PIK3CG, MARCKS, LIMK1, PLA2G4A, WAS, INPP5D, PIK3CD, ASAP1, VAV1, PLCG2, LYN, PAK1, PIK3R5, PRKCA, SYK, ARPC1A, PIKFYVE, LAT, PLD2, ARPC3, AKT3, PIK3CA
7	Propanoate metabolism	0.009	ACACA, ACSS2, ACAT2, ACACB, EHHADH

FDR q-value = adjusted p-value; core enrichment gene = subset of genes that contributes most to the enrichment result