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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

From: RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

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