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Table 2 Main commonly affected biological processes across four tissues

From: A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

GO termsa Nb DEG E score p-value Clustered DEG
GO:0046907 ~ intracellular transport 17 2.06 <0.001 PSEN1, YWHAZ, TOMM5, MLX, DST, RAB35, PIKFYVE, MYL6, PEX6, STAM2, OPTN, CDK5, CCHCR1, YWHAG, JAK2, STAM, NUP43
 (GO:0015031 ~ protein transport) (13)   (0.025)
GO:0006955 ~ immune response 13 1.81 0.050 HLA-A, HLA-B, HLA-C, HLA-H, CTSC, YWHAZ, PSEN1, TRAF6, POLR3B, BST1, COL4A3BP, ADAM17, XCL1
 (GO:0048002 ~ antigen processing and presentation of antigen) (4)   (0.001)
GO:0006643 ~ membrane lipid metabolic process 4 1.43 0.030 CLN3, PSAP, SGMS1, COL4A3BP
GO:0009057 ~ macromolecule catabolic process 17 1.14 0.005 PSEN1, YME1L1,CD40, TRAF6, USP33, USP30, UBE2V1, PSMA3, PSMD1, MUTYH, CLN3, TMEM189, CDK5, RNASET2, NEURL2, ADAM9, ADAM17
 (GO:0030163 ~ protein catabolic process) (12)   (0.015)
GO:0006414 ~ translational elongation 4 1.13 0.052 RPL6, RPL14, RPS18, RPL35
GO:0008219 ~ cell death 14 1.08 0.007 PSEN1, NTN1, CD40, TRAF6, SOD2, YWHAG, POLR3D, HSPE1, CLN3, TRIO, SGMS1, OPTN, PDCD4, CDK5, JAK2, BLCAP, ADAM9, ADAM17
GO:0045859 ~ regulation of protein kinase activity 9   0.008
GO:0001819 ~ positive regulation of cytokine production 5   0.007
GO:0006644 ~ phospholipid metabolic process 6 1.06 0.021 PON1, PIGL, PLA2G12A, SGMS1, PIKFYVE, CLN3
GO:0006979 ~ response to oxidative stress 6 1.00 0.048 PSEN1, SOD2, GPX3, JAK2, ADAM9, MUTYH
  1. aThe 147 differentially-expressed genes (DEG) (pigs from the low vs high RFI lines) which were commonly listed in muscle, liver, perirenal and subcutaneous adipose tissues, were clustered based on shared gene ontology (GO) terms for biological processes. The enrichment score (E ≥ 1) and P-value for each cluster are provided