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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