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Table 5 Main overrepresented biological processes shared by genes selected as predictors of feed efficiency traits

From: Analysis of merged whole blood transcriptomic datasets to identify circulating molecular biomarkers of feed efficiency in growing pigs

GO Terms

Nb genes

E

PValue

Clustered genes

Clustered pathways among 391 probes corresponding to 253 unique genes first selected to classify pigs on low/high RFI

GO:0006643 ~ membrane lipid metabolic process

6

1.93

0.004

TEX2, SPTLC2, PSAP, COL4A3BP, UGCG, SMPD3

GO:0006979 ~ response to oxidative stress

8

1.66

0.006

PLA2G4A, PSEN1, EPAS1, CLU, GPX3, JAK2, ADAM9, DHCR24

GO:0006869 ~ lipid transport

8

1.59

0.003

OSBPL3, PSAP, COL4A3BP, CLU, PCTP, ABCA1, APOM, CROT

GO:0016310 ~ phosphorylation

20

1.55

0.010

IRAK2, FCER1A, ND2, TGFBR1, BMPR2, EIF2A, ULK4, GALK2, NDUFV3, VRK1, PSEN1, GCK, COL4A3BP, TGFBR3, JAK2, ATP5O, CIT, THBS1, MYLK, ADAM9

GO:0031349 ~ positive regulation of defense response

6

1.34

0.003

FCER1A, IRAK2, PLA2G4A, CADM1, IL6ST, JAK2

GO:0000267 ~ cell fraction

23

1.33

0.036

JPH4, CADM1, CYP51A1, SLC22A7, UGCG, HPS1, CCDC47, ATP1A1, NMB, ABCA1, NPR3, IL15, KARS, DCT, JUP, PLA2G4A, PSEN1, GCK, GPX3, SRR, ENO3, JAK2, ACSL3

GO:0009725 ~ response to hormone stimulus

10

1.27

0.055

PLA2G4A, ENPP1, SOCS3, TGFBR1, TGFBR3, JAK2, PIK3R3, THBS1, BRCA1, ADAM9

GO:0008361 ~ regulation of cell size

5

1.25

0.295

ENPP1, TGFBR1, SMAD4, TGFBR3, NTN1

GO:0030278 ~ regulation of ossification

4

1.16

0.085

PLA2G4A, ENPP1, IL6ST, BMPR2

GO:0017015 ~ regulation of transforming growth factor beta receptor signaling pathway

4

1.09

0.015

HTRA1, CHST11, SMAD4, THBS1

GO:0051091 ~ positive regulation of transcription factor activity

4

1.05

0.045

IRAK2, UBE2V1, TGFBR3, JAK2

GO:0042470 ~ melanosome

5

1.03

0.033

DCT, STOM, SERPINF1, RAB35, ATP1A1

GO:0007498 ~ mesoderm development

4

1.02

0.075

MACF1, BMPR2, EOMES, JAK2

Clustered pathways among 728 probes corresponding to 477 unique genes first selected to predict FCR

GO:0002694 ~ regulation of leukocyte activation

13

1.89

0.002

CD83, CD86, CD80, STAT5A, IL27, IL4R, IL1B, CD4, IL15, CD40, PAG1, THY1, SYK

GO:0009100 ~ glycoprotein metabolic process

14

1.79

0.003

ATP7A, B3GNT9, MGAT4A, GALNT1, TRAK2, HPSE, CHST11, ACAN, CD4, FUT1, OGT, UGGT2, ST6GALNAC2, DHCR24

GO:0001817 ~ regulation of cytokine production

15

1.65

0.000

CADM1, PANX1, IGF2, STAT5A, IL27, CD40, NLRP3, DDX58, CD83, CD86, CD80, IL1B, CD4, CLEC7A, SYK

GO:0051223 ~ regulation of protein transport

8

1.65

0.034

CADM1, PANX1, IGF2, ANG, IL1B, CD40, NLRP3, DNAJC1

GO:0002673 ~ regulation of acute inflammatory response

5

1.51

0.002

PLA2G4A, C3, IGF2, SERPING1, CCL5

GO:0052547 ~ regulation of peptidase activity

7

1.39

0.028

SLC11A2, CYCS, BCL2L13, HBXIP, NLRP3, EIF2AK3, DHCR24

GO:0046777 ~ protein amino acid autophosphorylation

6

1.32

0.079

FYN, CLK4, KIT, LRRK2, EIF2AK3, SYK

GO:0050778 ~ positive regulation of immune response

10

1.15

0.017

CADM1, C3, FYN, STAT5A, IL1B, SERPING1, IL15, CLEC7A, THY1, SYK

GO:0031349 ~ positive regulation of defense response

6

1.01

0.047

PLA2G4A, CADM1, C3, STAT5A, CLEC7A, CCL5

GO:0032881 ~ regulation of polysaccharide metabolic process

3

1.01

0.060

PPP1R3C, ENPP1, IGF2

  1. Very important genes for prediction of feed efficiency traits (RFI: residual feed intake; FCR: feed conversion ratio) were clustered into functional groups using DAVID tool. The enrichment score (E > 1) for each cluster and P-value of the enrichment for the corresponding Gene Ontology (GO) terms are provided. Iterative steps for model reduction have been further applied on these transcripts of genes to obtain smaller sets of predictors