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Table 3 Significantly over-represented KEGG pathways and candidate genes

From: Whole genome association study identifies regions of the bovine genome and biological pathways involved in carcass trait performance in Holstein-Friesian cattle

Trait

Pathway name

p-value

Candidate genes

CWT

Jak-STAT signaling pathway

0.00503

IL12RB2, IL23R, JAK1, LEPR

CWT

Cell cycle

0.01768

ANAPC1, GADD45A, SMC1B

CWT

Metabolism of xenobiotics by cytochrome P450

0.01861

ALDH1A3, CYP1B1

CWT

p53 signaling pathway

0.03380

GADD45A, GTSE1

CWT

Adipocytokine signaling pathway

0.04000

LEPR, PPARA

CWT

Sulfur relay system

0.04560

TRMU

CFAT

PPAR signaling pathway

0.00114

CYP4A11, CYP4A22, FADS2

CFAT

Protein digestion and absorption

0.00129

PGA3, PGA4

CFAT

Biosynthesis of unsaturated fatty acids

0.00165

FADS1, FADS2

CFAT

Vascular smooth muscle contraction

0.00460

CYP4A11, CYP4A22

CFAT

Fatty acid metabolism

0.00716

CYP4A11, CYP4A22

CFAT

Retinol metabolism

0.00854

CYP4A11, CYP4A22

CFAT

Glycerolipid metabolism

0.00890

AGPAT4, DAK

CFAT

Arachidonic acid metabolism

0.01081

CYP4A11, CYP4A22

CFAT

Non-homologous end-joining

0.03864

FEN1

CONF

Inositol phosphate metabolism

0.01392

INPP5B, PI4KB, PIP5K1A

CONF

Biotin metabolism

0.01727

HLCS

CONF

Lysosome

0.01892

CTSK, CTSS, LAMP3, MAN2B1

CONF

Phosphatidylinositol signaling system

0.03030

INPP5B, PI4KB, PIP5K1A

CONF

Intestinal immune network for IgA production

0.04489

TNFSF13B

CONF

Proteasome

0.04913

PSMB4, PSMD4

CULL

Mucin type O-Glycan biosynthesis

0.00178

GALNT8, GALNTL2, GALNTL6

CULL

Vibrio cholerae infection

0.00981

ATP6V1C2, GNAS, KCNQ1

CULL

p53 signaling pathway

0.01664

CCNB1, CCND2, RRM2

CULL

Gap junction

0.03030

GNAS, MAP3K2, TUBB1

ALL

PPAR signaling pathway

0.00672

SLC27A6, FADS2, CYP4A22, RXRA, PPARA, CYP4A11

ALL

Phosphatidylinositol signaling system

0.01284

DGKD, PI4KB, PIP5K1A, INPP5D, INPP5B, CALM1

ALL

p53 signaling pathway

0.01862

GTSE1, GADD45A, CCND2, CCNB1, RRM2

ALL

Mucin type O-Glycan biosynthesis

0.03132

GALNT8, GALNTL2, GALNTL6

ALL

Protein digestion and absorption

0.03135

KCNQ1, KCNJ13, PGA4, PGA3

ALL

Vibrio cholerae infection

0.03729

KCNQ1, SLC12A2, GNAS, ATP6V1C2

ALL

Arachidonic acid metabolism

0.03964

PTGDS, CBR3, CYP4A22, CYP4A11

ALL

Non-homologous end-joining

0.03992

FEN1, LIG4

ALL

Biotin metabolism

0.04896

HLCS

  1. Candidate genes are genes that occurred in the over-represented pathway and were within 500kbs of a QTL significantly associated with the trait using the Bayesian approach.
  2. CWT = carcass weight; CFAT = carcass fat; CONF = carcass conformation; CULL = cull cow carcass weight; ALL = significantly over-represented KEGG pathways using combined trait gene dataset.
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BMC Genomics

ISSN: 1471-2164

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