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Table 2 Summary of identified pathways, DEGs and genes with significant SNPs

From: Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs

SNP ID Candidate Gene Pathway Differentially expressed genes
Pathway name P-Value FDR
rs80811321 GRIP1 GABAergic synapse 1.1E-6 2.4E-5 GNG13,ADCY1,GABRB2, ADCY8, ADCY7,GABRD,GABRE,GABRQ,GABBR2,GAD2,HAP1,PRKCG
Glutamatergic synapse 4.0E-7 1.3E-5 GNG13,DLGAP1,SHANK3,
ADCY1,ADCY8,ADCY7,GRM4,
HOMER2,KCNJ3,PRKCG,SLC17A6,SLC17A7
rs339913443 TPH2 Serotonergic synapse 1.6E-3 1.2E-2 ALOX5,GABRB2,KCNN2,KCND2,KCNJ3,PTGS1,PRKCG
Oxytocin signaling pathway 1.2E-4 1.6E-3 ADCY1,ADCY8,ADCY7,CACNG5,CAMK4,CAMKK2,CDKN1A,NPR1,OXT,KCNJ3,PRKCG,CACNB4,
rs80811321
rs332237334
rs81344478
rs323754097
GRIP1
FRS2
FRS2
TRHDE
CNOT2
Thyroid hormone synthesis 1.8E-2 8.0E-2 ADCY1,ADCY8,ADCY7,GPX3,PRKCG,TSHR,
Thyroid hormone signaling pathway 3.4E-1 6.7E-1 TRH,PIK3CG,PLCD4,PRKCG,
Autoimmune thyroid disease 8.1E-1 8.2E-1 SLA-DMB,SLA-DMA
  1. *CNOT2: There were no significant SNP located within the gene, but there were significant SNPs located in the upstream and downstream of the gene