Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs

Table 4 Description of the most enriched gene ontology (GO) and metabolic pathways (MP) terms across the evaluated scenarios

Gene Set	Scenario	Action	Term	Description	FDR
ssc05204	S2	Cis	MP	Chemical carcinogenesis	4E-05
GO:0007264	S2	Trans	BP	Small GTPase mediated signal transduction	1E-04
GO:0031252			CC	Cell leading edge	1E-04
GO:0005509			MF	Calcium ion binding	4E-05
ssc04520			MP	Adherens junction	2E-08
ssc00982	S4	Cis	MP	Drug metabolism	5E-02
ssc04913	S6	Cis	MP	Ovarian steroidogenesis	4E-04
GO:0072359	S6	Trans	BP	Circulatory system development	3E-11
GO:0019898			CC	Extrinsic component of membrane	1E-04
GO:0042802			MF	Identical protein binding	7E-05
ssc05205			MP	Proteoglycans in cancer	5E-08

MP Metabolic pathways, BP Biological process, CC Cellular component, MF Molecular function, FDR False Discovery Rate, S2 SNPs from the RNA-seq data of the skeletal muscle, S4 SNPs from the GGP-50K plus the SNPs from the RNA-seq data of the skeletal muscle, liver, and brain tissues, S6 SNPs from the RNA-seq data of the skeletal muscle after linkage disequilibrium pruning (r² threshold of 0.70); cis: genes locally modulated by eQTLs used for the enrichment analyses; trans: genes distantly modulated by eQTLs used for the enrichment analyses

ISSN: 1471-2164