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Table 4 Summary of the main muscle-specific biological processes

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
Over-expressed in pigs from the low RFI line
GO:0006412 ~ translation 97 39.8 <0.001
GO:0022613 ~ ribonucleoprotein complex biogenesis 33 4.3 <0.001
GO:0003012 ~ muscle system contraction process 26 4.1 <0.001
GO:0006091 ~ generation of precursor metabolites and energy 31 3.1 <0.001
 (GO:0006006 ~ glucose metabolic process) (26) (0.007)
GO:0032268 ~ regulation of cellular protein metabolic process 52 2.8 0.001
 (GO:0006417 ~ regulation of translation) (23)   (<0.001)
GO:0030163 ~ protein catabolic process 67 2.7 <0.001
 (GO:0006511 ~ ubiquitin-dependent catabolic process) (28) (0.010)
GO:0008104 ~ protein localization 84 2.7 0.003
 (GO:0046907 ~ intracellular transport) (73)   (<0.001)
GO:0005977 ~ glycogen metabolic process 8 1.6 0.009
GO:0046324 ~ regulation of glucose import 10 1.5 <0.001
Under-expressed in pigs from the low RFI line
GO:0006955 ~ immune response 62 10.1 <0.001
GO:0002250 ~ adaptive immune response 18 5.4 <0.001
GO:0001817 ~ regulation of cytokine production 22 4.6 <0.001
GO:0010033 ~ response to organic substance 61 4.0 <0.001
GO:0070482 ~ response to oxygen levels 17 4.0 <0.001
GO:0001501 ~ skeletal system development 25 3.4 <0.001
GO:0042981 ~ regulation of apoptosis 55 3.0 <0.001
GO:0009743 ~ response to carbohydrate stimulus 10 2.1 <0.001
GO:0006631 ~ fatty acid metabolic process 27 1.7 0.006
 (GO:0008610 ~ lipid biosynthetic process) (19) (0.05)
  1. aGenes that were differentially expressed between pigs from the low or high RFI lines in muscle only were clustered according to gene ontology (GO) terms for biological processes and Genomes biological pathways (hsa). Significantly-enriched clusters (E ≥ 1; P < 0.05) were listed with the enrichment (E) score, the number (Nb) of differentially expressed genes (DEG) in each cluster and P-value. Overlapping clusters with a similar biological significance were removed