pone.0121732.g003: Hierarchical clustering of biological process GO terms associated with genes located in outlier loci (regions) detected by XP-EHH method in comparisons between Yucatan miniature pig and Duroc (A), Landrace (B) and Yorkshire (C).The gene list of each GO term clustered using DAVID was compared to calculate the distance between the GO terms. For a distance value of > 0.4~0.5, GO terms were re-clustered, and GO term groups are shown in boxes. The representative GO terms manually selected are shown in red. The numbers of genes in the GO terms are in brackets with the corresponding p-values.

Mentions: For outlier loci (genes) in each comparison, we performed Gene Ontolgy (GO) term enrichment analyses with EASE < 0.05 to investigate their representation of functional groups (Fig 3). There were 45 enriched GO terms in all three comparisons. To reduce GO term list to the most relevant terms, we picked up representative GO terms based on the list of genes involved in. Representative GO terms associated with genes located in outlier loci (regions) detected by XP-EHH are shown in Table 1. The outlier loci (genes) between YMP and Duroc were mainly associated with detection of fungus, sensory perception of smell, ion transport, protein amino acid phosphorylation, cell proliferation, microtubule-based process and cell cycle in GO term. The outlier genes detected between YMP and Landrace were mainly associated with neuron fate commitment, response to organic substance, transcytosis, sensory perception of smell, regulation of cyclase activity and neurological system process. The outlier genes detected between YMP and Yorkshire were mainly associated with glutamate signaling pathway, vesicle-mediated transport, regulation of cell migration and learning. Nucleotide diversity plot of 14 genes in the intersection of all three XP-EHH analyses and 5 genes of interest which are known for their relation to growth is shown in S8 Fig.