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Fig. 5 | BMC Genomics

Fig. 5

From: Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis

Fig. 5

Detailed analysis of the association network centered on eQTL-SNP ALGA0034786 on SSC6. a: Circo plot produced by R package RCirco which maps eQTL-SNPs and associated genes according to their genomic positions. Links in red correspond to associations between the eQTL-SNP ALGA0034786 and genes mapping to SSC6, and links in blue represent associations with genes on other chromosomes. b: The distribution of all (grey) and significant (red) correlation coefficients calculated from pairwise comparisons of expression variation in probes associated with ALGA0034786, performed by PCIT. Red areas of the histogram correspond to coefficient correlations involving significant edges, as determined by PCIT, and gray areas represent non-significant edges. c: Boxplots of expression variations in probes annotated for porcine genes, depending on the eQTL-SNP genotype. Each dot represents one animal. Pink dots correspond to pigs homozygous for the most-frequent allele (genotype A/A), green dots to heterozygous pigs (genotype A/G), and blue dots to animals homozygous for the less-frequent allele (genotype G/G). d: Ingenuity Pathway Analysis of the genes included in the association network. The functional network comprised nine of the ten genes that were distant-associated to eQTL-SNP ALGA0034786. The symbols of these nine genes are colored in gray. The IPA-drawn network revealed functions linked to “cellular assembly and organization”, “cell death and survival”, and “endocrine system disorder”. e: eGWAS results for probe A_72_P211467, which was annotated for the gene COX6B1, visualized with a Manhattan plot. The association peak on SSC6 corresponds to the eQTL represented by eQTL-SNP ALGA0034786. The red horizontal line corresponds to an FDR threshold <0.01 and the horizontal blue line to an FDR threshold <0.05

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