Fig. 2: molQTL discovery.
From: A compendium of genetic regulatory effects across pig tissues
a, Pearson’s r between the proportion of detectable eGenes and sample size across 34 tissues. b, Proportions of detectable eMolecule (blue) and specific molQTL (red) for different molecular phenotypes in 34 tissues. * indicates the interaction of cis-eQTLs (ieQTL). Cell type* and Ancestry* are for cell-type ieQTL (cieQTL) and breed/ancestry ieQTLs (bieQTL), respectively. c, Distribution and the average number of independent cis-eQTL per gene. Tissues (x axis) are ordered by increasing sample size. The color key is the same as in a. d, Number of eGenes (triangle) and average number of independent cis-eQTL (square). e, The comparison of cis-h2 (blue) and median expression levels (red) of genes with different numbers of detectable independent cis-eQTL across tissues. The top labels show nominal P values (uncorrected for multiple testing) from one-sided Student’s t tests. f, Internal validation of cis-eQTL. Bars represent Pearson’s r of the normalized effects of cis-eQTL between validation and discovery groups. Points represent the π1 statistic measuring the replication rate of cis-eQTL. g, Spearman’s ρ of effect sizes (aFC in log2 scale) between cis-eQTL and ASE at matched loci (n = 4,417) in muscle. h, A cis-eQTL (rs331530041) of EMG1 in muscle is shared across eight ancestry groups. i, Spearman’s correlation of the cis-eQTL effects between eight breeds of the muscle (left) and between muscle and other 33 tissues (right). The P value is obtained from a two-sided Wilcoxon rank-sum test. j, Proportion of bieQTL that are validated with the ASE approach. The number of validated bieQTLs out of the total number of bieQTLs tested is shown to the right of each bar. k, Effect of eVariant (rs344529295) of GRHPR interacted with the Duroc ancestry enrichment in muscle. The two-sided P value is calculated by the linear regression bieQTL model. The lines are fitted by a linear regression model using the geom_smooth function from ggplot2 (v3.3.2) in R (v4.0.2). l, Proportion of cieQTL that are validated by the ASE approach. m, Effect of eVariant (rs344431919) of FGD2 interacted with monocyte enrichment in blood. The two-sided P value is calculated by the linear regression cieQTL model. The lines are fitted using the same method as in k. aFC, allelic fold change.
