Table 1.
Cis- and Trans-eQTLs Detected in LV, Fat, Kidney, and Adrenal Datasets at Different Genome-Wide Thresholds of Significance
Figure 1.
Genetic Architecture of Genetic Variation in Gene Expression
For each considered transcript the major eQTL was identified by linkage analysis (genome-wide significance, p = 0.05) and characterised as cis or trans. Additive allelic effect and heritability (h2QTL) for each cis-eQTL (black symbol) and trans-eQTL (grey symbol) were plotted for LV, fat, kidney, and adrenal tissues.
Figure 2.
Proportion of eQTLs That Are Excluded when Transcripts are Filtered Based on h2trait
Percentages were calculated as follows: (1 − (eQTLTOT − eQTLh2cut-off)/eQTLTOT) × 100, where eQTLTOT is the total number of eQTLs detected at p = 0.05 without filtering based on h2trait (see Table 1), and eQTLh2 cut-off is the total number of eQTLs observed when transcripts were filtered based on a given trait heritability cut-off. For any trait heritability cut-off, the number of excluded eQTLs is higher for trans-acting eQTLs, since they are usually detected for transcripts with low heritability of gene expression.
Figure 3.
Power to Detect a Major eQTL in the RI Strains
(A) Statistical power to detect an eQTL of given allelic effect is shown for various estimates of heritability of gene expression in 30 RI strains with four biological replicates. The eQTL allelic effect is an estimate of the absolute change in the transcript abundance that would be produced by substituting a single allele of one type with that of another type in the population (see Materials and Methods). Absolute FCs, corresponding to the allelic effects on the primary x-axis, are also reported on the secondary x-axis.
(B) Statistical power to detect cis-eQTLs (solid line) and trans-eQTLs (dashed line) (detected with genome-wide significance, p = 0.05) is shown for various heritabilities of gene expression (h2trait) in LV, fat, kidney, and adrenal tissues. Specific allelic effects for cis- and trans-eQTLs were defined in accordance with those observed in this study at p = 0.05 (reported in Table 1).
Figure 4.
FDR in LV, Fat, Kidney, and Adrenal Tissues
(A) For each major eQTL detected in LV, fat, kidney, and adrenal tissue, the expected FDR was calculated and plotted against different p-value thresholds in the range 10−6–0.05. Insert: FDR for various p-values in the range 10−6–10−3.
(B) Vase box-plots for the FDRs of the cis- and trans-acting eQTLs detected at p = 0.05 in LV, fat, kidney, and adrenal tissue. Vase box-plots are box-plots where the width of the box at each point is proportional to the density of the data there. The thick line indicates the median FDR for each distribution.