TABLE 1

Results from a simulation study on regulator–target pair identification in a single-eQTL region with three causal polymorphisms and with multiple candidate regulator and target genes (true network structure is in Figure 1)

MethodsSD = 0.5SD = 0.25SD = 0.125SD = 0.5/0.125SD = 0.5/0.25SD = 0.25/0.125
Cis-link, power (%)100, 100100, 100100, 10055.3, 59.8589.4, 98.6597.8, 98.5
Cis-link, FDR (%)0.6, 0.90.7, 0.670.67, 0.570.48, 0.530.6, 0.720.62, 0.57
Cis-reg cis, power (%)99, 9999, 9999, 9954.8, 59.488.6, 97.897.2, 97.8
Cis-reg cis, FDR (%)0.35, 0.130, 00, 038.6, 0.253.27, 0.151.8, 0.1
Cis-reg, power (%)99, 98.899, 98.998, 98.554.9, 59.288.2, 97.496.9, 97.5
Cis-reg, FDR (%)0.93, 0.40, 00, 045, 25.824.82, 1.332.85, 1.3
Trans-reg, power (%)99, 99.2100, 100100, 10041.8, 45.192.9, 96.196.3, 96.5
Trans-reg, FDR (%)0.85, 1.11.1, 1.151.57, 1.5226.95, 62.5210.92, 2.522.3, 2.77
  • Power, percentage of replicate data sets in which the regulation type was found; FDR, percentage of replicate data sets in which a regulation of a certain type was found that did not exist in the underlying network; Cis-link, cis-regulation of target in eQTL region; Cis-reg, cis–trans-regulation of target not in eQTL region; Cis-reg cis, cis–trans-regulation of target in eQTL region; Trans-reg, trans-regulation. For the last three columns, even-numbered gene nodes (Figure 1) received the left amount of error variance and odd-numbered nodes the right amount. The two numbers in each cell correspond to 0% recombination and 9% recombination among the three causal polymorphisms in the single-eQTL region, respectively. A P-value cutoff of 0.01 was used.