We calculated the significance of the excess number of genes attaining the specified thresholds in two main ways. The first was empirically, the second was based upon the assumption that, under the null hypothesis of no association, the number of significant genes in a scan is a normally distributed random variable whose mean and standard deviations can be obtained from the permutations. Given computational restrictions required by genome-wide permutation, we could only perform 1000 permutations and therefore based on the first method, significance can be reported only up to a threshold p>10−3. These were calculated by bootstrapping, as follows. From 1000 permutations, we choose a replicate at random as a ‘true study’. We then calculated the significance for each gene, and therefore the total number of significant genes, by comparing the ‘true study’ with 999 replicates obtained by sampling at random (with replacement) from the remaining 999 permutations. This process was repeated 1000 times. The empirical test of the number of significant genes being higher than expected under the null hypothesis of no association was carried out by comparing the
