We further applied GPA to study all pairs of disorders using the CNS gene set as the annotation data. The estimated () are given in Table 3 and remained almost the same as those estimated without the annotation data. The p-values of hypothesis test (14) are provided in the last column of Table 3. The p-value should be interpreted with caution: as shown in Table 1, the CNS gene set is enriched in all these disorders except ADHD. Hence, the significant p-values listed in Table 3 may be simply due to the significant enrichments for individual traits. On the other hand, the ratio between and could be more interesting. Take BPD-SCZ as an example. The ratio between and is 1.503 (s.e. 0.025), which suggests that enrichment of the CNS set for the BDP-SCZ shared risk variants was even stronger than that for BPD-only (1.467 (s.e. 0.033)) or SCZ-only (1.391 (s.e. 0.022)), although the differences are not statistically significant.
