The following analytical steps were taken to identify transcripts that may be modulated by the variant in Per3 locus and are potential downstream targets of Per3: (1) We rank ordered all transcripts with expression levels >8 units that had significant point-wise linkage with the marker (rs4140148) closest to Per3. In all, 3880 transcripts were then selected that had trans QTLs near Per3 at a nominal linkage P-value <0.01. (2) Pearson's product correlation was then computed between Per3 and these potential downstream transcripts. Only transcripts that had significant expression correlations with Per3 (P<0.01) were selected for further analysis. (3) We performed partial correlation analysis controlling for the Per3 transcript and removed the transcripts that mapped back to the marker near Per3. (4) Finally, we used prior literature based information on these genes to nominate those transcripts most plausibly linked to Per3 function.
