Table 1. JunctionSeq results.

Adjusted P-value threshold	In vivo			In vitro				No stimulus (in vivo)
	Ctrl day/night	Sham day/night	Overlap, in vivo	CN versus NE	CN versus DBcAMP	Overlap, in vitro	Overlap, All four	SCGX Day/Night	DCN day/night	Overlap, no stimulus
0.01	447	320	168	144	195	90	42	38	9	2
0.001	300	202	116	89	127	61	28	24	5	0
0.0001	227	151	94	67	91	48	18	20	2	0
0.00001	182	119	79	51	74	38	15	14	2	0
0.000001	151	98	61	43	65	34	14	11	2	0

The numbers of genes found to exhibit significant differential exon or splice junction usage for the four rat pineal gland analyses at various P-value thresholds.