Table 1. The false discovery rate (FDR) of Differentially Processed Genes (DPGs) and Differentially Expressed Genes (DEGs).

	P-Value
	T-test	F-test	# of genes	FDR (%)
DPGs	0.05	0.05	1013	7.3
	0.01	0.05	515	3.0
	0.01	0.01	176	2.8
	0.001	0.05	142	1.9
	0.0001	0.05	68	1.0
DEGs	0.05	0.05	3546	14.8
	0.01	0.05	1554	7.9
	0.001	0.05	485	5.0
	0.0001	0.05	220	3.5
	0.00001	0.05	114	1.8

Note: T-test and F-test, as depicted in Figure 1b and c; the p-value for the T-test on the whole transcript level (Figure 1d) was set at 0.05 (see Results section).