Table 2.

Design of simulation 3 for evaluation

Gene ID	Treatment Group	Control Group
1	Exon 5~N (0, 1)	All exons ~N (1.5,1), correlated
	Exon 6~N (0, 1)
	Others ~N (2.5, 1), correlated
2	Exon 5~N (0, 1)	All exons ~N (2.5,1), correlated
	Exon 6~N (0, 1)
	Others ~N (1.5, 1), correlated
3	Exon 5~N (2.5, 1)	Exon 5~N (0, 1)
	Exon 6~N (0, 1)	Exon 6~N (1.5, 1)
	Others ~N (2.5, 1), correlated	Others ~N (1.5, 1), correlated
4	Exon 5~N (1.5, 1)	Exon 5~N (0, 1)
	Exon 6~N (0, 1)	Exon 6~N (2.5, 1)
	Others ~N (1.5, 1), correlated	Others ~N (2.5, 1), correlated

The design of alternatively spliced exons is same with simulation 1, but the power of normal distribution is different between two sample groups to simulate the differential expression in gene level.