Table 1.

Design of simulation 1 for evaluation

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

Exon 5 and Exon 6 are simulated as cassette exons in alternatively spliced gene 1 and 2, while they are defined as mutually exclusive exons in alternatively spliced gene 3 and 4.