By executing this code with some modifications, one can obtain the results shown in Additional files 1-4. By default, it produces the results under the following conditions: Ngene = 10,000, P_DEG = 0.25, P_G1 = 0.8, P_G2 = 0.1, P_G3 = 0.1, Nrep = 3, and four possible expression patterns (nonDEG, DEG_G1, DEG_G2, and DEG_G3). It corresponds to a part of Table 1b.

This code was used for analyzing the first real dataset (Blekhman et al., Genome Res., 2010). It was obtained from the Supplemental Material. By executing this code, one can obtain the results shown in Table 2.

This code was used for analyzing the second real dataset (Prudencio et al., Nat Neurosci., 2015). The count dataset (SRP056477) was obtained from the recount2 website (Collado-Torres et al., Nat Biotechnol., 2017). By executing this code, one can obtain the results shown in Additional file 5.