Molecular Vision: Zhang, Mol Vis 2014; 20:56-72. Table 3

Table 3. Contrasts for selecting Smarca4-regulated RPE genes.

Question	Contrast	Number of genes	Appendix
1. Gene differentially expressed in WT RPE	H₀: T_RPE=0	6306	-
2. Gene differentially expressed in smarca4 RPE	H₀: T_RPE + M*T_RPE=0	4851	-
3. Gene differentially expressed in WT OR smarca4 RPE	H₀: T_RPE=0 OR H₀: T_RPE + M*T_RPE=0	8536	-
4. Smarca4-regulated RPE genes that are differentially expressed in RPE	H₀: M + MT_RPE=0 AND (H₀: T_RPE=0 OR H₀: T_RPE + MT_RPE=0)	591	5

These contrasts are listed in the sequential order of building up the final conclusion (Question 4). Each row lists the question, the corresponding contrast that was tested, and the number of genes less than the q-value cutoff (< 0.001). The final 591 selected genes that were selected in Question 4 are listed in Appendix 5. This group of genes is also illustrated in the black circle in Figure 1. These candidate genes are both differentially expressed in the RPE compared with the whole embryo and at the same time regulated by Smarca4 in the RPE.