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 412 selected genes that were selected in Question 4 are listed in Appendix 7. This group of genes is also illustrated in the dark blue circle in Figure 1. These genes are both differentially expressed in the retina compared with the whole embryo and at the same time regulated by Smarca4 in the retina.