(A) Proportion of transcription factors among different groups of switch-on (green) and switch-off (orange) genes. All expressed genes were ordered by their log2 fold changes between P0-P5 and P7-P12 and the 100, 200, 300, 400, 500 and 600 most strongly on- or off-switching genes were grouped. The last group ‘total’ contains all expressed genes (for conceptual consistency there are two separate bars but there is no difference between the orange and the green bar). The grey lines mark the frequency of transcription factors that is significantly higher or lower than expected (permutation analysis). (B) Comparison of log2 fold changes and log2 maximum expression levels during P0-P12 of all expressed genes (grey) with genes associated with a particular pathway (black): pathways needed for cone function, signaling pathways, axon guidance pathway, and metabolic pathways. The grey line marks the mean fold change of all expressed genes (−0.18). P-values from permutation analyses; n is the number of genes associated with each pathway. Orange boxes mark pathways that switch off, and green boxes mark pathways that switch on.