Fig. 4
Analysis of the transcriptomes of eyes from Ftx–/– mice. a Scheme for microarray analysis. WT female eyes (n = 4), WT male eyes (n = 3), Ftx–/– female eyes (type 1, n = 11) and Ftx–/Y male eyes (type 1, n = 3) were used for the analysis. All eyes were removed from E13.5 embryos and were of normal appearance. b Numbers of genes whose expression level altered between WT and Ftx-deficient mice. Comparing between WT and Ftx–/– female mice or between WT and Ftx−/Y male mice, the numbers of upregulated genes (fold change, FC, >1.2, P < 0.05) and downregulated genes (FC < 0.8, P < 0.05) are shown respectively (upper, autosomal genes; lower, X-linked genes). A two-tailed, unequal variance t-test (P < .05, WT n = 3 vs. KO n = 11) was used for statistical analysis to calculate FC values. c Physical location map of X-linked genes on the X chromosome. FC values of the Ftx–/– females vs. WT females are plotted in the upper panel, and FC values of WT females vs. WT males are plotted in the lower panel. Red dots show upregulated genes with FC >1.2, and blue dots show downregulated genes with FC < 0.8. Red arrows show genes known to escape from XCI. Xa, active X chromosome; Xi, inactive X chromosome marked with shaded circles. Ftx was not indicated in this panel because of its low signal intensity (signal intensity <500). d List of upregulated X-linked genes sorted in descending order of their FC values. The grey rows show genes containing repetitive sequences. Lists of all the X-linked genes and autosomal genes (signal intensity >500) are provided in Supplementary Data 1 and 2, respectively. e RT–qPCR analysis of Tmem29, Mecp2, Ogt, Gab3 and Slc16a2 in WT and Ftx–/– eyes (n = 3, E13.5). Significance levels of the mean differences between WT and Ftx–/– eyes were calculated using two-tailed, unequal variance t-tests. Error bars, s.d.; B2m, beta-2 microglobulin
