Fig. 3. Significant overlap of derepressed genes in Ring1A/B-dKO and Oct3/4-KO ES cells. (A) Scatter diagrams representing the correlation for changes in gene expression between respective KO ES cells. Each dot represents a specific probe. Fold changes of expression given by each probe in each KO against parental ES cells are dotted in the scatter diagram. Pearson's correlation coefficient (r) in each comparison is indicated in each panel. The distribution of dots is approximated by dotted ellipses. We prepared RNA from Oct3/4-KO ES cells 1 day after gene deletion was induced; Ring1A/B-dKO RNA was isolated at 4 days. Diagrams indicate the correlation of gene expression in Eed-KO versus Ring1A/B-dKO (green), Oct3/4-KO versus Ring1AB-dKO (red), Dnmt1-KO versus Ring1A/B-dKO (yellow), and Dnmt1-KO versus Oct3/4-KO (blue). (B) Pearson's correlation of expression changes for probes that belong to specific GO classifications are shown by bars. The same color codes are used as in A. Annotations are indicated above each graph. Error bars represent 95% confidence intervals of correlation coefficients calculated by Z transformation. (C) Graphical representation of correlation of derepressed genes in Oct3/4-KO and Ring1A/B-dKO ES cells in terms of the degree of Ring1B binding. Based on the genome-wide gene expression profiling, we first identified groups of genes more than 2-fold derepressed (red circles) or repressed (blue circles) in Oct3/4-KO ES cells. Average expression changes in Ring1A/B-dKO cells among those genes were plotted according to the degree of Ring1B binding determined by ChIP-chip and compared with the average of total genes (yellow circles). Where average expression changes in respective groups were statistically significant, relative to the total, the circles are solid; the open blue circles indicate that the difference from total genes is not statistically significant. P-values over 5-, 10- and 15-fold enrichment for Ring1B binding are shown. For actual values, see Table S6 in the supplementary material. (D) A significant fraction of the genes repressed by Oct3/4 is bound by Ring1B. The number of genes in each category of the Venn diagram is indicated.