Fig. 3

RA-induced cell-differentiation markers in HR-NB over-represent the PRC2-silencing targets and somatic mutations. a Identification and functional enrichment analysis of RA-dependently expressed genes. Sub-panel 1 is Venn diagrams demonstrating how to identify the core set of RA-dependent differentiation markers. Sub-panel 2 is a bar plot of the Fisher’s exact test results for the enriched functions among the RA-induced biomarkers (Ingenuity pathway analysis). b Venn diagram of the targets of PRC2, RA-induced genes, and genes harboring recurrent somatic mutations in HR-NB. Significance of enrichment is estimated using the Fisher’s exact test against approximately 21,000 human genes. c The mRNA levels of the five markers pinpointed in Panel B1 increased after RA-induced cell differentiation. The mRNA levels of the PRC2 components decreased after RA-induced cell differentiation. Box-and-whisker plots represent individual value distributions that are categorized as vehicle (left) and RA-treated (right) along with treated hours (x-axis) in the SK-N-BS cells (GSE45587). The central box represents the values of an expression (y-axis) from the lower to upper quartile. The middle line represents the median. The horizontal line extends from the minimum to the maximum value within 1.5 times of the interquartile range from the box. d The mRNA levels of three genes encoding PRC2 component increased after RA-induced cell differentiation