Fig. 3
Characterization of valproic acid (VPA)-deregulated probe sets on day 14 of differentiation in human embryonic stem cells (hESCs) and human induced pluripotent stems cells (hiPSCs) using gene ontology categories (GOs) and KEGG pathway analysis, as well as Dp and Di indice values. a The differentially regulated probe sets on day 14 by VPA were compared with non-treated 14-day differentiated cells (absolute fold change ≥ 2, false discovery rate-corrected p value < 0.05). The number of up- and downregulated genes overrepresented in GOs in hESCs and hiPSCs are shown on top of the bars. b, c Venn diagrams obtained for up- or downregulated developmental GOs, for hESCs and hiPSCs, respectively. d KEGG pathways of the VPA regulated up- or downregulated developmental probe sets, respectively. e Overlap analysis of well-annotated three germ layer-specific genes obtained from Partek Genomics Suite, showing the overlap among VPA-deregulated “developmental” genes. f Values for the D p index calculated using the ratio O/D, the D i g calculated using the ratio (O x A)/(T x D), and the significance of overlap calculated using Fisher's exact test (*** p < 0.001). In this figure, A represents the total probe sets available on the microarray chip; O represents VPA deregulated developmental probe sets; T represents the VPA deregulated probe sets; D represent “developmental” probe sets deregulated on day 14, compared with day 0. The total number of the deregulated probe sets in (f) and (g) is indicated on the top of the columns