Figure 6

IPA analyses for differentially expressed genes found in E15.5 GOF embryonic cortex. (A) The smear plot demonstrates the log-fold change (FC) against average log counts per million reads (CPM). The black and red dots represent genes with FDR > 0.05 and FDR < 0.05, respectively. Blue lines indicate the twofold change lines. (B) Transcriptional changes of genes associated with RGCs (Pax6, Fabp7, Nestin), IPCs (Eomes), and postmitotic neurons (Tbr1, Cux1, Satb1, Satb2, Bcl11b) summarized from RNA-seq data. (C) Top 10 significant canonical pathways identified by IPA classified by physiological function. These pathways are involved in regulating cellular assembly and organization, cell cycle, cellular development, and embryonic development (shown in the left panel). (D,E) Schematic diagrams show the partial pathways related to cell cycle and axonal guidance with the molecule activation prediction (MAP) analysis. Molecules are indicated by standard abbreviations. Relative changes in gene expression are depicted by graduated shades of color coding: red, up; green, down; white, no change, or not applicable. MAP analysis in IPA predicts the activation status of each pathway component based on the transcriptional state of the relevant genes. Relative activation and inhibition status are depicted by graduated shades of color coding: orange, activation; blue, inhibition; yellow, inconsistent with the state of the downstream molecule; grey, effect not predicted.