Additional file 2 of Transcriptional consequences of MBD5 disruption in mouse brain and CRISPR-derived neurons

Additional file 2: Figure S1. Enrichments of differentially expressed genes in gene sets with relevance to neurodevelopment and neuronal function. The description of gene lists and corresponding publications is provided in Supplementary Tables 5 & 6. The color represents -log10(p-value). Figure S2. Enrichments of co-expression modules with evidence of Mbd5 knock-down relevance in gene sets with relevance to neurodevelopment and neuronal function. Only sets with significant enrichments are shown. The description of gene lists and corresponding publications is provided in Supplementary Tables 5 & 6. The color represents -log10(p-value). Figure S3. Protein-protein interaction network of genes from co-expression module Cx15 from String-db database. The nodes filled with red represent the genes that belong to GO “cilium”. Nodes circled in red are differentially expressed in cortex at nominal p-value <0.05. The boxplot shows the mean expression of the genes in module Cx15 as normalized log10-transformed counts. Figure S4. Heatmap of gene expression of cell-type specific markers as normalized log-transformed scaled counts. The values are scaled by row. Figure S5. Differential expression analysis of cell lines and overlaps with mouse brain regions. A-B - Volcano plots of differential expression tests for NPCs (A) and Neurons (B). X-axis shows estimated log2 fold change and y-axis shows -log10(FDR). Horizontal grey dashed line shows -log10(0.05), marking the significance cut-off for FDR. Vertical grey dashed line shows the log2 fold change = 0. Red points show the genes that have FDR < 0.05 and absolute log2 fold change less or equal to 1, green points show the genes with FDR < 0.05 and absolute log2 fold change greater than 1. C - Table of number of differentially expressed genes in NPCs and Neurons at FDR < 0.05 and nominal p < 0.05. D - Overlap of nominal differentially expressed genes in cell lines and mice. Genes that are expressed in all 5 comparisons (NPCs, neurons, mouse cerebellum, mouse cortex, mouse striatum) were considered as background for enrichment tests. The number inside the cell shows number of background genes in corresponding overlap, and the color of the cell shows the -log10(p) from Fisher's test for overrepresentation. Figure S6. Meta analysis of cell lines using Fisher’s method and comparison of nDEGs with Gigek et al. A - Genes with FDR < 0.05 in meta-analysis on all mouse regions and cell lines. The heatmap shows the direction and significance of each gene in the corresponding cell type/brain region. B –Enrichment of DEGs identified in Gigek et al. among nDEGs from mouse brain regions, and human NPCs and neurons. The color indicates -log10(p) of Fisher’s enrichment test between two sets, and the number shows the number of genes in common. Figure S7. Principal Component Analysis of mouse brain regions. This shows that the primary component of the variability in gene expression is brain region, contributing as much as 79% to overall variation.