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.

补充文件2：图S1。与神经发育及神经元功能相关基因集的差异表达基因富集分析。基因列表及相关文献的详细说明见补充表5与6。颜色代表-log₁₀(p值)。
图S2。与神经发育及神经元功能相关的基因集中，具备Mbd5敲低关联证据的共表达模块富集分析。仅展示具有显著富集的基因集。基因列表及相关文献的详细说明见补充表5与6。颜色代表-log₁₀(p值)。
图S3。来自String-db数据库的共表达模块Cx15的基因蛋白质相互作用网络。填充红色的节点代表属于基因本体（Gene Ontology, GO）“纤毛（cilium）”类别的基因。红色圈出的节点为在皮层中名义p值<0.05的差异表达基因。箱线图展示了模块Cx15中基因的平均表达水平，以经过标准化的log₁₀转换计数表示。
图S4。细胞类型特异性标志物基因表达量热图，数值为经标准化log转换后的标准化计数，且按行进行标准化。
图S5。细胞系的差异表达分析及其与小鼠脑区的重叠情况。A-B：神经前体细胞（Neural Progenitor Cells, NPCs，图A）与神经元（图B）的差异表达检验火山图。横轴为估算的log₂倍变化值，纵轴为-log₁₀(错误发现率, False Discovery Rate, FDR)值。灰色水平虚线代表-log₁₀(0.05)，以此作为FDR的显著性阈值。灰色垂直虚线代表log₂倍变化值为0。红色点代表FDR<0.05且|log₂倍变化|≤1的基因，绿色点代表FDR<0.05且|log₂倍变化|>1的基因。C：神经前体细胞与神经元中，满足FDR<0.05且名义p值<0.05的差异表达基因数量统计表。D：细胞系与小鼠中名义差异表达基因的重叠情况。在全部5组比较（神经前体细胞、神经元、小鼠小脑、小鼠皮层、小鼠纹状体）中均有表达的基因被用作富集分析的背景基因集。单元格内的数字代表对应重叠区域的背景基因数量，单元格颜色代表Fisher过度表征检验的-log₁₀(p值)。
图S6。采用Fisher方法的细胞系荟萃分析，以及与Gigek等人研究中差异表达基因数（nDEGs）的对比。A：在所有小鼠脑区与细胞系的荟萃分析中，FDR<0.05的基因。热图展示了各基因在对应细胞类型/脑区中的表达方向与显著性。B：Gigek等人研究中鉴定的差异表达基因（DEGs）在小鼠脑区、人类神经前体细胞与神经元的名义差异表达基因（nDEGs）中的富集情况。颜色代表两组间Fisher富集检验的-log₁₀(p值)，数字代表共有的基因数量。
图S7。小鼠脑区的主成分分析。结果显示，基因表达变异的首要成分为脑区类型，其对总变异的贡献可达79%。