Fig. 3
From: B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation
Dysregulation of plasma cell gene expression without Dnmt3a and Dnmt3b. a Principle component analysis of gene expression. The percentage in parenthesis is the proportion of variation explained by each component and 95% confidence intervals for each group are drawn. b K-means clustering of differentially expressed genes organized into seven categories uniquely. Samples are represented by columns and genes by rows. c Gene ontology analysis of genes contained in the K-clusters from b. Select ontologies are shown, and the significance of each ontology in each K-cluster (represented by columns) is denoted by color. d Number of Dnmt3-specific differentially expressed genes (DEGs) found between Dnmt3-sufficient and -deficient naive B cells (nB), germinal center B cells (GCB), and bone marrow plasma cells (BMPC). Genes upregulated in Dnmt3-deficient cells are shown above and those downregulated are shown below. e Average level of expression of all Dnmt3-specific differentially expressed genes shown in d. (f, g) Examples of Dnmt3 differentially expressed genes both downregulated (f) and upregulated (g) in Dnmt3-deficient BMPC. **FDR ≤ 0.01, ***FDR ≤ 0.001; mean and standard defviation are shown f, g. Data are from 3 experiments and 24 mice where nB were isolated from 6 mice, GCB were from 12 mice (2 mice were pooled per sample), and BMPC were from 6 mice. Each cell type contained 4 female and 2 male (nB, GCB) or 4 male and 2 female (BMPC) mice split evenly between the genotypes. Differentially expressed genes had an FDR ≤ 0.01 and a fold change ≥ 2
