Supplementary Figure 9: Differentially expressed genes in mouse Smarcd2-deficient early progenitors affect myeloid pathways.

(a) Differentially expressed genes in Smarcd2^+/+ versus Smarcd2^−/− mouse LSK cells cluster in 11 groups by Reactome FI spectral clustering. Pathways cluster significantly in immune system and myeloid pathways. Smarcd2 is highlighted in red. Relevant pathways and interactions between pathways are indicated. The sources of pathway annotations are indicated in parentheses: C, CellMap; R, Reactome; K, KEGG; N, NCI PID; P, Panther; B, BioCarta. A complete list of pathways enriched per cluster is shown in Supplementary Table 6a. (b) Venn diagram of differentially expressed genes in Smarcd2^+/+ versus Smarcd2^−/− LSK cells and CEBPɛ target genes (Supplementary Table 6c). (c) Differentially expressed genes in Smarcd2^+/+ versus Smarcd2^−/− mouse LSK cells overlap with CEBPɛ targets (13 genes) and interact via MYC, FOS, EP300, and the ubiquitin system. Genes in green diamonds have been introduced as linker genes; differentially expressed genes are color-coded by continuous mapping of log(fold change) generated in LSK Smarcd2^+/+ versus Smarcd2^−/− RNA–seq experiments (blue, reduced expression in knockout; red, increased expression in knockout). Analysis and display of the network were carried out using Cytoscape 3.3.0 and the Reactome Functional Interaction (FI) plugin (solid line with arrow for activating/catalyzing FI, solid line with block for inhibitory FI, solid line (alone) for FIs extracted from complexes or inputs, and dotted lines for predicted FIs). The genes for all intersections are listed in Supplementary Table 6c.