a, Cell–cell correlation matrix based on all analysed genes across all malignant cells in MGH54 (n = 1,174). Cells are ordered by average linkage hierarchical clustering, and coloured boxes indicate distinct clusters. Clusters are marked based on the identity of differentially expressed genes as OC-like (blue), AC-like (yellow), cycling (pink) stem-like (purple) and intermediate cells that do not score highly for any of those expression programs (orange). b, Most differentially expressed genes. Shown is the average expression in each of the OC-like, AC-like, stem-like and intermediate cell clusters (columns) of differentially expressed genes (rows) defined by comparing cells from each of the OC-like, AC-like and stem-like clusters to cells from the remaining clusters with a t-test. Similar genes are highlighted as in Fig. 1 (OC-like: OMG, OLIG1, OLIG2, SOX8; AC-like: ALDOC, APOE, SOX9; Stem-like: SOX4, SOX11, CCND2, SOX2). Stem-like genes also include CTNNB1, USP22, and MSI1. c, Overlap with human GBM stemness program. We previously6 identified a GBM stemness program and determined the association of each gene with that program by the correlation between the expression of that gene and the average expression of the stemness program’s genes across individual cells (‘CSC gradient’) in each of five GBM tumours. Shown is the average correlation (x axis) of each analysed gene (green dots) across the five cases and the P values of those correlations as determined with a t-test (y axis). Genes identified in the oligodendroglioma stemness program (this work) are marked in black and are significantly enriched for the GBM stemness genes (1.5 × 10−4, hypergeometric test), defined as those with P < 0.05 and an average correlation above 0.1. d, Preferential expression of the oligodendroglioma stemness program in neurons but not in OPCs. Genes expressed in the oligodendroglioma single cells were divided into six bins (bars) based on their relative expression (log2-ratio) in stem-like cells with high PC2/3 and intermediate PC1 scores compared to all other cells. Each panel shows for each bin the average relative expression in each of three normal brain cell types (y axis) based on data from the Barres laboratory RNA-seq database9,18: mice oligodendrocyte progenitor cells (mOPC, top), mouse neurons (mNeurons, middle), and human neurons (hNeurons, bottom). Relative expression of each gene in each cell type was defined as the log2-ratio between the respective cell type divided by the average over AC, OC and neurons. Error bars denote standard error as defined by bootstrapping. Asterisks denote bins with significantly different relative expression (in the respective normal cell type) compared to all genes expressed in oligodendroglioma, based on P < 0.001 (by t-test) and average expression change of at least 30%. e, Correlation with mouse activated NSC program. Shown is the distribution of correlation values (x axis) of either all genes (grey) or genes from the oligodendroglioma stemness program (black) with the expression program of mice NSC activation states, as previously quantified by ‘pseudotime’, across single mouse NSCs19. The average correlation of the NSC activation program genes with oligodendroglioma stemness genes is significantly higher than with all other genes (P = 3 × 10−6; t-test). f, Correlation with human NPC program. Shown is the distribution of correlation values (x axis) of either all genes (grey) or genes from the oligodendroglioma stemness program (black) with an expression program of human NPCs identified by PCA (Extended Data Fig. 4). Each gene’s correlation to the average expression of the NPC program genes was calculated across single human NPCs. The average correlation with oligodendroglioma stemness genes is significantly higher than with all other genes (P = 2 × 10−35, t-test).