Gene characterization of 4 D/THL cell lines compared with the other lymphoma/leukemia cell lines. (A) t-SNE clustering of the COH cell lines along with other 74 cell lines of 11 types. (B) The number of differentially expressed genes (|log₂fold change| >1, false discovery rate <0.1) for contrasts between D/THL and activated B-cell like (ABC)-DLBCL, GCB-DLBCL, or BL. (C) Heatmap showing gene set enrichment analysis results with hallmark gene sets for differentially expressed genes between D/THL , ABC-DLBCL, GCB-DLBCL, and BL. Gradient colors represent the net enrichment score. *P < .05; **P < .01. (D) Waterfall plot showing the recurrent mutations in the 4 D/THL cell lines and the other 4 double-hit GCB-DLBCL cell lines. Different colors represent different types of mutations or CNA. The top bar plot shows the total number of mutations in each sample. The right bar plot shows the number of different alterations for each gene labeled by the percentage of samples that have genetic alteration in the gene. “Multi_Hit” means genes with cooccurring mutations of different types. “Complex_Event” means genes with both mutations and CNAs. (E) Bar plot showing expressed gene number covered by regions with copy number gain or loss of D/THL cell lines studied here along with another 4 double-hit cell lines. (F) Heatmap showing the distribution of the MCRs identified by GISTIC among the 8 cell lines. (G) The significant gene ontology (GO) terms (P < .05) enriched by the expressed genes in the MCRs ranked according to −log₁₀ (P values) from top to bottom. The color and size of the dots indicate the enrichment score and ratio between gene number in MCRs and gene number in each GO term, respectively.