Fig. 2: Gene set enrichment analysis and analysis of differentially expressed genes in lineage-switched AML. | Nature Communications

Fig. 2: Gene set enrichment analysis and analysis of differentially expressed genes in lineage-switched AML.

From: Multi-omics analysis identifies an M-MDSC-like immunosuppressive phenotype in lineage-switched AML with KMT2A rearrangement

Fig. 2

a Ontology gene sets ranked in the top 15 and bottom 15 normalized enrichment scores (NESs) calculated by gene set enrichment analysis (GSEA). LS AML and LC AML in Cluster 2 were compared. Adaptive immune-related gene sets are shown in purple; antigen presentation-related gene sets are shown in blue. GOCC gene ontology cellular component, GOBP gene ontology biological process, GOMF gene ontology molecular function, HP human phenotype. Source data are provided as a Source Data file. b, c Leading edge analysis of adaptive immune-related gene sets (b) and antigen presentation-related gene sets (c) ranked in the bottom 15 when comparing LS AML and LC AML in Cluster 2. Expression values are represented by colors, where the range of colors (red, pink, light blue, dark blue) reflects the range of expression values (high, moderate, low, lowest, respectively). d Enrichment analysis of M-MDSC signatures comparing LS AML and LC AML. The “M-MDSC Signature Cell Rep” comprises ORM1, S100P, SLCO4C1, CYP1B1, CLEC4D, CHD7, CKAP4, MSRB1, CLU, CD82, CPEB4, TLK1, OSBPL8, ABHD2, ATP6V1E1, and ROCK1. NOM: nominal; FDR: false discovery rate. Nominal (NOM) p-value represents the credibility of the enrichment result, and false discovery rate (FDR) q-value is the p-value adjusted after multiple hypothesis testing (Benjamini-Hochberg method, two-sided). e Enrichment analysis (pre-ranked) of M-MDSC signatures comparing LS AML with KMT2A::AFF1 and LC AML with KMT2A::AFF1. NOM p-value represents the credibility of the enrichment result, and FDR q-value is the p-value adjusted after multiple hypothesis testing (Benjamini-Hochberg method, two-sided). f Volcano plot showing differentially expressed genes (DEGs) between LS AML and LC AML. The significance-adjusted p-value (calculated by DESeq2 using multiple comparisons; Benjamini-Hochberg method, two-sided) is set as <0.05, and a significant-fold change is defined as > |2| (orange dotted lines). The names of the M-MDSC-related genes are displayed as dark red or gray dots.

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