Fig. 3
Identification of differentially expressed genes in subgroup A versus B TAMs by edgeR. a Scatter plot showing the expression of genes identified by the edgeR tool (FDR <0.05) in TAM subgroups A or B identified by PCA in Fig. 2. Data represent the ratio (FC) of median TPM values for subgroup A versus subgroup B. b Functional annotation of genes upregulated in subgroup A (red) or subgroup B (blue) by gene ontology (GO) enrichment analysis. p values are plotted against fold enrichment. Only specific non-redundant terms with p values <0.01 and enrichment >3 are shown. c Upstream Regulator Analysis (Ingenuity Pathways Analysis database) of upregulated genes with p < 10−8. d Expression of the IFN signaling-associated genes of signature B identified by GO enrichment analysis (c). Boxes show the upper and lower quartiles, whiskers the 95% CI, and horizontal lines the median. e Validation of RNA-Seq data. Analysis by RT-qPCR of signature A and B genes (Additional file 2: Datasets S3 and S4) in TAM samples from subgroup A and B (n = 6). Error bars show the standard deviation and horizontal lines the mean. Red: cluster A samples; blue: cluster B samples. Asterisks indicate the statistical significance determined by unpaired t test (cluster A versus B samples); ns: not significant