Additional file 1 of Tumor antigens and immune subtypes guided mRNA vaccine development for kidney renal clear cell carcinoma

Additional file 1: Figure S1. The workflow of the study. OE, overexpressed genes; APCs, antigen-presenting cells; TMB, tumor mutation burden; CNV, copy number alterations; DEGs, differentially expressed genes; RIS, renal cancer immune subtype. Figure S2. a, volcano plot; b, heatmap of overexpressed genes in normal and KIRC samples; c, overlapped genes identified through intersection; d-f, KEGG (d), Hallmark (e) and reactome (f) enrichment analysis of 572 genes after intersection of overexpressed and mutated genes. KEGG, Kyoto Encyclopedia of Genes and Genomes. Figure S3. a, cumulative distribution function curve; b, delta area of immune-related genes; c, principal component analysis; d, association of immune subtypes with G-score; e-f, Bar graph of copy number variation in RIS1 (e) and RIS2 (f). Figure S4. the differences of immune infiltration score among subtypes in immune cells. Figure S5. a-b, the differential enrichment fraction of immune cells in the above subgroups. RIS, renal cancer immune subtype; ns, not significant. * p < 0.05, ** p < 0.01, *** p < 0.001 and **** p < 0.0001. Figure S6. WGCNA module identification. a, sample clustering; b, scale-free fitting index of various soft threshold powers (β); c, the average connectivity; d, Dendrogram of all differentially expressed genes clustered based on a dissimilarity measure (1-TOM). e, number of genes in each module; f, difference distribution of feature vectors of each module in RIS1 and RIS2. RIS, renal cancer immune subtype; ns, not significant. * p < 0.05, ** p < 0.01, *** p < 0.001 and **** p < 0.0001. Figure S7. Identification of immune hub genes in KIRC. a, univariate Cox regression analysis of the 10 modules; b-d, Gene Ontology analysis of Blue (b), Yellow (c) and Green (d). Figure S8. a, risk score distribution; b, survival state distribution; c, prognosis of risk models; d, heatmap of RDX, IREB2, UBR1 and PIK3CA. Figure S9. a, heatmap of differentially expressed genes in immune subtypes; b-e, GO (b-d) and KEGG (e) enrichment of differentially expressed genes in immune subtypes. GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes. Figure S10. a, univariate Cox regression analysis; b-d, Lasso regression model; e, risk score distribution; f, survival state distribution; g, Survival curves of risk model; h, heatmap of genes in the risk model; i, risk score distribution between immune subtypes; j, Distribution of high and low risk group samples among subtypes; k, immune response inference based on SKCM. RIS, renal cancer immune subtype; SKCM, human skin cutaneous melanoma; CTLA-4, Cytotoxic T-Lymphocyte Associated Protein 4; PD-1, programmed cell death protein 1; nonR, non-responder; R, responder.