Integrative Bulk-to-Single-Cell Transcriptomics Defines Melanoma Subtypes and a Prognostic Signature for Immunotherapy Guidance
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Supplementary Figures: Supplementary Figure S1. The sample similarity of each subgroup was assessed by calculating the Silhoutte score. Supplementary Figure S2. The cluster prediction index and gap statistical analysis of the multi-omics clusters. Supplementary Figure S6-S11. The TWAS analysis validation results of TCGA and meta-GEO cohorts. Supplementary Figure S6-S11. The single-gene expression analysis and OS survival analysis of CLMS in TCGA cohorts. Supplementary Figure S12-S17. The single-gene expression analysis and OS survival analysis of CLMS in meta-GEO cohorts. Supplementary Tables: Supplementary Table S1. The main characteristic of datasets used in this study Supplementary Table S2. The significant TWAS analysis results between Skin Not Sun Exposed Suprapubic and melanoma. Supplementary Table S3. The significant TWAS analysis results between Skin Sun Exposed Lower leg and melanoma. Supplementary Table S4. The significant TWAS analysis results between Whole Blood and melanoma.
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1. Data Acquisition Download RNA-seq expression data and corresponding clinical information of melanoma patients from TCGA and meta-GEO cohorts. Detailed dataset characteristics are listed in Supplementary Table S1. 2. Sample Similarity Assessment Assess the sample similarity within each identified multi-omics subgroup using the Silhouette score. The results are visualized in Supplementary Figure S1. 3. Multi-omics Clustering Analysis Perform integrative clustering using algorithms such as iClusterPlus or Similarity Network Fusion. Evaluate the optimal number of clusters using the cluster prediction index and gap statistic analysis, as shown in Supplementary Figure S2. 4. TWAS Analysis Conduct transcriptome-wide association studies (TWAS) using reference expression models (e.g., GTEx v8) and melanoma GWAS summary statistics. Significant gene-trait associations for different tissues are provided in: Supplementary Table S2: Skin Not Sun Exposed Suprapubic Supplementary Table S3: Skin Sun Exposed Lower Leg Supplementary Table S4: Whole Blood 5. TWAS Result Validation Validate TWAS-identified gene associations in both TCGA and meta-GEO cohorts. The validation results are presented in Supplementary Figures S6–S11. 6. Gene Expression and Survival Analysis in TCGA Analyze the expression levels of key TWAS genes in TCGA samples and evaluate their prognostic value using overall survival (OS) analysis. Results are shown in Supplementary Figures S6–S11. 7. Gene Expression and Survival Analysis in meta-GEO Repeat the expression and OS survival analyses in the meta-GEO cohort. The corresponding results are displayed in Supplementary Figures S12–S17.
Institutions
- Southwest Medical University