Supplementary Figures S1-S13 from Whole Exome and Transcriptome Analyses Integrated with Microenvironmental Immune Signatures of Lung Squamous Cell Carcinoma

Supplementary Figure S1. Transcriptomic analyses for molecular subtypes Supplementary Figure S2. Identification of the subtypes in LUSC TCGA cohort (n=431) Supplementary Figure S3. The genomic difference across subtypes in LUSC. Supplementary Figure S4. Estimation of Stromal and immune score and distribution of infiltrating immune cells for tumor and noncancer control sample in LUSC Supplementary Figure S5. The immune landscape and micro-environmental signature in LUSC TCGA cohort (n=431) Supplementary Figure S6. The dual roles of stroma are described by distinct gene expression patterns in tumor(subtype A and B) and noncancer control samples. Supplementary Figure S7. Distribution of infiltrating immune cells for tumor and noncancer control sample in LUSC Supplementary Figure S8. Distinct expression pattern of M1 and M2 signature genes in LUSC subtypes Supplementary Figure S9. Comparison of immune contents between subtypes in our LUSC cohort (n=101) and TCGA LUSC cohort (n=431) Supplementary Figure S10. Immune related pathways enriched for genes which have copy number variants. Supplementary Figure S11. Comparison of the LUSC expression subtypes with the previously defined subtypes Supplementary Figure S12. Clinical association analysis across subtypes Supplementary Figure S13. Survival analysis across subtypes