Additional file 2 of Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment

Additional file 2: Table S1. Cancer drivers used in the analysis. Table S2. Canonical and candidate drivers damaged in 7,730 TCGA samples. Table S3. Gene signatures used to compute TIME features. Table S4. Predicted TIME drivers using Lasso regularised ordinal regression. Table S5. True positive TIME drivers collected from the literature. Table S6. Frequency of TIME and non-TIME driver alterations per cancer type. Table S7. Proportion of oncogenes and tumour suppressors predictive of TIME levels. Table S8. Comparison of clonality between TIME and non-TIME drivers. Table S9. Literature support for TIME differences across HNSC subtypes. Table S10. Comparison of TIME levels between HNSC molecular subtypes. Table S11. TIME driver-TIME TF functional networks in HNSC subtypes. Table S12. Components of HNSC TIME drivers - TIME TFs functional networks. Table S13. Functional annotation of TIME TF gene targets in selected coherent subnetworks.

附加文件2：表S1 本分析中使用的癌症驱动基因。表S2 7730份癌症基因组图谱（The Cancer Genome Atlas, TCGA）样本中发生变异损伤的经典驱动基因与候选驱动基因。表S3 用于计算肿瘤微环境（Tumor Immune Microenvironment, TIME）特征的基因特征集。表S4 采用套索（Lasso）正则化序数回归预测得到的肿瘤微环境驱动基因。表S5 从文献中搜集得到的真阳性肿瘤微环境驱动基因。表S6 各癌型中肿瘤微环境驱动基因与非肿瘤微环境驱动基因的变异频率。表S7 可预测肿瘤微环境水平的癌基因与抑癌基因的占比。表S8 肿瘤微环境驱动基因与非肿瘤微环境驱动基因的克隆性比较。表S9 头颈部鳞状细胞癌（Head and Neck Squamous Cell Carcinoma, HNSC）各亚型间肿瘤微环境差异的文献佐证。表S10 头颈部鳞状细胞癌分子亚型间的肿瘤微环境水平比较。表S11 头颈部鳞状细胞癌亚型中肿瘤微环境驱动基因-肿瘤微环境转录因子（Transcription Factor, TF）功能网络。表S12 头颈部鳞状细胞癌肿瘤微环境驱动基因-肿瘤微环境转录因子功能网络的构成要素。表S13 选定的连贯子网中肿瘤微环境转录因子基因靶标的功能注释。