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。在7730份癌症基因组图谱（TCGA）样本中发生功能受损的经典驱动基因与候选驱动基因。表S3。用于计算肿瘤免疫微环境（Tumor Immune Microenvironment, TIME）特征的基因特征集。表S4。采用Lasso正则化序数回归预测得到的TIME驱动基因。表S5。从已发表文献中收集的真阳性TIME驱动基因。表S6。按癌症类型分类的TIME驱动基因与非TIME驱动基因的变异发生频率。表S7。可预测TIME水平的致癌基因与肿瘤抑制基因的占比情况。表S8。TIME驱动基因与非TIME驱动基因的克隆性差异对比分析。表S9。针对头颈部鳞状细胞癌（Head and Neck Squamous Cell Carcinoma, HNSC）各亚型间TIME差异的文献支持证据。表S10。头颈部鳞状细胞癌（HNSC）分子亚型间TIME水平的比较分析。表S11。头颈部鳞状细胞癌（HNSC）亚型中TIME驱动基因-TIME转录因子（Transcription Factor, TF）功能调控网络。表S12。头颈部鳞状细胞癌（HNSC）TIME驱动基因-TIME转录因子功能调控网络的组成元件。表S13。选定的共调控子网络中TIME转录因子基因靶标的功能注释。