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（Cancer drivers）。表S2。7730份癌症基因组图谱（TCGA, The Cancer Genome Atlas）样本中发生功能损伤的经典及候选驱动基因。表S3。用于计算肿瘤免疫微环境（TIME, Tumor Immune Microenvironment）特征的基因特征集。表S4。采用Lasso正则化序数回归（Lasso regularised ordinal regression）预测得到的肿瘤免疫微环境驱动基因。表S5。从已发表文献中收集的真阳性肿瘤免疫微环境驱动基因。表S6。各癌症类型中肿瘤免疫微环境驱动基因与非肿瘤免疫微环境驱动基因的变异发生频率。表S7。可预测肿瘤免疫微环境水平的致癌基因与肿瘤抑制基因的占比情况。表S8。肿瘤免疫微环境驱动基因与非肿瘤免疫微环境驱动基因的克隆性差异对比。表S9。头颈部鳞状细胞癌（HNSC, Head and Neck Squamous Cell Carcinoma）亚型间肿瘤免疫微环境差异的文献支持证据。表S10。头颈部鳞状细胞癌分子亚型间的肿瘤免疫微环境水平对比。表S11。头颈部鳞状细胞癌亚型中肿瘤免疫微环境驱动基因-肿瘤免疫微环境转录因子（TF, Transcription Factor）功能调控网络。表S12。头颈部鳞状细胞癌肿瘤免疫微环境驱动基因-肿瘤免疫微环境转录因子功能调控网络的组成成分。表S13。选定的共表达子网络中肿瘤免疫微环境转录因子基因靶标的功能注释。