Additional file 1 of A machine learning framework develops a DNA replication stress model for predicting clinical outcomes and therapeutic vulnerability in primary prostate cancer

Additional file 1: Table S1. Gene sets of DNA replication stress. Table S2. Hyperparameters used in the machine learning algorithms. Table S3. Collection of prostate cancer signatures. Table S4. Gene lists of pathways. Table S5. The list of curated targetable genes. Table S6. The result of univariate Cox regression analysis of DNA replication stress-related genes. Table S7. The result of Bootstrapping-based Cox regression analysis. Table S8. The result of machine learning benchmark. Table S9. The result of signatures comparison. Table S10. Somatic copy number alterations in RSS-high and RSS-low groups. Table S11. Somatic mutation characteristics in the RSS-high and RSS-low groups. Table S12. Clinicopathologic characteristics of prostate cancers in the included cohorts. Table S13. The result of single sample gene set enrichment analysis in the Meta-cohort. Table S14. The CIBERSORT result of 905 prostate cancer samples. Table S15. The result of Spearman’s rank-order correlation between replication stress signature and druggable genes in the TCGA-PRAD cohort. Table S16. The result of Spearman’s rank-order correlation between replication stress signature and druggable genes in the DKFZ-PRAD cohort. Table S17. The result of a meta-analysis of differential gene analysis. Table S18. The result of CMap analysis. Table S19. Comparison of clinical characteristics among included cohorts.

附加文件1：表S1 DNA复制应激（DNA replication stress）相关基因集。表S2 机器学习算法所用超参数。表S3 前列腺癌特征基因集合集。表S4 通路相关基因列表。表S5 经整理注释的可靶向基因列表。表S6 DNA复制应激相关基因的单因素Cox回归分析结果。表S7 基于自举法（Bootstrap）的Cox回归分析结果。表S8 机器学习基准测试结果。表S9 特征集对比结果。表S10 RSS高表达组与RSS低表达组的体细胞拷贝数变异情况。表S11 RSS高、低表达组的体细胞突变特征。表S12 纳入队列中前列腺癌患者的临床病理特征。表S13 荟萃队列中的单样本基因集富集分析（single sample gene set enrichment analysis）结果。表S14 905例前列腺癌样本的CIBERSORT分析结果。表S15 TCGA-PRAD队列中复制应激特征与可靶向基因的斯皮尔曼等级相关分析结果。表S16 DKFZ-PRAD队列中复制应激特征与可靶向基因的斯皮尔曼等级相关分析结果。表S17 差异基因分析的荟萃分析结果。表S18 CMap分析结果。表S19 纳入队列间临床特征对比结果。