Additional file 1 of Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks

Additional file 1: Table S1A. Differential expression genes obtained from healthy and moderate comparative analysis based on GEM. Table S1B. Differential expression genes obtained from healthy and severe comparative analysis based on GEM. Table S1C. Differential expression genes obtained from healthy and convalescent comparative analysis based on GEM. Table S1D. Differential degree genes obtained from healthy and moderate comparative analysis based on CNDM. Table S1E. Differential degree genes obtained from healthy and severe comparative analysis based on CNDM. Table S1F. Differential degree genes obtained from healthy and convalescent comparative analysis based on CNDM. Table S1G. DGs. Table S1H. 'dark' genes. Table S1I. DDGs.Table S1J. DEGs. Supplementary Note 1. Construct of CCSN and obtain CNDM from CCSN. Supplementary Note 2. Network-based cell clustering, gene dimension-reduction analysis and cell counts. Supplementary Note 3. ‘Dark’ genes revealed by CNDM. Supplementary Note 4. Validation of experimental results based on the COVID-19 single-cell sequencing dataset GSE155673. Supplementary Note 5. The prognosis analysis of ‘dark’ genes. Supplementary Note 6. Cell-cell communication analysis. Supplementary Note 7. The underlying signaling mechanisms revealed by ‘dark’ genes.

附加文件1：
表S1A：基于基因表达矩阵（GEM）开展健康对照组与中度病例组对比分析得到的差异表达基因。
表S1B：基于GEM开展健康对照组与重度病例组对比分析得到的差异表达基因。
表S1C：基于GEM开展健康对照组与康复组对比分析得到的差异表达基因。
表S1D：基于细胞邻域差异模型（CNDM）开展健康对照组与中度病例组对比分析得到的差异程度基因。
表S1E：基于CNDM开展健康对照组与重度病例组对比分析得到的差异程度基因。
表S1F：基于CNDM开展健康对照组与康复组对比分析得到的差异程度基因。
表S1G：差异基因（DGs）。
表S1H：暗基因（dark genes）。
表S1I：差异分布基因（DDGs）。
表S1J：差异表达基因（DEGs）。
补充说明1：细胞-细胞信号网络（CCSN）的构建及从CCSN获取细胞邻域差异模型（CNDM）。
补充说明2：基于网络的细胞聚类、基因降维分析及细胞计数。
补充说明3：基于CNDM揭示的暗基因。
补充说明4：基于新型冠状病毒肺炎（COVID-19）单细胞测序数据集GSE155673的实验结果验证。
补充说明5：暗基因的预后分析。
补充说明6：细胞间通信分析。
补充说明7：暗基因揭示的潜在信号传导机制。