Data Statistics and tSNE/UMAP Visualization

  • Overview of the dataset
  • tSNE/UMAP - unsupervised clustering
  • The dataset included a total of 1210 cells, the parameters adopted were as follows: resolution=1, PCs=1:20, MT<10%.

Tumor Microenvironment

  • Cell components
  • Subtype Cell Count Percentage
    CD4+ naive T cells 78 6.450%
    CD4+ effector T cells 113 9.340%
    CD4+ Tcm 100 8.260%
    CD4+ Tem 29 2.400%
    Tregs 8 0.660%
    CD8+ naive T cells 16 1.320%
    CD8+ effector T cells 46 3.800%
    CD8+ Tem 29 2.400%
    NK cells 65 5.370%
    Plasma cells 103 8.510%
    Macrophages 2 0.170%
    Monocytes 416 34.380%
    Dendritic cells 1 0.080%
    Erythrocytes 34 2.810%
    GMPs 103 8.510%
    Unassigned 67 5.540%
  • Differential expression analysis
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    Gene Symbol
    Avg_logFC
    Pct.1
    Pct.2
    p-value
    adj_pvalue
    RPS60.5710.9793.420e-247.376e-20
    IL7R0.950.7080.2612.254e-234.862e-19
    AC005912.10.700.9470.6821.597e-223.445e-18
    AC073861.10.590.9910.8778.590e-221.852e-17
    RPS180.5410.932.141e-204.617e-16
    ETS10.850.6550.2634.367e-199.416e-15
    RPS27AP160.560.9650.8831.414e-183.049e-14
    AC007688.20.610.9380.8172.063e-184.449e-14
    RPS120.5110.891.612e-173.477e-13
    RPL210.510.9730.8843.516e-177.583e-13
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  • GO and KEGG enrichments

Functional Genes' Expression

  • Receptor and ligand genes' expression
  • Receptor genes and their paired ligand genes were collected from CelltalkDB, SingleCellSingalR, Cellinker, Cell-Cell Interaction Database and Armingol E, et al., 2021. The following figures only demonstrated the expression of receptor genes and ligand genes supported by three or more databases or other sources, and the corresponding relationship between ligands and receptors were shown in the following table.

  • Oncogenes and suppressor genes' expression
  • Oncogenes and tumor suppressor genes (TSGs) were collected from Cancer Gene Census (CGC), OncoKB, Network of Cancer Genes (NCG), TSGene, IntOGene and Volkan Okur and Wendy K. Chung, 2017. The following figures only displayed the expression of oncogenes and TSGs supported by three or more databases or other sources.