Data Statistics and tSNE/UMAP Visualization

  • Overview of the dataset
  • tSNE/UMAP - unsupervised clustering
  • The dataset included a total of 3466 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 307 8.860%
    CD4+ effector T cells 135 3.890%
    CD4+ Tcm 571 16.470%
    CD4+ Tem 123 3.550%
    Tregs 4 0.120%
    CD8+ naive T cells 20 0.580%
    CD8+ effector T cells 146 4.210%
    CD8+ Tcm 10 0.290%
    CD8+ Tem 239 6.900%
    NK cells 44 1.270%
    Monocytes 9 0.260%
    Erythrocytes 242 6.980%
    HSCs 271 7.820%
    Unassigned 1345 38.810%
  • Differential expression analysis
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    Gene Symbol
    Avg_logFC
    Pct.1
    Pct.2
    p-value
    adj_pvalue
    XIST0.480.570.3191.012e-092.505e-05
    RPLP20.270.9480.8982.512e-070.00
    AP000936.30.270.8670.752.848e-050.70
    RPL180.350.6890.5883.737e-050.92
    TMSB100.290.8440.7395.340e-051
    AC005912.10.260.8440.7495.589e-051
    AC007688.20.260.7410.6469.733e-051
    PCED1B-AS10.420.3110.190.001
    RPL39L0.380.430.3020.001
    BX679664.10.260.6740.5570.001
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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.