Data Statistics and tSNE/UMAP Visualization

  • Overview of the dataset
  • tSNE/UMAP - unsupervised clustering
  • The dataset included a total of 1883 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 134 7.120%
    CD4+ effector T cells 142 7.540%
    CD4+ Tcm 97 5.150%
    CD4+ Tem 41 2.180%
    Tregs 13 0.690%
    CD8+ naive T cells 19 1.010%
    CD8+ effector T cells 106 5.630%
    CD8+ Tcm 6 0.320%
    CD8+ Tem 84 4.460%
    NK cells 122 6.480%
    Naive B cells 30 1.590%
    Activated B cells 22 1.170%
    Memory B cells 2 0.110%
    Plasma cells 1 0.050%
    Monocytes 23 1.220%
    Erythrocytes 806 42.800%
    GMPs 195 10.360%
    Unassigned 40 2.120%
  • Differential expression analysis
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    Gene Symbol
    Avg_logFC
    Pct.1
    Pct.2
    p-value
    adj_pvalue
    MS4A12.820.8640.0371.563e-763.546e-72
    HLA-DOA1.950.3180.012.669e-356.054e-31
    BANK11.730.3640.0192.496e-275.660e-23
    IGHM2.020.4550.0318.338e-271.891e-22
    SWAP701.720.4090.0267.055e-261.600e-21
    RALGPS21.930.4550.057.945e-181.802e-13
    HLA-DRA1.920.5450.0763.640e-178.255e-13
    SNX21.630.4090.0653.071e-116.965e-07
    REL2.030.3640.0584.252e-109.644e-06
    MEF2C1.330.3640.0574.643e-101.053e-05
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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.