Fig. 5

Identification of tumor cluster with high expression of ligands. A t-SNE plot displaying classification of tumor cells. B Inferred copy number variations of tumor cells were used to estimate the robustness of classifications. Blue indicates low modified expression, inferring to genomic loss; red indicates high modified gene expression, inferring genomic gain. Internal reference cells refer to mast cells. Observations refer to putative malignant epithelial cells. Genomic regions (chromosomes) are labeled and color-coded. C Violin plot demonstrates the distribution of ligand expression among cancer cells, Welch’s t test: *P < 0.05; **P < 0.01; ***P < 0.001, ****P < 0.0001 D Gene set variation analysis (GSVA) showing the enriched pathways of tumor cluster 3 compared with other tumor clusters. E CCCs between tumor cluster 3 with myeloid cells and T Cells. The bars to the right suggest that the pathways are upregulated in tumor cluster3, with longer bars suggesting more significant variance values. F The expression programs of transcription factors are heterogenous among different tumor clusters, the colors indicate the AUCell regulon activity of the transcription factors (TFs) as red (highly active) and blue (lowly active). TFs upregulated in tumor cluster 3 are marked on the right. G GO analysis of highly expressed transcription factors of tumor cluster 3 targeting downstream genes. The vertical coordinate represents the enriched pathways, and the horizontal coordinate represents the genes regulated downstream of the transcription factor (the number is the number of genes) predicted from the cistarget database