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. 2019 Feb 21;4(4):e121387. doi: 10.1172/jci.insight.121387

Figure 2. Expression of genes in the cell cycle pathway and antigen presentation pathway among single cancer cells are coregulated.

Figure 2

(A and C) Gene pathway clusters from metagene analysis of single cells from PDX LC-PT-45 or from LC2/ad-R and LC2/ad cell lines. K-means clustering of metagenes on SOMs into 6 clusters and 8 clusters, respectively. A hypergeometric test was performed on each cluster of metagenes to determine enrichment of canonical pathways. (A) For PDX LC-PT-45, cluster A was enriched for cell cycle pathways, while cluster B was enriched for antigen presentation pathways. (C) For LC2/ad-R and LC2/ad cell lines, cluster G/H was enriched for cell cycle pathways, while cluster F was enriched for antigen presentation pathways. P values in the parentheses are FDR corrected. (B and D) Second-level clustering of SOMs for (B) 77 single cells from PDX LC-PT-45 or (D) 159 single cells from LC2/ad-R and LC2/ad cell lines. Each square is a unique SOM pattern with the heatmap indicating the gene expression level of metagenes. Cells with the same SOM are collapsed with only 1 representative SOM. SOMs are arranged by mapping all cells together into a 2-dimensional mosaic pattern based on metagene expression. Coexpression of cell cycle pathway and antigen presentation pathway further separates cells into 3 major groups: cell cycle pathway high (I), antigen presentation pathway high (II), and both pathways low (III).