Figure 3: Using the treeness test as a tool to identify distinct cell types. | Nature Communications

Figure 3: Using the treeness test as a tool to identify distinct cell types.

From: The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Figure 3

(a) Comparison of pairs of replicates between normal cell types. If the two cell samples are in fact two cell types, we expect the tetrad to have significant tree structure, meaning that replicates are more similar to each other than each is to a replicate from a different cell type. (b) To test whether cancer cells remain similar to their normal cell types from which they originate, we compare cancer cell transcriptomes with that of normal cell types from which the cancer originated, that is, each tetrad has two pairs, each consisting of a normal cell with their cognate cancer cell. (c) Results for ENCODE data. (d) Results for FANTOM5 data. Note that cancer cells are not more similar to their cells of origin than to unrelated cell types, indicating that cancer cells diverge more radically than novel cell types in evolution. Fibroblasts from different body parts have marginally significant tree structure, suggesting that they might be representing the same cell type in different locations of the body. Finally, replicates of the other normal cell types are highly significant, showing that their replicates are much more similar than they are to other cell types. In the box-and-whisker plot, the bottom and top of the box are the first and third quartiles. The ends of whiskers are the lowest datum still within 1.5 interquartile range of the lower quartile, and the highest datum within 1.5 interquartile range of the upper quartile. The red dotted line indicates α=0.05.

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