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Fig. 4 | Genome Biology

Fig. 4

From: Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

Fig. 4

Identification of PDX cell subclones using single-cell RNA-seq data. a Top: normalized RS. Middle: heatmaps of expression of 69 prognostic markers. Bottom: KRAS mutation status of each patient (training set, n = 86) or single cell (LC-PT-45, n = 34; LC-PT-45-Re, n = 43). b Scatter plots demonstrating the effect of the KRAS mutation on the RSs of LUAD patients and PDX single cells. Horizontal lines represent the mean. *P < 0.05; **P < 0.01. c Semi-supervised clustering of single cells into four groups with estimated RS and KRAS mutant status. d Principal component analysis of the genes discriminating the subgroups. Ellipsoids were generated with standard deviations around each group. eh Comparative features among the classified single cell subgroups. e KRAS gene expression (Log2 ratio of transcripts per million + 1). Gene set signature scores (computed by gene set variation analysis) corresponding to the KRAS over-expression signature [39] (f), KRAS mutation signature [40] (g), and MAPK pathway signature (gene sets from BioCarta) (h). For the boxplots in (eh), boxes = the interquartile range between the first and third quartiles, and error bars = 10th–90th percentiles

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