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Figure 2 | Genome Biology

Figure 2

From: Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment

Figure 2

Diversity in the expression levels between different individual cells and different genes. (A) Distribution of the average gene expression levels (solid line) and the relative standard deviations (vertical lines). (B) Relation between average expression levels and the relative divergence. Statistical significance calculated by Fisher’s exact test (f-test) is shown in the margin. (C) Dependency of the calculated relative divergence on the varying sequence depth per cell. Average values for the indicated populations are shown. A total of 2,370, 1,014, 3,489, 541 and 429 genes were used for genes with average expression levels of 1 to 5, 5 to 10, 10 to 50, 50 to 100, and 100 to 500 rpkm, respectively. The inset represents magnification of the main plot at the region of small values on the x-axis. (D) Reproducibility of the experiments with regard to expression variation. Relative expression variation obtained from two independent experiments is shown. Pearson’s correlation is shown in the plot. (E,F) Validation analysis using real time RT-PCR assays in individual cells of LC2/ad. A total of 13 genes were analyzed. Pearson’s correlation coefficients are shown in the plot. (E) Relation between Ct values of real time RT-PCR assays and the results of single-cell RNA-Seq analyses. Each dot represents the average of triplicate experiments. (F) Relation between the relative divergence calculated based on the real time RT-PCR analyses and the single-cell RNA-Seq analyses. (G) Relative divergence in different genes. Genes were sorted according to their relative divergence and genes that were ranked at 1, 10, 100, 1,000 and 5,000 are shown. The horizontal bar represents the average expression level. The EGFR gene, which was ranked 2830, is also shown. CV, coefficient of variation. (H) Gene Ontology terms (upper panel) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways (lower panel) for genes that showed highly diverse expression between individual cells.

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