Fig. 3: The transcriptome landscape of PSCCE. | Nature Communications

Fig. 3: The transcriptome landscape of PSCCE.

From: Multi-omics profiling of primary small cell carcinoma of the esophagus reveals RB1 disruption and additional molecular subtypes

Fig. 3

a Volcano plot of differentially regulated genes (DEGs). Up- and downregulated DEGs are plotted in red and cyan, respectively. Key genes are plotted in purple with symbols annotated. Source data are provided as a Source Data file. b Pathways that were largely discordant between PSCCE, EAC, and ESCC. c Heatmap of gene expressions of three principle clustering groups. Key signature genes associated with clustering are marked on the right side. d Expression of neuroendocrine differentiation marker genes and lineage transcription factors across three groups. PSCCE and SCLC samples are plotted separately to show that there was no hijacking of either cancer by the other. The upper bound, centerline, and lower bound of boxplot represent the 75 percentile, the median and the 25 percentile of data; the upper and lower whiskers extend to the largest and smallest value within 1.5 times of interquartile range (IQR) from corresponding bound. Data beyond the whiskers are plotted as outlier dots. ***P < 0.001, by the Wilcoxon rank-sum test. e GSEA revealed that E2F target genes were specifically expressed in Group NE. f GSEA revealed that RB1-loss associated genes were specifically expressed in Group NE.

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