Fig. 7: Validation of the tumorigenic routes.
From: Club cells employ regeneration mechanisms during lung tumorigenesis
a Violin plot depicting cNMF module scores in human LUAD based on single-cell transcriptome of patient-specific tumour cells. Patients 3 to 7 had a LUAD52. b Violin plot depicting cNMF module scores in human LUAD based on single-cell transcriptome. TS1-TS3 represent 3 tumour-specific transcription states of LUAD, and non-lung metastases labelled as “Malignant cells”53. c Forest plot depicting the Hazard Ratio (HR) and its confidence interval (CI) based on a Cox proportional hazards model in LUAD patients in TCGA for each gene expression module (n = 533). d Correlation-based heatmap of the cluster composition of our original clusters and the clusters from ref. 55. The rows are the integrated clusters, while columns are the original clusters from both studies. To avoid confusion, the clusters from ref. 55, are referred by name and coloured in blue. e AT1-like, Regeneration-like and Stem-like tumour module z-scores for cells belonging to the original clusters from this study and the one from ref. 55. The clusters from the Yang study are referred by name and coloured in blue. Cluster 13 vs. AT1-like, AT1-like tumour module, p-value 2.11 × 10−41; Cluster 12 vs. Late Gastric, Regeneration-like tumour module p value = 2.29 × 10−31. n1 = 3502, n2 = 4710, n3 = 3091, n4 = 3027, n5 = 2717, n6 = 1706, n7 = 2684, n8 = 506, n9 = 518, n10 = 594, n11 = 64, n12 = 1526, n13 = 103, nMesenchymal-1 = 9950, nMesenchymal-2 = 9028, nMesenchymal-1 (Met)=818, nMesenchymal-2 (Met)=3829, nEarly EMT-1 = 3513, nEarly EMT-2 = 460, nAT2-like = 4680, nPre-EMT = 2108, nEarly gastric = 2175, nLung progenitor-like = 1074, nGastric-like = 4906, nEndoderm-like = 10272, nLate Gastric = 714, nHigh plasticity = 2439, nAT1-like = 1788. The p values were calculated based on a two-sided t test with the following results: t = 20.677, df = 120.21, 95% CI = 0.554–0.671 and t = 5.2966, df = 1678.6, 95% CI = 0.0497–0.108, respectively.
