Fig. 3: Integrative omics analyses of early ESCC samples.

a The significant arm events of 102 samples in ESCC progression. The gain and loss events are highlighted in red and blue, respectively. b Volcano plot showing the cis- correlation of the SCNA (x-axis) and the associated –log₁₀ (p value) (y-axis) on the genes at chr3q gain (two-sided Spearman’s correlation test). c The cis SCNA-protein regulations of significantly correlated genes (top) on their corresponding proteins expression (bottom) (two-sided Spearman’s correlation test, p < 0.05). d Dependency map-supported (https://depmap.org) panels showing relative survival averaged across all available ESCC cell lines after depletion of the indicated genes by RNAi or CRISPR. The right shows Pearson’s correlation and p value of these genes with PCNA and MKI67 at the protein level (two-sided Pearson’s correlation test). e A brief summary of the impacts of chr3q gain. f Volcano plot showing the impacts of the top ten mutations of ESCC progression on proteins expression (log₂-transformed Intensity) (x-axis) and the associated –log₁₀ (FDR) (y-axis) (two-sided Student’s t-test). g Scatterplot showing the relationship between log₁₀ GSK3A and log₁₀ MACF1 expression at the protein level in the Fudan cohort (two-sided Pearson’s correlation test, mean ± SD). h Represented pathway enrichment of proteins that was positively correlated with MACF1 in the Fudan cohort (top) and the TCGA ESCC cohort (bottom). Biological pathways are analyzed from the GO/KEGG database. i Heatmap showing the impacts of the mutation of MACF1 on the expression of Wnt signaling-related proteins in ESCC progression (Kruskal–Wallis test, BH-adjusted *p < 0.05). The square directs to a subset of patient samples used for WES (n = 102). j A brief summary of the impacts of the mutation of MACF1. ****p < 1.0E–4, ***p < 1.0E–3, **p < 0.01, *p < 0.05, ns. > 0.05. Source data are provided as a Source data file.