Fig. 3: The impacts of chr8q gain in the D subtype.
a Volcano plot showing the cis- correlation of the SCNA (x-axis) and the associated −log10 (p-value) (y-axis) on the genes at chr8q gain (two-sided Spearman’s correlation test). SCNA somatic copy number alterations. b The cis SCNA-protein regulations of significantly correlated genes (top) on their corresponding proteins expression (bottom). The genes are related to MAPK signaling. The right represents relative survival averaged across all available DC cell lines after depletion of the indicated genes by RNAi (Dependency map-supported (https://depmap.org) panels) and shows the correlation between the genes and CAGs. CAGs cancer-associated genes. The square directs to a subset of patient samples in the D subtype used for WES (n = 120). c The impacts of the MAPK signaling associated SCNAs on their corresponding protein expression in gastrointestinal cancers (two-sided Spearman’s correlation test). d Venn diagram depicting the amplification of LYN positive associated proteins (top), and the represented signaling pathways (bottom). e Heatmap showing the represented proteins in MAPK signaling at the protein (top) and phosphoprotein (bottom) levels (two-sided Pearson’s correlation test). f The represented kinases in MAPK signaling were overrepresented in the LYN amplification group (two-sided Wilcoxon signed-ranked test, BH-adjusted p < 0.05). The red frame shows the significant correlation between LYN and the represented kinases (two-sided Pearson’s correlation test). g Kinase-substrate regulation network showing the substrates of LYN and MAPK1. The asterisk shows the overrepresented expression of the substrates in the LYN amplification group (two-sided Wilcoxon signed-ranked test, BH-adjusted p < 0.05). h Scatterplot showing the relationship between LYN and cell proliferation at the protein level (two-sided Pearson’s correlation test). i A brief summary of the impacts of the chr8q gain in the IFT phase of the D subtype. ****p < 1.0E−4, ***p < 1.0E−3, **p < 1.0E−2, *p < 0.05, ns. >0.05. Source data are provided as a Source data file.
