Figure 2 from Decoding the Genomic and Functional Landscape of Emerging Subtypes in Ovarian Cancer
Year: 2025
Type: other
Abstract: Biological and clinical associations of the SCN signatures. A, Correlation plot between COSMIC mutational and extracted signatures. Cell color indicates correlation strength and direction. Significance is assessed using Spearman’s correlation with FDR correction. B, Distribution of signature SCN-E (top) and SCN-A (bottom). Each panel displays the signature activity across HRP samples, HRD samples without the respective BRCA mutation (BRCA1 for SCN-E and BRCA2 for SCN-A), and samples with the corresponding BRCA mutation. Samples with BRCA1 deficiency exhibit significantly higher SCN-E signature activity, whereas BRCA2-mutated samples show the same trend with SCN-A signature activity. Interactive visualization is available at GenomeSpy_3. C, Kaplan–Meier survival analysis of HRD-related signatures with log-rank P-values. Signature activities are first summarized per patient using the sample median. Patients are then divided into high and low signature activities using the median signature activity among all patients as a threshold. Elevated HRD-related signature activity is associated with improved treatment response. PFI, platinum-free interval. D, SCN-F signature activities for patients bearing CDK12 mutation and patients not having it. Mann–Whitney U-test with FDR correction significance level is reported (P = 8.49e−10). E, Correlation between copy number alterations and signature activity. Bar plots display the number of amplifications (left), gains (middle), and deletions (right) derived from GISTIC, whose copy number–ploidy ratio correlates with the activity of each SCN signature. The length of each bar segment represents the number of copy number events in each correlation category. SCN-I and SCN-J display the highest number of positive correlations with amplified regions. Similarly, SCN-C exhibits a high number of positive correlations with gains and deletions, excluding HRD-related signatures. In contrast, SCN-K exhibits negative correlations with most deletion and gain peaks. F, Difference in breakpoints abundance in chromosome 19 between CCNE1amp samples and normal CCNE1 samples. The counts are referred to bins of 0.5 Mb. G, GenomeSpy visualization of the signature SCN-K displaying the segmentation profiles of the five samples with the highest value for SCN-K activity, also available at GenomeSpy_5.
Language: English
Subfield: Reproductive Medicine
Field: Medicine
Domain: Health Sciences
Open Access status: gold
OpenAlex ID: W4415786959