Supplementary Figures from Pooled Clustering of High-Grade Serous Ovarian Cancer Gene Expression Leads to Novel Consensus Subtypes Associated with Survival and Surgical Outcomes
Authors: Wang Chen , Armasu Sebastian M. , Kalli Kimberly R. , Maurer Matthew J. , Heinzen Ethan P. , Keeney Gary L. , Cliby William A. , Oberg Ann L. , Kaufmann Scott H. , Goode Ellen L. 
Published: April 2023

<p>Supplementary Figure 1. Analytical workflow of the present study. Supplementary Figure 2. Principal component analysis plots of public expression datasets before (A) and after (B) batch-correction Supplementary Figure 3. Consensus clustering results of non-negative matrix factorization from K= 2 to K = 9. The stable clustering relationships can be observed from K=2 to K=5. Supplementary Figure 4. Overall survival plots according to late-stage HGSOC cases in public cohort, n=1946. Supplementary Figure 5. Overall survival plots according to late-stage HGSOC cases with optimal debulking surgeries, in (A) public cohort, n=936; (B) Mayo Clinic cohort, n=250. Supplementary Figure 6. Overall survival plots according to late-stage HGSOC cases with sub-optimal debulking surgeries, in (A) public cohort, n=660; (B) Mayo Clinic cohort, n=88. Supplementary Figure 7. Overall survival plots according to surgical outcomes in Mayo clinic cohorts, for (A) all the late-stage HGSOC patients, (B-F) for late-stage patients belonging to each subtype. Supplementary Figure 8. Volcano plot of S1.MES subtype vs. other molecular subtypes. X-axis is the log-scaled expression fold-change (FC) and Y-axis is the significance level of differential expression analysis, defined as -log10(q-value). Two identical volcano plots were presented, where the larger one plotting according to gene symbols, and the smaller one plotting using dots. Red-color and green-color are used to indicate significantly up-regulated (FC{greater than or equal to}0.5 & q-value{less than or equal to}0.01) and down-regulated genes (FC{less than or equal to} -0.5 & q-value{less than or equal to}0.01), respectively. Supplementary Figure 9. Volcano plot of S2.IMM subtype vs. other molecular subtypes. X-axis is the log-scaled expression fold-change (FC) and Y-axis is the significance level of differential expression analysis, defined as -log10(q-value). Two identical volcano plots were presented, where the larger one plotting according to gene symbols, and the smaller one plotting using dots. Red-color and green-color are used to indicate significantly up-regulated (FC{greater than or equal to}0.5 & q-value{less than or equal to}0.01) and down-regulated genes (FC{less than or equal to} -0.5 & q-value{less than or equal to}0.01), respectively. Supplementary Figure 10. Volcano plot of S3.PRO subtype vs. other molecular subtypes. X-axis is the log-scaled expression fold-change (FC) and Y-axis is the significance level of differential expression analysis, defined as -log10(q-value). Two identical volcano plots were presented, where the larger one plotting according to gene symbols, and the smaller one plotting using dots. Red-color and green-color are used to indicate significantly up-regulated (FC{greater than or equal to}0.5 & q-value{less than or equal to}0.01) and down-regulated genes (FC{less than or equal to} -0.5 & q-value{less than or equal to}0.01), respectively. Supplementary Figure 11. Volcano plot of S4.DIF subtype vs. other molecular subtypes. X-axis is the log-scaled expression fold-change (FC) and Y-axis is the significance level of differential expression analysis, defined as -log10(q-value). Two identical volcano plots were presented, where the larger one plotting according to gene symbols, and the smaller one plotting using dots. Red-color and green-color are used to indicate significantly up-regulated (FC{greater than or equal to}0.5 & q-value{less than or equal to}0.01) and down-regulated genes (FC{less than or equal to} -0.5 & q-value{less than or equal to}0.01), respectively. Supplementary Figure 12. Volcano plot of S5.ANM subtype vs. other molecular subtypes. X-axis is the log-scaled expression fold-change (FC) and Y-axis is the significance level of differential expression analysis, defined as -log10(q-value). Two identical volcano plots were presented, where the larger one plotting according to gene symbols, and the smaller one plotting using dots. Red-color and green-color are used to indicate significantly up-regulated (FC{greater than or equal to}0.5 & q-value{less than or equal to}0.01) and down-regulated genes (FC{less than or equal to} -0.5 & q-value{less than or equal to}0.01), respectively. Supplementary Figure 13. Enriched pathways (q-value {less than or equal to}0.1) for S1.MES subtype vs. other molecular subtypes. Green and red colors are used to represent significantly down- and up-regulated pathways, respectively. Supplementary Figure 14. Enriched pathways (q-value {less than or equal to}0.1) for S2.IMM subtype vs. other molecular subtypes. Green and red colors are used to represent significantly down- and up-regulated pathways, respectively. Supplementary Figure 15. Enriched pathways (q-value {less than or equal to}0.1) for S3.PRO subtype vs. other molecular subtypes. Green and red colors are used to represent significantly down- and up-regulated pathways, respectively. Supplementary Figure 16. Enriched pathways (q-value {less than or equal to}0.1) for S4.DIF subtype vs. other molecular subtypes. Green and red colors are used to represent significantly down- and up-regulated pathways, respectively. Supplementary Figure 17. Enriched pathways (q-value {less than or equal to}0.1) for S5.ANM subtype vs. other molecular subtypes. Green and red colors are used to represent significantly down- and up-regulated pathways, respectively. Supplementary Figure 18. Expression scatterplot between PD-L1 and TAP1 genes; the figure was generated using cBioPortal (http://www.cbioportal.org/) according to TCGA HGSOC data. Supplementary Figure 19. Distribution boxplots of four genomics scores with respect to five de novo subtypes for TCGA HGSOC cases.</p>