Additional file 4 of Lifetime ovulatory years and ovarian cancer gene expression profiles

Additional file 4: Supplementary Figure 3

Additional file 3 of Lifetime ovulatory years and ovarian cancer gene expression profiles

Additional file 3: Supplementary Figure 2

Additional file 1 of Lifetime ovulatory years and ovarian cancer gene expression profiles

Additional file 1: Supplementary Table S1. Association between individual gene expression and ovulatory years

Additional file 2 of Lifetime ovulatory years and ovarian cancer gene expression profiles

Additional file 2: Supplementary Figure S1

S1 Fig -

The relationship between the percent of CD3+ cells and degree of spatial clustering has an exponentially decaying relationship (A). Plots (B) and (D) (colored red in plot A), and (C) and (E) (colored green in plot A) are two ROIs which have two approximately the same percent of CD3+ but different levels of spatial clustering. (PDF)</p

Results of co-localization/co-clustering of CD3+CD8+ (cytotoxic T-cells) and CD3+ FOXP3+ (regulatory T-cells) using bivariate Ripley’s K for the ROIs and TMAs.

Degree of spatial clustering based on permutation-based estimate of CSR. Models were adjusted for age at diagnosis and stage. The no cytotoxic T-cells and no regulatory T-cells (none) group/category is the reference group. The overall p-value is the joint association of the five categorial variable based on immune abundance and spatial clustering on overall survival.</p

S1 Table -

Summary of the demographics of the African American women with EOC in AACES included in the study. (XLSX)</p

S2 Fig -

Scatter plots showing the cytoplasm intensity, which is used to classify cell positivity, for FOXP3 (Opal 540) and CD8 (Opal 570). These four plots show varying degree of phenotype misclassification and illustrates the challenge of making univariate or bivariate intensity threshold for classifying higher dimensional spaces. (PDF)</p

Results from survival analysis of the immune marker abundance and spatial clustering from the ROIs and TMAs determined to be high abundance.

Models were adjusted for age at diagnosis and stage. Group high abundance/ low spatial clustering (“HL” group) is the reference group.</p

S5 Fig -

Predicted survival curves for patients with high abundance stratified by level of spatial clustering from Cox proportional hazard models for the CD3+, CD3+CD8+, and CD3+FOXP3+ cells where the degree of spatial clustering was based the permutation-based estimate of Ripley’s K under CSR (i.e., observed Ripley’s K–the mean of the empirical distribution of Ripley’s K under CSR); (A) results from intra-tumoral ROIs (B) results from tumor compartment of TMAs. Models adjusted for age at diagnosis and stage within a repeated measures analysis framework. (PDF)</p