Fig. 2: Analysis 2: Development of the molecular staging model to assign cycle stage for the whole menstrual cycle.

Figure 2a. Example of a spline curve fitted to menstrual, combined proliferative and early secretory expression data. The error bands surrounding the regression line represent the 95% confidence interval. Figure 2b. Menstrual, proliferative and early secretory samples with estimated molecular cycle stage calculated from minimum mean squared error data. Figure 2c. Combined proliferative samples reassigned into early, mid and late proliferative groups containing equal numbers. Figure 2d. Example of a spline curve fitted to data from all 7 stages of the cycle using reclassified proliferative cycle stage information and pathology-derived menstrual and secretory staging. The error bands surrounding the regression line represent the 95% confidence interval. Figure 2e. Comparison of cycle time within the 7 cycle stages estimated from the model and pathology-derived cycle stage. Figure 2f. Under the assumption that 236 women underwent surgery at random stages of the menstrual cycle, data from 236 samples were transformed to be uniformly spaced along the x-axis on a 0–100 scale. This transformation allows each sample to be identified as being a percentage of the way through the menstrual cycle. Figure 2g. Plot showing relationship between pathology staging and the percentage of cycle from the molecular staging model. Menstrual is 0–8%, proliferative is 8–58% and secretory is 58–100% of the molecular staging model cycle respectively. Figure 2h, i. Expression data for ENSG00000187231 replotted using derived ‘percentage’ cycle times and then normalised across the menstrual cycle. The error bands surrounding the regression line represent the 95% confidence interval. Source data are provided as a Source Data file.