Additional file 1: of Analysis of menstrual effluent: diagnostic potential for endometriosis

Table S1. ME FACS Statistics. Table S2. Important Genes Upregulated During 6 h cAMP Stimulation. Table S3. Pr Values for Decidualization Time course Experiment. (DOCX 17 kb

Additional file 3: of Analysis of menstrual effluent: diagnostic potential for endometriosis

Figure S2. Decidualization capacity can be determined after only 6 h of cAMP stimulation. Log of IGFBP-1 secretion at 6 h, 24 h, and 48 h of cAMP (0.5 mM) stimulation per subject (n = 7 control, n = 7 endometriosis). (TIFF 170 kb

Additional file 2: of Analysis of menstrual effluent: diagnostic potential for endometriosis

Figure S1. ME-derived SFCs obtained from endometriosis subjects exhibit reduced decidualization capacity when exposed to cAMP+MPA + E2. Time course of IGFBP-1 secretion by vehicle- and 0.5 mM cAMP+ 1 μM MPA+ 10 nM E2-treated ME-derived SFCs isolated from endometriosis (Endo) and control subjects (n = 7 control, n = 7 endometriosis). Data are shown as IGFBP-1 values for each subject’s SFC culture and the horizontal lines represent group means and vertical lines represent the standard error of the mean. ** posterior probabilities (Pr) < 0.01 *Pr < 0.05. Statistics were performed on log transformed data, as described in the methods. (TIFF 113 kb

Demographic, clinical and pathological characteristics of subjects in this study.

<p>*IQR = interquartile range; NYBB = New York Brain Bank.</p><p>∧TCGA GBM cases did not include CWRU TCGA GBM cases.</p><p># Publicly available brain tissue controls were from Brain Banks at the University of Maryland, Johns Hopkins University and National Institute of Aging.</p

Principal component analyses (PCA) of the discovery and validation datasets.

<p>a. In the discovery dataset, the 5 tumor and 1 control methylation classes were represented by the first 3 principal components (PCs) in x, y and z axes in 3 dimensional space. b. In the validation dataset, 5 tumors and 2 control classes were represented by the first 3 PCs in 3 dimensional space.</p

The most significant canonical pathways represented in our validated gene list.

<p>a. The horizontal blue bars showed the top10 significant canonical pathways that were altered epigenetically in the hypomethylated gene set, using Ingenuity Pathway Analysis (IPA). The orange square denotes the ratio of number of genes presented in our dataset over the total number of genes in that pathway. The top horizontal axis represents FDR (Benjamin-Hochberg) corrected P value, and the bottom one denotes ratio of number of genes presented in the dataset over the total number of genes. The vertical dotted line (in orange) represents the threshold of statistical significance. b. The 5 significant canonical pathways enriched in the hypermethylated gene set. Annotation is the same as the hypomethylated gene list.</p

Levels of global methylation markers among methylation classes.

<p>a. Levels of 5m-dC between brain controls and tumors, and among methylation classes. Red, yellow and green lines (dotted) denoted pairwise comparison between two classes and the P values of their comparisons. b. Levels of LINE1 between brain controls and tumors, and among methylation classes. c. Levels of 5hm-dC between brain controls and tumors, and among methylation classes.</p

Adjusted Cox proportional hazard survival curves based on ESC index percentiles.

<p>a. Adjusted Cox survival curve of the discovery dataset, illustrating survival of subjects at the 25^th, 50^th and 75^th percentiles of ESC index. b. Adjusted Cox survival curve of the validation dataset, illustrating survival of subjects at the 25^th, 50^th and 75^th percentiles of ESC index.</p

Histograms of median |Δβ| distributions.

<p>a. The histogram showing a range of median |Δβ| of significant CpG sites from the discovery dataset; b. the histogram of a range of median |Δβ| of significant CpG sites from the validation dataset. Red bars denote the number of hypermethylated CpGs, and blue bar represented hypomethylated CpGs.</p

Heat map of differential methylation in the validation dataset.

<p>Heat map based on a set of 2445 CpG sites that significantly segregated GBM and control brain tissues into seven methylation classes in the validation dataset. Annotations were the same as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089376#pone-0089376-g001" target="_blank">Figure 1</a>.</p