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For this analysis, protein expression was grouped as low or high based on median values; the 4- and 5-high groups were determined by having either 4 or 5 of the indicator univariate proteins highly expressed. Anonymized benign (n = 20) and malignant (n = 51) ovarian cancer patient effusion cell pellets obtained from therapeutic or diagnostic effusion sampling were used. Table 1 describes the clinicopathologic characteristics of the patient cohort. Most patients had high grade, advanced stage serous cancers at diagnosis, consistent with the normal distribution of epithelial ovarian cancer worldwide. Approximately equal http://www.selleckchem.com/products/BI-2536.html numbers of patients underwent optimal or suboptimal debulking and most effusions were ascites. Each case was printed in 5-point 1:1 serial dilution in triplicate. Quality control was validated before examination of specific protein endpoints. Intraslide reliability was examined by determining the CV of total protein measures in control lysates and randomly selected patient lysates, consisting of 6 controls and 8 patient samples. Table 2 shows the CV within each slide and across the 4 slides stained with colloidal gold. The mean and median CV were less than 4% for each slide (range, 0.55%-5.72%), and mean and median CV for all samples was http://www.selleck.cn/products/gsk126.html over a series of 4 slides (slides 1, 8, 16, and 25). An equivalence plot is shown in Figure 1, demonstrating results for RPPA slide 1 versus RPPA slide 25 (R2 = 0.905; inset table shows all equivalence regressions). Excellent reproducibility in total protein printing was observed between slides, with a median http://www.selleckchem.com/products/Cyclopamine.html regression coefficient of 0.91 (range, 0.88-0.93). We first tested the ability of the expression values of cell adhesion and adhesion-related target proteins to discriminate benign from malignant effusions using unsupervised hierarchical clustering. Figure 2A shows near complete segregation of the benign and malignant samples. The aggregate protein expression data were then median-centered and used to define a cell adhesion protein (CAP) signature. Evaluation of clustering of benign versus malignant cases as a function of protein distribution clusters was examined. The biology leading to a differential distribution of the benign and cancer samples between the 2 protein clusters is significantly different (P = 2E-05) (Figure 2B). The relative organization of protein expression in all samples weighted by the CAP signature is shown in Figure 2C. A statistically significant difference in expression of the average CAP signature was found between the benign (n = 20) and malignant (n = 51) samples (P = 6.18E-06) (Figure 2D). Proteins with statistically significant differences in expression between benign and malignant samples are presented in the inset in Figure 2.