The WGCNA* and COX mortality group definitions. A. Classification trees were used to identify a subset of markers (3 out of 26 total) and their optimal thresholds for approximating the WGCNA groups. Nearly 88% (72 matches out of 82) of the mortality group assignments matched between WGCNA* and WGCNA. The markers and approximate thresholds included: p53 (dichotomized at the 75th percentile), Na-KATPase-β1 (33rd percentile) and TGF β receptor II (66th percentile). High mortality was defined by high p53 and low Na-KATPase-β1. The group with a 17% mortality rate is called "low" because 10 of these 12 patients were assigned to the low mortality group by WGCNA. B. We also conducted a more traditional multimarker analysis by dichotomizing each of the 26 markers at an optimal threshold for survival prediction and then using a step-wise marker selection approach to achieve low, moderate and high mortality "COX" patient groups. This approach defined high mortality as high MED28, and moderate mortality as low MED28 and high Smad4. In both diagrams "cyt" indicates expression in the cytoplasm.
Presson et al. BMC Cancer 2011 11:230 doi:10.1186/1471-2407-11-230