Fig. 3

Pro-angiogenic VEGF/Sema gene expression in prostate cancer metastasis. a-b: A greater number of VEGF/Sema genes have recurrent expression alterations when comparing metastases to normal samples (b) than to primary tumor samples (a). The p-values are displayed according to the same criteria as in Fig. 1, and red and blue boxes on the right hand sides of panels a and b indicate recurrent up- and down-regulation, respectively. c-d: PLS-DA scores plots show separation of metastases and primary tumors in GSE35988 (c) and of metastases and normal tissues in GSE38241 (d). Each dot represents a sample with colors as indicated. Arrows correspond to gene loadings in the PLS-DA models, with the names of the genes displayed in the vicinity of the arrowhead. Only the genes with the largest magnitude loadings vectors are displayed. Accuracy refers to the accuracy of the LOOCV predictions; AUC refers to the area under the curve of the LOOCV ROC curve. In both cases, values of one indicate perfect prediction