Figure 2: Immunosignature performance.
From: Scalable high-density peptide arrays for comprehensive health monitoring
Heatmaps (top left and right) indicate groupwise specificity of peptide signals with hierarchical clustering performed on 350 peptides (y axis) and 60 patients plus 10 controls (x axis) with Euclidean distance used as the measure of separation. The order of each patient and peptide is calculated from the distance measure using hierarchical clustering. Classification of all samples was 100% accurate using either linear discriminant analysis or support vector machine (SVM) with leave-one-out cross-validation. Top left: serum from six different cancers with 10 patients in each group (BC, breast cancer, GBM, Glioblastoma multiformae, MM, multiple myeloma, EC, oesophageal cancer, OV, ovarian cancer, LNG, lung cancer) was analysed using the 330,000 peptide microarray. The striking stair-step pattern is because of the clustering algorithm alone. Top right: Sera from six different infectious diseases, with 10 patients in each group except BP, with five patients (Dengue, dengue virus, VF, Coccidioides immitis, BP, B. pertussis, Lyme, Borrelia burgdorferi, WNV, West Nile Virus, TP, T. pallidum and healthy donors (ND) were likewise analysed. Each sample set achieved 100% accuracy using SVM as the classifier and leave-one-out cross-validation. Below left: a plot of log10 P value (x axis) versus log2 fold-change (y axis) between 10 randomly selected patients at the time of diagnosis with oesophageal cancer (numerator) and 10 otherwise healthy controls (denominator) displays the distribution of significant peptides and the resulting ratios. In all, 562 peptides with P-val <3 × 10−7 are coloured red, yielding a 0.017% false-positive rate. Lower right is a power plot demonstrating the minimum detectable fold-change (delta, black line, calculated using the command power.t.test() in R) along the x axis. This power plot is reviewed in detail in ref. 30. The blue bars (y axis) represent every peptide’s average log2 ratio between 10 oesophageal cancer patients (numerator) and 10 healthy controls (denominator). The red circles indicate the same peptides as in the graph to the left (P<3 × 10−7).
