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Table 2 Comparison of prediction performance for Nearest-Centroid classifiers built from unique VIP genes, top 50 p-value ranked genes, and 50 VIP genes. The classifier performance metrics, including accuracy (Acc), specificity (Spec), Sensitivity (Sens), and Matthew's correlation coefficient (MCC) were calculated based on averages of 50 repetitions of sample splitting, gene selection, and validation dataset prediction.

From: Very Important Pool (VIP) genes – an application for microarray-based molecular signatures

  Unique VIP genes 50 p-value ranked genes 50 VIP genes
Data set Number of genes Acc (%) Spec (%) Sens (%) MCC Acc (%) Spec (%) Sens (%) MCC Acc (%) Spec (%) Sens (%) MCC
Beer 15 64.7 38.3 74.0 0.13 64.7 38.3 74.0 0.12 65.2 35.4 75.6 0.11
Bhattacharjee 17 58.7 57.8 59.6 0.18 58.0 59.2 56.8 0.16 58.6 59.4 57.8 0.18
Chen 14 96.5 99.9 93.6 0.93 95.3 100.0 91.2 0.91 95.8 100.0 92.1 0.92
Pomeroy 20 60.8 54.0 64.2 0.19 60.8 51.7 65.3 0.18 62.4 55.7 65.8 0.22
Rosenwald 18 55.5 58.1 53.6 0.12 56.8 63.2 52.2 0.15 57.4 62.3 53.8 0.16
Shipp 18 51.6 50.8 52.5 0.03 47.9 51.8 43.0 -0.05 49.0 47.4 51.0 -0.02
Singh 15 94.3 98.3 91.7 0.89 98.1 100.0 96.9 0.96 97.8 100.0 96.4 0.96
Yeoh 22 74.6 37.8 80.2 0.15 78.2 31.0 85.4 0.15 80.2 35.0 87.0 0.21
van't Veer 20 64.8 64.8 64.9 0.30 65.2 61.5 68.6 0.31 66.9 66.1 67.6 0.34