Table 2.
Modules associated with kidney histopathology
| Histopathology | Module ID | Ng | MCC | TP | TN | FN | FP | Sen | Spc | PPV | NPV | BAc |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cast (hyaline) | KM1 | 26 | 0.40 | 6 | 459 | 6 | 11 | 0.50 | 0.98 | 0.35 | 0.99 | 0.74 |
| Cellular infiltration | KM2 | 53 | 0.52 | 7 | 462 | 9 | 4 | 0.44 | 0.99 | 0.64 | 0.98 | 0.71 |
| Degeneration | KM3 | 72 | 0.66 | 12 | 458 | 9 | 3 | 0.57 | 0.99 | 0.80 | 0.98 | 0.78 |
| Dilatation | KM4 | 9 | 0.67 | 16 | 451 | 11 | 4 | 0.59 | 0.99 | 0.80 | 0.98 | 0.79 |
| Fibrosis | KM5 | 147 | 0.84 | 5 | 475 | 0 | 2 | 1.00 | 1.00 | 0.71 | 1.00 | 1.00 |
| Hypertrophy | KM6 | 18 | 0.41 | 5 | 463 | 5 | 9 | 0.50 | 0.98 | 0.36 | 0.99 | 0.74 |
| Intracytoplasmic inclusion body | KM7 | 46 | 0.65 | 7 | 467 | 1 | 7 | 0.88 | 0.99 | 0.50 | 1.00 | 0.93 |
| Necrosis | KM8 | 16 | 0.44 | 9 | 452 | 10 | 11 | 0.47 | 0.98 | 0.45 | 0.98 | 0.72 |
Ng = number of genes; MCC = Matthews correlation coefficient; TP = true positives; TN = true negatives; FN = false negatives; FP = false positives; Sen = sensitivity or TP/(TP + FN); Spc = specificity or TN/(FP + TN); PPV = positive predictive value or TP/(TP + FP); NPV = negative predictive value or TN/(TN + FN); BAc = Balanced Accuracy or ½ (Sen + Spc). The gene complement of each module is provided as an Excel file in the Supplementary Materials.