Table 1.
Comparative performance analysis of the enhancer predictions in the pilot ENCODE region of untreated and IFN-γ treated HeLa cells showing the number of regions recovered over the number of total predictions and sensitivity values in parentheses
| Cell | Method Marker | PM(%) | HMM(%) | CSI-ANN(%) | ChromaGenSVM(%) |
|
|---|---|---|---|---|---|---|
| Adapted cut-off | Optimum cut-off | |||||
| Untreated HeLa cells | P300 (n = 94) | 77/389 (81.9) | 82/389 (87.2) | 79/389 (84.0) | 66/391 (70.2) | 80/1022 (85.1) |
| DHS (n = 587) | 165/389 (28.1) | 179/389 (30.5) | 243/389 (41.4) | 152/391 (25.9) | 224/1022 (38.2) | |
| TRAP220 (n = 76) | 43/389 (55.8) | 47/389 (61.0) | 54/389 (71.0) | 40/391 (52.6) | 54/1022 (71.1) | |
| p300 or DHS or TRAP220 | 206/389 (52.9)* | 213/389 (54.8)* | 258/389 (66.3)* | 223/391 (57.0)* | 299/1022 (30.1)* | |
| IFN-γ treated HeLa cells | P300 (n = 151) | 116/324 (76.8) | 109/324 (72.2) | – | 109/325 (72.0) | 133/1001 (88.0) |
Note. ChromaGenSVM also reports the number of predictions in untreated HeLa cells at the cut-off of maximum F-score.
*Precision [TP/(TP + FP)] in brackets (Equation 3).