Table 1.
Comparison analysis of enhancer predictions obtained by different methods across six ENCODE cell lines
| Method 1 versus Method 2 | Gm12878 | H1hesc | K562 | HeLa | HepG2 | HUVEC | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Coverage 1 versus. Coverage 2 (million bases) | Overlap (million bases) | Jaccard inde× (%) | Coverage 1 versus Coverage 2 (million bases) | Overlap (million bases) | Jaccard inde× (%) | Coverage 1 versus Coverage 2 (million bases) | Overlap (million bases) | Jaccard inde× (%) | Coverage 1 versus Coverage 2 (million bases) | Overlap (million bases) | Jaccard index (%) | Coverage 1 versus Coverage 2 (million bases) | Overlap (million bases) | Jaccard inde× (%) | Coverage 1 versus Coverage 2 (million bases) | Overlap (million bases) | Jaccard index (%) | |
| CSI-ANN versus ENCODE annotation | 10.7 versus 42.69 | 5.3 | 11.0 | 19.1 versus 56.5 | 2.2 | 3.0 | 34.5 versus 28.1 | 8.0 | 14.8 | 26.6. versus 42.9 | 5.3 | 8.3 | 40.8 versus 24 | 6.4 | 11.0 | 49.4 versus 47.1 | 21.3 | 28.3 |
| RFECS versus ENCODE annotation | 344.1 versus 42.69 | 31.6 | 8.9 | 124.7 versus 56.5 | 29.5 | 19.4 | 130.6 versus 28.1 | 18.5 | 13.1 | 87.4 versus 42.9 | 26.4 | 25.4 | 253.1 versus 24 | 12 | 4.5 | 191.2 versus 47.1 | 33.6 | 16.4 |
| ChromHMM versus ENCODE annotation | 82.7 versus 42.69 | 37.7 | 43.0 | 80.5 versus 56.5 | 36.9 | 36.8 | 111.4 versus. 28.1 | 24.8 | 21.6 | 70.9 versus 42.9 | 36.0 | 46.2 | 72.88 versus 24 | 10.8 | 12.6 | 107.2 versus 47.1 | 40.0 | 35.0 |
| Segway versus ENCODE annotation | 119.5 versus 42.69 | 39.1 | 31.7 | 404.9 versus 56.5 | 20.3 | 4.6 | 282.5 versus 28.1 | 27.6 | 9.7 | 124.8 versus 42.9 | 41.1 | 32.7 | 230.3 versus 24 | 11.6 | 4.5 | 189.6 s. 47.1 | 39.1 | 19.7 |
| CSI-ANN versusRFECS | 10.7 versus 344.1 | 6.1 | 1.7 | 19.1 versus 124.7 | 2.2 | 1.5 | 34.5 versus 130.6 | 11.4 | 7.4 | 26.6 versus 87.4 | 5.71 | 5.2 | 40.8 versus 253.1 | 12.6 | 4.4 | 49.4 versus 191.2 | 21.9 | 10.0 |
| RFECS versus ChromHMM | 344.1 versus 82.7 | 55.9 | 15.0 | 124.7 versus 80.5 | 40.3 | 24.4 | 34.5 versus 111.4 | 51.1 | 26.7 | 87.4 versus 70.9 | 42.1 | 36.1 | 253.1 versus 72.88 | 45.2 | 16.2 | 191.2 versus 107.2 | 73.7 | 32.7 |
| RFECS versus Segway | 344.1 versus 119.5 | 71.6 | 18.2 | 124.7 versus 404.9 | 52.3 | 10.9 | 130.6 versus. 282.5 | 80.5 | 24.2 | 87.4 versus 124.8 | 51.1 | 31.7 | 253.1 versus 230.3 | 77.8 | 19.1 | 191.2 versus 189.6 | 92.4 | 32.0 |
| CSI-ANN versus ChromHMM | 10.7 versus 82.7 | 6.0 | 6.8 | 19.1 versus 80.5 | 1.6 | 1.6 | 34.5 versus 111.4 | 12.0 | 8.9 | 26.6 versus 70.9 | 5.8 | 6.3 | 40.8 versus 72.88 | 10.9 | 10.6 | 49.4 versus 107.2 | 25.8 | 19.7 |
| ChromHMM versus Segway | 82.7 versus 119.5 | 63.8 | 46.1 | 80.5 versus 404.9 | 52.5 | 12.1 | 111.4 versus 282.5 | 100.6 | 34.2 | 70.9 versus 124.8 | 61.4 | 45.7 | 72.88 versus 230.3 | 56.3 | 22.8 | 107.2 versus 189.6 | 99.0 | 50.0 |
| CSI-ANN versus Segway | 10.7 versus 119.5 | 8.0 | 6.5 | 19.1 versus 404.9 | 1.3 | 0.3 | 34.5 versus 282.5 | 19.74 | 6.6 | 26.6. versus 124.8 | 10.0 | 7.1 | 40.8 versus 230.3 | 18.1 | 7.1 | 49.4 versus 189.6 | 30.4 | 14.5 |
We report the total number of bases in millions predicted as belonging to enhancers. Coverage 1 corresponds to enhancers predicted by Method 1, while Coverage 2 corresponds to enhancers predicted by Method 2. The overlap column corresponds to the same enhancer predictions in million bases as obtained by Method 1 and Method 2. In the third column, we report similarity of predictions of Method 1 and Method 2 based on the Jaccard similarity index (as percentage)