Table 2 Summarized evaluation results in K562 cells, based on chromatin states, experimental data and annotated protein-coding TSSs. From left to right, each column shows the number of total positive predictions of each algorithm, the percentage overlapping with chromatin states associated with active and weak/repressed transcription, and at least one TF and H3K4me3 peak
Algorithm | Total positive predictions | ChromHMM active transcription | ChromHMM weak transcription | TF ChIP-Seq peaks | H3K4me3 ChIP-Seq peaks |
|---|---|---|---|---|---|
DeepTSS | 31,443 | 96.66% | 3.33% | 98.27% | 92.04% |
(30,376) | (1047) | (30,898) | (28,939) | ||
ADAPT-CAGE | 31,177 | 95.90% | 4.09% | 97.72% | 91.12% |
(29,885) | (1276) | (30,466) | (28,409) | ||
CAGER | 14,465 | 84.62% | 15.37% | 87.67% | 81.11% |
(12,195) | (2215) | (12,681) | (11,732) | ||
PARACLU | 9453 | 94.01% | 5.98% | 95.26% | 92.06% |
(8868) | (565) | (9,005) | (8702) | ||
RECLU | 11,558 | 93.35% | 6.64% | 94.32% | 89.96% |
(10,773) | (767) | (10,902) | (10,397) | ||
TOMETOOLS | 30,689 | 92.59% | 7.40% | 95.46% | 88.12% |
(28,395) | (2272) | (29,296) | (27,044) | ||
iTiSS | 1734 | 41.58% | 58.41% | 48.12% | 41.94% |
(721) | (1013) | (848) | (739) |