Table 2 Results of statistical overrepresentation analysis with GREAT a
From: The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
Method | MACS | Meta | QuEST | PeakRanger | TPic | Triform |
|---|---|---|---|---|---|---|
NRSF | ||||||
Peaks total (2894 common) | 9802 | 4750 | 3574 | 6123 | 37514 | 10583 |
Peaks used (1993 common) | 3500 | 3500 | 3500 | 3500 | 3500 | 3500 |
Genes | 4017 | 4017 | 4105 | 3956 | 3866 | 4033 |
GO – Neurotransmitter transport | 1.6 × 10-10 | 6.0 × 10-11 | 1.2 × 10-10 | 2.5 × 10-6 | 5.2 × 10-7 | 9.3 × 10 -13 |
TF – REST motif | 1.1 × 10-26 | 4.6 × 10-25 | 5.4 × 10-19 | 1.4 × 10-25 | 5.6 × 10-23 | 1.1 × 10 -31 |
SRF | ||||||
Peaks total (608 common) | 4012 | 1553 | 1383 | 1320 | 111305 | 9555 |
Peaks used (310 common) | 1300 | 1300 | 1300 | 1300 | 1300 | 1300 |
Genes | 1930 | 1887 | 1855 | 1816 | 1565 | 1837 |
GO – Actin cytoskeleton | 1.8 × 10-7 | 2.6 × 10 -9 | 1.2 × 10-6 | 2.1 × 10-8 | - | 3.8 × 10-9 |
TF – SRF-motif | 6.0 × 10-9 | 3.6 × 10-12 | 2.4 × 10-11 | 3.6 × 10-12 | 2.4 × 10-11 | 2.3 × 10 -18 |
MAX | ||||||
Peaks total (3306 common) | 21866 | 10323 | 6556 | 9383 | 61021 | 15137 |
Peaks used (2014 common) | 6500 | 6500 | 6500 | 6500 | 6500 | 6500 |
Genes | 6139 | 6393 | 6626 | 6283 | 6276 | 6668 |
GO – ncRNA processing | 4.3 × 10-18 | 5.9 × 10-14 | 2.0 × 10-18 | 3.9 × 10 -22 | 3.1 × 10-16 | 1.5 × 10-12 |
GO – DNA duplex unwinding | 9.7 × 10 -43 | 3.9 × 10-14 | - | 1.6 × 10-5 | 1.1 × 10-25 | - |
TF – MYC motif | 2.5 × 10-12 | 2.7 × 10-14 | 5.3 × 10-16 | - | - | 1.7 × 10 -17 |
TF – E2F1 motif | 2.7 × 10-12 | 1.8 × 10-12 | - | 7.3 × 10 -15 | 5.4 × 10-13 | 2.9 × 10-11 |
TF – c-MYC from ChIP-chip | 2.1 × 10-36 | 2.8 × 10-35 | 8.7 × 10-48 | 3.9 × 10-36 | 1.8 × 10-46 | 7.8 × 10 -58 |