Table 2

Results of statistical overrepresentation analysis with GREATa
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

aThe table shows (for each TF) the total number of peaks identified by each peak-finder (including the number of peaks common to all methods), the number of peaks used for GREAT analysis (including the number of common peaks), the number of associated genes identified by GREAT, and the binominal FDR Q-values identified by GREAT for the selected GO and TF-associated terms. The smallest Q-value for each term is shown in bold.

Kornacker et al.

Kornacker et al. BMC Bioinformatics 2012 13:176   doi:10.1186/1471-2105-13-176

Open Data