Table 5. oPOSSUM-3 results for FoxA2 ChIP-Seq dataset, using JASPAR CORE vertebrate profiles.
|
A. Single Site Analysis Results. Forkhead-box binding profiles rank the highest by both Z-score and Fisher score. | ||||
|---|---|---|---|---|
| Z-score | Name | Class:Family | Score | FDR |
| FoxA2 | Winged HTH:Forkhead | 203.4 | 0.00 | |
| FoxA1 | Winged HTH:Forkhead | 155.6 | 0.00 | |
| FoxF2 | Winged HTH:Forkhead | 113.8 | 0.00 | |
| FoxD1 | Winged HTH:Forkhead | 107.1 | 0.00 | |
| FoxO3 | Winged HTH:Forkhead | 90.1 | 0.00 | |
| Fisher score | FoxA2 | Winged HTH:Forkhead | 388.7 | 1.86E-167 |
| FoxA1 | Winged HTH:Forkhead | 219.0 | 4.62E-94 | |
| FoxD1 | Winged HTH:Forkhead | 131.4 | 3.20E-56 | |
| FoxF2 | Winged HTH:Forkhead | 82.4 | 4.97E-35 | |
| FoxO3 | Winged HTH:Forkhead | 77.2 | 6.71E-33 | |
| KS score | FoxA2 | Winged HTH:Forkhead | Inf | 0.00 |
| FoxA1 | Winged HTH:Forkhead | Inf | 0.00 | |
| FoxD1 | Winged HTH:Forkhead | Inf | 0.00 | |
| FoxF2 | Winged HTH:Forkhead | Inf | 0.00 | |
| FoxO3 | Winged HTH:Forkhead | Inf | 0.00 | |
| B. TFBS Cluster Analysis. Cluster C57, containing forkhead-box binding profiles, ranks highest by all three scores. Cluster C19, containing the Hnf4A hepatocyte-related TF profile, ranks second by Z and Fisher scores, while cluster C41 containing the Sox profiles ranks the same as C57 by KS score. | ||||
| Z-score | Name | Class:Family | Score | FDR |
| C57 (FoxA2) | Winged HTH:Forkhead | 214.0 | 0.00E+00 | |
| C19 (Hnf4A) | Zinc-coord:NucReceptor | 67.2 | 0.00E+00 | |
| C9 | Zipper-type:LeuZip | 54.3 | 0.00E+00 | |
| C41 (Sox2, Sry) | Other Alpha-helix:HMG | 31.6 | 5.29E-218 | |
| C17 | Zinc-coord:NucReceptor | 29.3 | 1.92E-187 | |
| Fisher score | C57 (FoxA2) | Winged HTH:Forkhead | 69.2 | 1.44E-28 |
| C19 (Hnf4A) | Zinc-coord:NucReceptor | 9.2 | 8.88E-03 | |
| C9 | Zipper-type:LeuZip | 1.3 | 1.00E+00 | |
| C41 (Sox2, Sry) | Other Alpha-helix:HMG | 0.012 | 1.00E+00 | |
| C17 | Zinc-coord:NucReceptor | 0.005 | 1.00E+00 | |
| KS score | C57 (FoxA2) | Winged HTH:Forkhead | Inf | 0.00 |
| C41 (Sox2,Sry) | Other Alpha-helix:HMG | 35.6 | 9.66E-15 | |
| C113 | HTH:Homeo | 20.7 | 1.98E-08 | |
| C19 | Zinc-coord:NucReceptor | 18.6 | 1.22E-07 | |
| C17 | Zinc-coord:NucReceptor | 17.7 | 2.48E-07 | |
| C. Anchored Combination Site Analysis. FoxA2 associates closely with other forkhead-box binding profiles, and the profile of Hnf4A, a hepatocyte-related TF. (Anchor: FoxA2, Maximum inter-binding distance = 100 bp) | ||||
| Z-score | Name | Class:Family | Score | FDR |
| FoxA1 | Winged HTH:Forkhead | 334.8 | 0.00 | |
| FoxA2 | Winged HTH:Forkhead | 265.3 | 0.00 | |
| Hnf4A | Zinc-coord:NucReceptor | 247.1 | 0.00 | |
| FoxD1 | Winged HTH:Forkhead | 238.7 | 0.00 | |
| FoxO3 | Winged HTH:Forkhead | 213.4 | 0.00 | |
| Fisher score | FoxA2 | Winged HTH:Forkhead | 245.7 | 2.23E-105 |
| FoxA1 | Winged HTH:Forkhead | 238.0 | 2.56E-102 | |
| Zeb1 | Zinc-coord:ZnF | 236.5 | 7.57E-102 | |
| Znf354C | Zinc-coord:ZnF | 223.0 | 4.14E-96 | |
| FoxD1 | Winged HTH:Forkhead | 208.0 | 1.07E-89 | |
| D. Anchored Combination TFBS Cluster Analysis. Cluster C19 containing the Hnf4A hepatocyte-related TF profile is ranked high by both scores. (Anchor: FoxA2, Maximum inter-binding distance = 100 bp) | ||||
| Z-score | Name | Class:Family | Score | FDR |
| C57 (FoxA2) | Winged HTH:Forkhead | 189.3 | 0.00 | |
| C19 (Hnf4A) | Zinc-coord:NucReceptor | 180.1 | 0.00 | |
| C17 | Zinc-coord:NucReceptor | 151.1 | 0.00 | |
| C41 | Other Alpha-helix:HMG | 135.0 | 0.00 | |
| C9 | Zipper-type:LeuZip | 133.5 | 0.00 | |
| Fisher score | C57 (FoxA2) | Winged HTH:Forkhead | 72.6 | 5.02E-30 |
| C19 (Hnf4A) | Zinc-coord:NucReceptor | 42.2 | 4.00E-17 | |
| C55 | WingedHTH:Homeo | 31.5 | 1.18E-12 | |
| C113 | HTH:Homeo | 26.5 | 1.32E-10 | |
| C9 | Zipper-type:LeuZipper | 25.0 | 4.72E-10 | |
FoxA2 is bolded. FDR (false discovery rate) column lists the adjusted p-values calculated using the Benjamini & Hochberg algorithm. (Matrix Score Threshold: 85%, JASPAR CORE vertebrate profiles, minimum information content = 8 bits.)