Table 2.
Functional heterotypic motif pairs (anchor ≠ neighbor) where the neighbor motif may be mapped to known TRANSFAC matrices
|
Anchor motif |
Neighbor motifa |
Window size, bp |
Orientationb |
NSc |
PECd |
|---|---|---|---|---|---|
| M00071 (E47) | M00271 (AML-1a) | 50 | Down | 1.6E-7 | 1.0E-6 |
| M00135 (Oct-1) | M00287 (NF-Y) | 50 | Up | 1.5E-3 | 9.8E-7 |
| M00178 (CREB) | M00216 (TATA) | 50 | Down | 1.5E-6 | 1.9E-6 |
| M00287 (NF-Y) | M00195 (Oct-1) | 50 | Up | 5.2E-7 | 1.3E-6 |
| M00425 (E2F) | M00287 (NF-Y) | 50 | Down | 4.0E-7 | 1.5E-6 |
| M00466 (HIF-1) | M00025 (Elk-1) | 50 | Up | 2.0E-3 | 1.0E-6 |
| M00615 (c-Myc/Max) | M00069 (YY1) | 50 | Down | 4.4E-3 | 1.2E-6 |
| M00651 (NF-muE1) | M00179 (CRE-BP1) | 50 | Up | 9.1E-6 | 1.0E-6 |
| M00136 (Oct-1) | M00622 (C/EBP) | 100 | Down | 2.2E-11 | 1.0E-6 |
| M00177 (CREB) | M00069 (YY1) | 100 | Down | 2.2E-3 | 2.0E-6 |
| M00289 (HFH-3) | M00045 (E4BP4) | 100 | Down | 7.3E-8 | 1.2E-6 |
| M00341 (GABP) | M00281 (RFX1) | 100 | Up | 3.5E-4 | 7.7E-6 |
| M00425 (E2F) | M00287 (NF-Y) | 100 | Down | 6.8E-8 | 1.0E-6 |
| M00464 (POU3F2) | M00216 (TATA) | 100 | Down | 1.4E-13 | 9.8E-7 |
| M00466 (HIF-1) | M00069 (YY1) | 100 | Down | 2.2E-5 | 9.4E-7 |
| M00476 (FOXO4) | M00422 (FOXJ2) | 100 | Down | 5.1E-3 | 9.8E-7 |
| M00615 (c-Myc/Max) | M00651 (NF-muE1) | 100 | Down | 1.8E-3 | 3.7E-6 |
| M00678 (Tel-2)
|
M00069 (YY1)
|
100
|
Down
|
7.3E-4
|
1.0E-6
|
-
↵a The best TRANSFAC matrix match (CompareACE > 0.85).
-
↵b The orientation of neighbor motif with respect to anchor (i.e., down = neighbor motif was derived from sequences downstream of anchor; up = neighbor motif was derived from sequences upstream of anchor).
-
↵c Neighbor specificity score.
-
↵d P-value on the hypothesis that the genes with motif combination are equally or less correlated in expression than either anchor or neighbor-containing genes without the combination.
