Table 3 Results for Rel/NF-κ B target genes. Most significant TFBSs detected in Rel/NF-κ B target genes set by TFM-Explorer, TOUCAN, OTFBS, and oPOSSUM. The data set comprised 99 human Rel/NF-κ B target genes that have experimentally verified binding sites. Both 2-kb-upstream sequences and 5-kb-downstream/5-kb-upstream sequences were used. The TRANSFAC vertebrate matrix collection was used with TFM-Explorer, TOUCAN, and OTFBS, and JASPAR vertebrate matrices were used with oPOSSUM. TFs of the Rel/NF-κ B family are marked with *. Other TFBSs (such as TATA-box) are also likely to be biologically valid.
TFM-Explorer, region -5000, 5000 | ||||
|---|---|---|---|---|
Rank | PWM | Window | P-value | |
1 | * | NFKAPPAB65_01 | [-0520: +0115] | 8.875e-27 |
2 | * | NFKAPPAB_01 | [-0698: +0116] | 1.026e-20 |
3 | * | NFKB_C | [-0522: -0020] | 9.148e-19 |
4 | TATA_01 | [-0056: -0010] | 5.585e-18 | |
5 | * | NFKB_Q6 | [-0537: +0092] | 2.241e-16 |
6 | TATA_C | [-0055: -0015] | 4.128e-16 | |
7 | * | CREL_01 | [-0501: -0020] | 3.510e-15 |
8 | CDXA_01 | [-0071: -0018] | 4.262e-15 | |
9 | * | NFKAPPAB50_01 | [-0521: +0012] | 8.601e-13 |
10 | SP1_Q6 | [-0094: -0043] | 1.451e-11 | |
TFM-Explorer, region -2000, 0 | ||||
Rank | PWM | Window | P-value | |
1 | * | NFKAPPAB65_01 | [-0520: -0019] | 7.706e-27 |
2 | * | NFKAPPAB_01 | [-0698: -0019] | 9.418e-20 |
3 | TATA_0l | [-0056: -0023] | 1.118e-19 | |
4 | * | NFKB_C | [-0522: -0020] | 9.148e-19 |
5 | TATA_C | [-0055: -0015] | 4.128e-16 | |
6 | * | CREL_01 | [-0501: -0020] | 3.510e-15 |
7 | * | CDXA_01 | [-0071: -0018] | 4.262e-15 |
8 | * | NFKB_Q6 | [-0537: -0021] | 3.574e-14 |
9 | * | NFKAPPAB50_01 | [-0521: -0019] | 1.066e-12 |
10 | SP1_Q6 | [-0094: -0043] | 1.451e-11 | |
TOUCAN, region -5000, 5000 | ||||
Rank | PWM | P-value | ||
1 | HFH3_01 | 0.0 | ||
2 | BRACH_01 | 4.667e-01 | ||
3 | RORA2_01 | 8.596e-01 | ||
4 | NRSF_01 | 9.956e-01 | ||
5 | E47_01 | 1.0 | ||
6 | VMYB_01 | 1.0 | ||
7 | AP4_01 | 1.0 | ||
8 | MEF2_01 | 1.0 | ||
9 | ELK1_01 | 1.0 | ||
10 | EVI1_06 | 1.0 | ||
TOUCAN, region -2000, 0 | ||||
Rank | PWM | P-value | ||
1 | * | NFKAPPAB65_01 | 1.381e-05 | |
2 | * | NFKB_C | 6.975e-05 | |
3 | * | NFKAPPAB_01 | 3.139e-04 | |
4 | ARP1_01 | 1.257e-03 | ||
5 | SREBP1_01 | 6.795e-03 | ||
6 | * | NFKB_Q6 | 4.683e-02 | |
7 | * | NFKAPPAB50_01 | 8.661e-02 | |
8 | RORA2_01 | 9.847e-02 | ||
9 | E47_02 | 1.628e-01 | ||
10 | HEN1_01 | 2.882e-01 | ||
OTFBS, region -5000, 5000 | ||||
Rank | PWM | P-value | ||
OTFBS, region -2000, 0 | ||||
Rank | PWM | P-value | ||
1 | FOXJ2_01 | 6.097e-49 | ||
2 | FOXD3_01 | 4.229e-45 | ||
3 | HFH3_01 | 5.356e-41 | ||
4 | HNF3B_01 | 7.352e-35 | ||
5 | IK2_01 | 3.031e-20 | ||
6 | SREBP1_01 | 1.969e-19 | ||
7 | * | NFKAPPAB65_01 | 3.708e-19 | |
8 | * | NFKB_C | 8.819e-19 | |
9 | * | CREL_01 | 2.571e-18 | |
10 | CHOP_01 | 1.004e-17 | ||
oPOSSUM, region -5000, 5000 | ||||
Rank | PWM | P-value | ||
1 | * | p65 | 1.941e-08 | |
2 | * | NF-kappaB | 1.579e-05 | |
3 | * | c-REL | 7.877e-05 | |
4 | * | p50 | 1.510e-04 | |
5 | c-FOS | 6.236e-04 | ||
6 | Irf-1 | 3.301e-03 | ||
7 | MZF_5-13 | 5.543e-03 | ||
8 | MZF_1-4 | 7.967e-03 | ||
9 | NRF-2 | 2.933e-02 | ||
10 | SPI-B | 3.239e-02 | ||
oPOSSUM, region -2000, 0 | ||||
Rank | PWM | P-value | ||
1 | * | p65 | 1.333e-14 | |
2 | * | NF-kappaB | 3.234e-11 | |
3 | * | c-REL | 4.835e-09 | |
4 | * | p50 | 3.272e-07 | |
5 | SPI-B | 5.137e-05 | ||
6 | c-FOS | 1.519e-04 | ||
7 | Elk-1 | 2.329e-04 | ||
8 | deltaEF1 | 2.877e-04 | ||
9 | MZF_1-4 | 3.731e-04 | ||
10 | Irf-1 | 6.815e-04 | ||