Table 2 Sequences used in this study. One "TFBS duplex stability score" is computed as the average of all the raw DNA duplex stability scores over a given TFBS. The TFBS duplex stability scores are computed for all the binding sites of a promoter sequence. Note that one sequence can have multiple binding TFs and TFBSs, one TF can bind to more than one site, and one TFBS may be recognized by multiple TFs.
Promoter sequence | Length | Binding TFs | TFBS duplex stability scores |
|---|---|---|---|
AF093878 | 501 | Sp1, Hnf1 | 5.44, 6.34 |
Ache | 2000 | Sp1, Ap2, Egr1 | 10.03, 9.98, 9.70, 10.03, 10.10, 9.66 |
Acta1 | 2000 | Srf, Tef, Sp1, Tead1, Sre, Tbp | 7.66, 7.71, 7.31, 7.69, 7.71, 7.94, |
7.66, 7.77, 7.46, 6.67, 8.09, 7.73, 5.18 | |||
Acta2 | 2000 | Carg-d, Prm, Carg-c | 9.70, 10.01, 9.76 |
Actc1 | 2000 | Sp1, Myod1, Srf, Tbp | 9.93, 9.82, 9.73, 9.72, 9.23, 9.94, 9.82, 8.90 |
Alb1 | 2000 | Tcf1, Cebp, Hnf1, Cebp | 9.17, 9.80, 9.44, 9.71, 9.64, 9.20 |
Chrna1 | 2000 | Myf, E1, E2, E3 | 9.85, 9.91, 9.93, 9.92, 9.92 |
Chrnb1 | 2000 | Myf, Tef, E1 | 9.59, 9.78, 9.77, 9.91 |
Chrnd | 2000 | Myf, E1 | 9.90, 9.88, 9.81, 9.76, 9.55, 9.61 |
Chrne | 2000 | E1 | 9.93 |
Chrng | 2000 | Myf, E1, E2, E3, E4 | 9.74, 9.84, 9.64, 9.28, 9.83, 9.86 |
Ckm | 2000 | Srf, Nvl, Mef, Prrx1, Myog, Myod1, | 9.78, 9.89, 8.15, 8.63, 8.06, 9.94, 9.94, 9.94, 9.95, |
Myf5, Mef1, Ap2, Myf, Carg3, | 9.95, 9.35, 9.94, 9.95, 9.80, 9.97, 9.74, 9.94, | ||
Mef2-left (-right), E-left (-right), Trp53 | 9.69, 8.34, 8.53, 9.80, 9.95, 9.96, 9.87, 9.70 | ||
Des | 2000 | E1, Mef2c, Myod1, Tbp | 9.88, 8.23, 6.49, 9.88, 9.88, 8.66 |
Id2 | 2000 | Cebpb | 9.47 |
Igfbp5 | 2000 | unknown | 9.77 |
M22326 | 501 | Srf | 4.69, 4.48, 3.92 |
M23768 | 500 | Srf, Ap1, Creb | 3.99, 5.71, 7.09 |
M29660 | 499 | Mef2, Caat | 5.27, 8.11 |
M62362 | 500 | Usf, Egr1, Ap2a, Tbp | 8.55, 9.60, 9.57, 4.16 |
M63335 | 500 | Cebp, Nfya, Tbp | 2.54, 2.50, 4.34 |
M86180 | 514 | Sp1 | 9.97 |
M86232 | 428 | Srf, Myod1 | 9.02, 9.87 |
Mb | 2000 | Myod1, Mef2, E2, Tbp | 8.90, 9.66, 9.73, 8.78, 9.62, 8.34 |
Myf6 | 2000 | Myf, Myog, Myf5, Myod1 | 9.62, 9.63, 9.77, 9.63, 9.77, 9.77, 9.63 |
Myh4 | 2000 | Myf | 9.88 |
Myh6 | 2000 | Mef, Tef, Srf, Mef2, Tead1 | 7.60, 9.75, 7.60, 8.80, 7.60, 9.75, 8.94 |
Myl4 | 2000 | E4, E1, Carg | 9.97, 9.94, 9.14 |
Myod1 | 2000 | Ap2, Gc2, Ccaat-box, Sp1, Tbp | 9.91, 9.98, 9.55, 9.99, 8.35, 9.55, 9.98 |
Myog | 2000 | Myf, Mef, Mef2, E1, Def-2, Myog, Tbp, Myod1 | 9.03, 7.21, 9.87, 7.00, 9.79, 7.01, 9.79, 9.79, |
9.02, 7.00, 7.03, 8.31, 9.79 | |||
Q8cfn5 | 2000 | Myf | 9.917 |
Tnnc1 | 2000 | Cef-2, Sp1, Mef2, Mef3, Gata4 | 9.04, 9.25, 6.54, 9.52, 9.19, 6.54, 9.49, 8.54 |
Ttr | 2000 | Cebp, Tcf1, Hnf2, Hnf3, Cebp, Hnf4, Hnf1 | 9.74, 9.47, 9.50, 9.38, 9.13, 9.74, 9.31, 9.38, |
9.50, 9.45, 9.12 | |||
U36238 | 501 | Sp1, Cebp, Tbp | 10.05, 9.85, 8.78 |
U69555 | 505 | E2f, Cets | 9.92, 9.93 |
Vim | 2000 | unknown | 9.64, 9.88 |
X03020 | 501 | Nfkb1, Ap1, Nfat | 6.52, 6.63, −0.40, −0.33 |
X04724 | 500 | Hnf1, Ipf1, Creb, Tbp | 5.43, 5.57, 7.27, 8.21 |
Y18062 | 500 | Hnf1, Cebp | 6.38, 0.35, 0.32 |
NM | 500 | Oct, Aml, Egr1 | 2.74, 3.65, 9.77 |
NM | 500 | Sp1 | 9.89, 9.84, 9.81, 9.89, 9.70 |
NM | 500 | Sp1, Ap2a, Tbp | 9.46, 6.08, 4.55, 3.14, 2.40, 4.10 |
NM | 500 | Sp1 | 10.03, 9.44, 10.02 |
NM | 500 | Myb, Caat, Tbp | 9.90, 9.74, 6.76, 6.25 |
NM | 500 | Sp1, Ap1 | 10.03, 9.94, 9.92 |
NM | 500 | Olf1 | 7.41 |
NM | 500 | Sp1 | 5.42, 8.60, 7.87, 9.87 |
NM | 500 | Myod1 | 8.41, 9.10, 8.80, 1.90 |
