Summary of results
Parameters
threshold = low FP (p < 10-4)
maxd = 25, 50, 200 bp
species = hs
conserved binding sites
    total n   % of each pattern hs[1]   % of each pattern mm[2]   Chi2 test[3] expression p value[4] TSS position bias[5] order p value (binomial) maxd[6] low FN[7]
name 1[8] name 2[9] hs mm 5'-3' 3'-5' 3'-3' 5'-5' 5'-3' 3'-5' 3'-3' 5'-5' p hs p mm hs mm hs scan stats mm*9591 hs mm hs mm  
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
NFY NFY 892 224 16% 18% 34% 31% 9% 16% 40% 34% <1E-16 2.00E-12 **** ** *        25 50 200 25 y
SP1 SP1 1323 1227 37% 40% 9% 14% 40% 38% 10% 12% <1E-16 <1E-16 ****            25 50 200 25 y
SP1 RREB1 414 301 12% 12% 39% 36% 9% 13% 48% 31% <1E-16 <1E-16     **** ****      25 50 200 25 y
SP1 PAX4 629 468 16% 11% 39% 34% 11% 13% 36% 40% <1E-16 <1E-16     **** ****      25 50 200 25 y
MEIS1A/HOXA9 TCF11 78 65 6% 9% 72% 13% 8% 5% 75% 12% <1E-16 <1E-16              25 50 25 y
TCF11 CREBP1CJUN 54 44 9% 9% 78% 4% 2% 7% 86% 5% <1E-16 <1E-16     **** ****      25 50 200 25 y
RREB1 MZF1 202 161 8% 10% 47% 34% 6% 8% 55% 31% <1E-16 <1E-16              25 50 200 25 y
RREB1 PAX4 471 344 34% 45% 13% 9% 33% 57% 4% 6% <1E-16 <1E-16              25 50 200 25 y
MZF1 PAX4 210 207 14% 7% 53% 25% 4% 11% 57% 29% <1E-16 <1E-16              25 50 200 25 y
TCF11 TAXCREB 43 42 0% 16% 79% 5% 14% 10% 74% 2% 5.60E-15 8.50E-12              25 50 25 n
EGR1 SP1 1191 575 31% 30% 19% 20% 36% 33% 16% 16% 1.30E-12 1.10E-16 ****   *** ***      25 50 200 25 y
EGR1 PAX4 298 217 14% 17% 28% 41% 14% 17% 27% 43% 4.40E-12 9.60E-10 *   **** ****      25 50 200 25 y
EGR1 RREB1 220 144 11% 16% 32% 41% 8% 13% 38% 42% 2.50E-11 2.50E-11     **** ****      25 50 200  25 50 n
RREB1 P300 194 147 12% 12% 39% 37% 12% 13% 45% 30% 3.30E-11 2.60E-09              25 50 200  25 50 y
P300 PAX4 367 167 16% 16% 35% 34% 16% 14% 37% 33% 4.50E-11 4.30E-06              25 50 200 25 y
AP2 SP1 832 520 20% 18% 33% 28% 24% 20% 30% 27% 1.30E-10 0.011 ****   *        25 50   y
TAXCREB RREB1 197 180 16% 14% 45% 25% 13% 11% 59% 17% 1.40E-10 <1E-16     **** ****      25 50 25 n
MZF1 MZF1 151 115 36% 41% 11% 13% 45% 34% 10% 10% 1.20E-09 4.10E-09              25 50 25 y
RREB1 GATA1 407 178 20% 14% 35% 30% 14% 12% 43% 30% 2.10E-09 6.60E-10              25 50 200  25 50 y
SP1 MZF1 210 152 36% 36% 11% 17% 43% 36% 9% 11% 5.20E-09 6.90E-12     **** ****      25 50 200 25 y
SP1 P300 365 164 34% 32% 15% 18% 35% 34% 17% 13% 6.80E-09 1.20E-05     **** ****      25 50 25 y
SP1 TAXCREB 377 327 37% 28% 18% 18% 30% 30% 22% 18% 1.80E-08 0.0022 **   *        25 50 25 n
NFY SP1 1309 1226 29% 21% 29% 21% 27% 23% 27% 23% 2.00E-08 0.0099 ****   **** ***      50 200   y
GATA1 PAX4 238 170 15% 16% 34% 35% 15% 21% 27% 37% 4.20E-08 0.00046              25 50   y
TAXCREB MZF1 507 416 33% 30% 20% 17% 26% 28% 25% 22% 8.40E-08 0.3     **** ****     200   n
CREL RREB1 223 188 22% 17% 42% 19% 24% 20% 38% 18% 8.50E-08 0.00024             50   y
AML1 EVI1 292 296 19% 20% 40% 21% 16% 17% 43% 25% 9.40E-08 7.10E-12             25 25 n
P300 GATA1 224 167 36% 33% 11% 21% 28% 34% 16% 22% 1.60E-07 0.0083              25 50   y
EGR1 AML1 281 267 31% 35% 15% 19% 31% 31% 21% 18% 4.40E-07 0.0023     **** ****      25 50   n
1-Oct AML1 245 232 20% 19% 40% 20% 23% 25% 30% 22% 8.10E-07 0.31             50   y
AML1 PAX4 277 311 20% 17% 25% 39% 21% 19% 27% 32% 8.70E-07 0.0041     **** ****     25   y
EGR1 MZF1 112 85 47% 21% 14% 17% 39% 27% 14% 20% 8.80E-07 0.0092     **** ****     25   y
LYF1 PAX4 73 59 8% 15% 51% 26% 20% 25% 22% 32% 1.10E-06 0.58     **** ****     25   y
SP1 GATA1 293 221 30% 35% 17% 17% 37% 32% 15% 17% 2.20E-06 8.80E-07 **   **** ****     25 25 y
SREBP1 RREB1 199 86 41% 24% 18% 17% 51% 28% 9% 12% 2.90E-06 2.30E-08             50 25 n
MZF1 GKLF 73 63 33% 47% 10% 11% 48% 27% 19% 6% 3.50E-06 4.80E-05       **     50   y
PAX4 GKLF 60 53 8% 17% 53% 22% 23% 8% 30% 40% 3.90E-06 0.0086             25   y
PAX5 SP1 397 266 36% 24% 22% 18% 30% 28% 21% 21% 7.10E-06 0.079     **** ****     25 25 y
GATA3 RREB1 94 86 11% 17% 46% 27% 8% 10% 40% 42% 7.80E-06 1.90E-07              25 50 25 y
    total n   % of each pattern hs[10]   % of each pattern mm[11]   Chi2 test[12] expression p value[13] TSS position bias[14] order p value (binomial) maxd[15]  
name 1[16] name 2[17] hs mm 5'-3' 3'-5' 3'-3' 5'-5' 5'-3' 3'-5' 3'-3' 5'-5' p hs p mm hs mm hs mm hs mm hs mm low FN
NOTES:
A) Click on header for brief explanation of entries in each column
B) Statistical significance:* = "p<0.01", ** = "p<0.001", *** = "p<0.0001", **** = "p<0.00001"
C) A gray shade in the TF names (columns 1 and 2) indicates that the order/orientation pattern was conserved between hs (humans) and mm (mouse, e.g. AP2-SP1 was significant both in hs and mm but TCF11-ARP1 was significant only in hs)
D) When an interaction was observed for multiple maxd values, here we report the values corresponding to the minimum Chi2 p value (i.e. the strongest evidence)
E) Entries marked in red correspond to the examples discussed in the text (Due to note D, the values reported here may not be the same as those quoted in the main text which may correspond to a different maxd)
F) For hs, 69% of the TF pairs reported here showed significant pattern biases for more than one value of maxd
G) 80% of the TF pairs shown here were also found with the low FN threshold parameter
[1]
Percentage of the total number of genes where the two motifs occurred within maxd showing each order/orientation pattern
[2]
Percentage of the total number of genes where the two motifs occurred within maxd showing each order/orientation pattern
[3]
p value for Chi2 test comparing actual distribution vs null hypothesis of uniform distribution
[4]
Permutation p value for the correlation between gene expression values for genes with the most prevalent order/orientation pattern
[5]
p value for t test comparing the distribution of positions with respect to the TSS of the two motifs
[6]
maxd parameter where the significant interactions were observed
[7]
Indicates whether the same motif pair was found with the low FN parameter set
[8]
TRANSFAC name for motif 1
[9]
TRANSFAC name for motif 2
[10]
Percentage of the total number of genes where the two motifs occurred within maxd showing each order/orientation pattern
[11]
Percentage of the total number of genes where the two motifs occurred within maxd showing each order/orientation pattern
[12]
p value for Chi2 test comparing actual distribution vs null hypothesis of uniform distribution
[13]
Permutation p value for the correlation between gene expression values for genes with the most prevalent order/orientation pattern
[14]
p value for t test comparing the distribution of positions with respect to the TSS of the two motifs
[15]
maxd parameter where the significant interactions were observed
[16]
TRANSFAC name for motif 1
[17]
TRANSFAC name for motif 2