Supplementary Figure 1 Calculation of motif displacements. Supplementary Figure 2 Parameters to binomial distribution. Supplementary Figure 3 Motivation for ...
Inferring transcription factor complexes from ChIP-seq data Tom Whitington, Martin C. Frith, James Johnson and Timothy L. Bailey
Supplementary figures and tables: Supplementary Figure 1
Calculation of motif displacements
Supplementary Figure 2
Parameters to binomial distribution
Supplementary Figure 3
Motivation for motif trimming
Supplementary Figure 4
Distribution of inter-motif distances
Supplementary Figure 5
Distribution of significant results count
Supplementary Figure 6
Distribution of number of significant intervals
Supplementary Table 1
Input datasets and motifs
Supplementary Table 2
Types of evidence
Supplementary Table 3
Table of all results
Supplementary Table 4
Motif database
1
Supplementary Figure 1. Calculation of motif distances. Schematic illustrating how motif displacement is calculated. Two hypothetical example sequences are shown, with primary motif hits highlighted in blue and secondary motif hits highlighted in green. If the secondary motif occurrence is located at the 3’ side of the primary motif occurrence, then the displacement is positive. In this case (as in the first example), the displacement is defined as d = g + 1, where g = the gap size between the motifs (in basepairs). If the secondary motif occurrence is at the 5’ side of the primary motif occurrence, then the displacement is negative. In this case (as in the second example), the displacement is defined as d = −1 × (g + 1).
!"#$%"&' ()*+'
,-.)/0%"&' ()*+'
CCGGAAGT
A
G
T
G
A
AC
TGA
C
G C
T G
1 2 3 4 5
1 2 3 4 5 6 7 8 9
A
ACCGGAAGTCTGTAATGAC! !"#$%&'()(*+,-,./,
,-.)/0%"&' ()*+'
TGA
C T
CCGGAAGT
A
G
G
1 2 3 4 5
G
A
T
AC
1 2 3 4 5 6 7 8 9
A
G C
!"#$%"&' ()*+'
ATGACCTGACCGGAAGT! !"#$%&'()(*+,-,01,
2
Supplementary Figure 2. Parameters to binomial distribution. Schematic explaining parameter q in the binomial distribution of number of sequences exhibiting displacement in a specified interval of size x. The maximum magnitude of the distance between the primary and secondary motifs is given by r. The schematic illustrates why p r = m−w − ws . Since the primary and secondary motif occurrences can occur on the same 2 strand or opposite strands, the fraction of sequences expected to exhibit displacements in a x given interval of width x at random is given by q = 4×r .
!"#
!$# &#
TGA
C T
1 2 3 4 5
G
CCGGAAGT
A
G
T
G
A
AC
1 2 3 4 5 6 7 8 9
A
G C
%#
3
'#
Supplementary Figure 3. Motivation for motif trimming. Schematic illustrating the motivation for trimming low information flanking columns from motifs. Some motifs, such as the two original untrimmed motifs shown in this example, consist of a set of columns with moderate or high information content (the “motif core”), with low information content columns occurring at either or both sides of the motif core. When the original, untrimmed motifs are considered, spacing enrichments cannot be detected involving short distances between the motif cores, as we do not allow motif overlap in our analysis. When low information flanking columns are trimmed from the motifs, spacing enrichments involving small inter-motif distances can be detected.
!"#$#%&'()*+,(-( A
T G
A
A
A G
1 2 3 4 5 6 7 8 9 10
T
A
CT T
A
A
T G
A
A
A G
GTA
1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8
C
GTA
1 2 3 4 5 6 7 8
CT
C
!"#$#%&'()*+,(.(
!"#$%&'()*+,-++&)./01)$/2+()3&4+,+$,#*5+) /"#0012()*+,(.(
/"#0012()*+,(-(
A
GTA
T G
A
1 2 3 4 5 6
T
A
1 2 3
CT
C
G
GTA
1 2 3 4 5 6
1 2 3
CT
C
T
A
A
T A
!"#$%&'()*+,-++&)./01)$/2+()#2+)&/-)4+,+$,#*5+)
4
Supplementary Figure 4. Distribution of inter-motif distances. We obtained the single spacing interval with the lowest p-value, from each of the 87 nonredundant spacing patterns that pass a p-value threshold of 0.01 (shown in Supplementary Table 3). We recorded the absolute value of the displacement value of each of those intervals, and made a histogram of these values. The vast majority of significant spacing enrichments have a distance of 1bp, with no gap between the primary and secondary motifs.
20 10 0
Count
30
40
Motif separataion distribution for all significant spacing results (N=87)
0
5
10 Inter−motif distance of strongest interval
5
15
20
Supplmenentary Figure 5. Distribution of significant results counts. Histogram of the number of non-redundant significant secondary motif results, for all 41 analyses.
0
5
Count
10
15
Distribution of number of significant results over all input ChIP−seq datasets (N=41)
0
2
4
6 Number of non−redundant secondary motif results at p < 0.01
6
8
10
12
Supplementary Figure 6. Distribution of number of significant intervals. Histogram of the number of significant intervals considering all 87 results significant at a p-value threshold of 0.01. For each significant secondary motif result, the maximum number of significant intervals is reported, considering same strand and opposite strand displacements.
30 20 10 0
Count
40
50
60
Distribution of number of significant intervals over all significant results (N=87)
0
2
4
6 Number of significant intervals
7
8
10
12
Supplementary Table 1. Input ChIP-seq datasets and primary motifs. Summary of input datasets, sorted first by Author, then by Assembly to resolve ties, then by Tissue, then by Factor. “TF” represents the factor targeted in the ChIP-seq experiment. “Assembly” represents the UCSC genome assembly for the ChIP-seq peak region sequences. “Tissue” represents the tissue in which the ChIP-seq was carried out. “Primary motif” represents the short name of the primary motif employed in the SpaMo analysis (full motif name and sequence logo is shown in Supplementary Table 4). “Number of ChIP-seq peaks” represents the number of peak regions declared by the authors, and used as input to SpaMo.
8
TF
Assembly
Tissue
Author
Primary motif
E2f1
mm8
ESC
[1]
J E2F1
20699
Esrrb
mm8
ESC
[1]
C Esrrb
21647
Klf4
mm8
ESC
[1]
U Klf7 i
10875
Nanog
mm8
ESC
[1]
C Nanog Loh2
10343
Oct4
mm8
ESC
[1]
C Oct4
3761
STAT3
mm8
ESC
[1]
C Stat3
2546
Smad1
mm8
ESC
[1]
U Smad3 i
1126
Sox2
mm8
ESC
[1]
C Oct4
4526
Tcfcp2l1
mm8
ESC
[1]
C Tcfcp2l1
26910
Zfx
mm8
ESC
[1]
C Zfx
10338
cMyc
mm8
ESC
[1]
J Mycn
3422
nMyc
mm8
ESC
[1]
J Mycn
7182
Gata1
mm9
G1EER4
[2]
U Gata6 i
14711
Jund
hg18
Gm12878
[3]
U Jundm2 ii
12958
Max
hg18
Gm12878
[3]
U Max i
6546
cFos
hg18
Gm12878
[3]
C NFYA
3284
cFos
hg18
Gm12878
[3]
U Jundm2 ii
3284
Tcf4
hg18
Hct116
[3]
U Tcf3 i
34522
Srebp1a
hg18
Hepg2
[3]
C Srebp
5461
Srebp2
hg18
Hepg2
[3]
C Srebp
3761
Jund
hg18
K562
[3]
U Jundm2 ii
1500
Max
hg18
K562
[3]
U Max i
10480
Nfe2
hg18
K562
[3]
C Nfe2
5071
cFos
hg18
K562
[3]
C NFYA
18963
cFos
hg18
K562
[3]
C Jundm2 ii
18963
cJun
hg18
K562
[3]
C Jundm2 ii
26920
cMyc
hg18
K562
[3]
J Mycn
15749
Gata1
hg18
K562b
[3]
U Gata6 i
5496
Znf263
hg18
K562b
[3]
C Znf263
27549
NRSF canonical
mm8
ESC
[4]
J REST
1698
NRSF canonical
mm8
NSC
[4]
J REST
692
STAT1
hg18
HeLaStim
[5]
C Stat3
41582
STAT1
hg18
HeLaUnstim
[5]
C Stat3
11004
FoxA2
mm8
Liver
[5]
U Foxa2 i
11475
STAT1
hg18
HeLaStim
[6]
C Stat3
36998
Srebp1
mm9
Liver
[7]
C Srebp
426
GABP
hg18
Jurkat
[8]
U Gabpa i
6442
NRSFmono
hg18
Jurkat
[8]
J REST
2596
NRSFpoly
hg18
Jurkat
[8]
J REST
2960
SRF
hg18
Jurkat
[8]
U Srf i
2429
Scl
mm8
HPC7
[9]
U Ascl2 i
199
9
Number of ChIP-seq peaks
Supplementary Table 2. Types of evidence. The class of evidence supporting the existence of a TF complex is shown, for each reference given in Tables 1, 2 or 3 of Results. “Reference” indicates the reference for the article as shown in the supplementary bibliography. “Type of evidence” indicates the experimental evidence supporting the interaction. “EMSA” indicates electrophoretic mobility shift assay. *: This paper supports an interaction between E2F family members and YY1. The authors do not find evidence for a direct E2F1/YY1 interaction. Therefore, the YY1 spacing enrichment observed in the E2F1 data is potentially due to an interaction between YY1 and other E2F TFs binding at the same locations as E2F1. Reference
PubMed ID
Type of evidence
[10]
14559893
X-ray crystallography
[11]
11846562
X-ray crystallography
[12]
9491997
EMSA
[13]
16272134
EMSA
[14]
9214632
EMSA
[15]
18026136
EMSA
[16]
15525604
EMSA with ortholog
[17]
14757430
Review paper
[18]
16007074
Luciferase assay
[19]
12411495
Y2H *
Immunoprecipitation,
10
Supplementary Table 3. Table of all results. All secondary motif results significant at a p-value threshold of 0.01 are reported. Results are grouped according to the input ChIP-seq dataset. In the first column, the assembly, TF, tissue and reference for the input ChIP-seq dataset is given. For “Primary motif” and “Secondary motif” columns, the seqlogos and summary names are provided. Same strand and opposite strand displacement histograms are shown. The x-axis of each histogram shows the motif displacement value. The y-axis shows the number of sequences that exhibited the given secondary-primary motif displacement value, and is scaled linearly with the origin corresponding to zero. The “Sig. Interval” specifies the displacement value and strand for the single most significant interval, with “Opp.” indicating opposite strand. The p-value of that interval is given. Secondary motifs that are highly similar to the primary motif (considering reverse complement) are highlighted in bold font. Factor
Primary PWM
Secondary PWM
Same Disps
Opp Disps
34
hg18 Gata1
GATAA
K562b [3]
U Gata6 i
A T
T
C
G
A C
T
C G
A T
CA TG C Ebox
150
34
0
150
28
hg18 Gata1
GATAA
K562b [3]
U Gata6 i
A T
T
C
G
A C
T
C G
A T
CTGG
T
G A
A TT
C
CAG
C A
T
T
T
G
A
T
G
C
150
J Hand1::Tcfe2a
hg18 Gata1
GATAA
K562b [3]
U Gata6 i
A T
T
G
A C
T
C G
A T
A
CA G
CC
CC
ACTGACGGG
G
AC T A
CG T
A
GT CG
A AT AGGA
C T
T
A
T
TG
150
U Myf6 ii
0
150
hg18 Gata1
GATAA
K562b [3]
U Gata6 i
A T
T
G
A C
T
C CAGCAGG
A
C
T
G
G
A T
A
TA
C
T
G
T
TG T
T
U Zic2 ii
150
0
150
hg18 Gata1
GATAA
K562b [3]
U Gata6 i
A T
T
G
A C
T
C G
A T
T C GGAA T GCT
C
G T A
A
A
T
G
T
G A
A
T G AGC C
C
C Stat3
150
0
150
T
AA T
G
hg18 Nfe2 K562 [3]
C TA
TG T AG C
AC
C
G
T CA
A
C
TC
C Nfe2
T
A
A
T
C
G
A
TGA TCA
G
TG
GA CT
C
C A
G
C
TC
A
U Jundm2 ii
11
C T
G
150
-9, Same 2.76e-16
150
0
150
-5, Same 7.02e-13
150
0
150
-7, Opp. 1.78e-04
150
0
150
-6, Opp. 3.59e-03
16
0
150
13
C
150
16
16
C
0
19
16
C
150
28
19
C
Sig. Interval
150
0
150
-2, Same 7.22e-03
13
0
150
150
0
150
+2, Opp. 1.08e-05
8
GC T TG GA TGTAGT C
C
G
hg18 Srebp1a
T
A
A
T
A CG C T TA
CG
T
G
Hepg2 [3]
G
A
G
A
T
A AC
A
G
T
T
C
C
A
C
G
A
T
C
CGCGCG
CG T
C
C
T AAG
G
C Srebp
CGG
GA
G C
A
T
T CG
A
CT
C
A T GG A A
T G
C
A
150
U Rsc30
8
0
150
28
T
T
T
hg18 Tcf4 Hct116 [3]
T AAA
AC G
G AC
G
G
AAT
T
T
A
AGG
TCAC C
G
T
T
U Tcf3 i
TGA TCA G
A
C
G
TG
GA CT
C
C A
TC
A
C T
G
150
U Jundm2 ii
G T
G
AC
G A
AC
T
GT
hg18 cFos Gm12878 [3]
AT G C
C CCTCG
C
A
C
A
T
T
G
T CC A
CCAAT
AG C G
AG
A
G
C
T
C NFYA
A
T
G
C A
A
CT
150
J NFYA
0
150
G T
G
AC
G A
AC
T
GT
hg18 cFos Gm12878 [3]
A TG C
C CCTCG
C
A
C
A
T
T
G
T CC A
GG
C
TA
G T
C
C NFYA
CTGTCA
AC
A
GG C
AT
CA
C
A
A
A
TC
G
G G
150
U Pknox2
0
150
G T
G
AC
G A
AC
T
GT
hg18 cFos Gm12878 [3]
AT G C
C CCTCG
C
A
C
A
T
T
G
T CC A
GG G
A C TG C
A G
A TT
C NFYA
T
T
C
GA
A T
C
T
G
GT
C
G G C
TT
C C
A
C
G
C
150
U Sp4 ii
0
150
G T
G
AC
G A
AC
hg18 cFos Gm12878 [3]
AT G C
C CCTCG T
GT
C
A
C
A
T
T
G
T CC A
C NFYA
T
A G
A
A
C
T
T
GT A
TG C
C C
C
A
CACGTG
G C
T
TC
AC T
C
A
A
G T TG A
150
U Cbf1 b
0
150
A
TGA TCA G
G
TG
GA
C
AC
hg18 cFos K562 [3]
C
TC
C
A
T
G
U Jundm2 ii
A TG
GGAA
A
CC
A
A G T
T
AT
T
J SPIB
150
0
150
A
TGA TCA
G
TG
GA
C
AC
hg18 cFos K562 [3]
G
C
TC
C
A
U Jundm2 ii
T
G
A
TGA TCA
G
TG
GA CT
C
C A
G
C
TC
A
U Jundm2 ii
12
C T
G
150
0
150
-1, Same 3.12e-04
150
0
150
-17, Opp. 2.87e-23
150
0
150
+2, Same 4.80e-20
150
0
150
-4, Opp. 3.11e-06
150
0
150
+6, Opp. 2.02e-05
41
0
150
21
CT
150
10
41
CT
3.58e-08
18
10
T CC G T T GG
-1, Opp.
21
18
T CC G T T GG
150
34
21
T CC G T T GG
0
28
34
T CC G T T GG
150
150
0
150
1, Opp. 9.24e-14
21
0
150
150
0
150
-1, Same. 6.6e-06
! "$# % &(' ) *+
21
A
TGA TCA G
G
TG
GA CT
C
AC
hg18 cFos K562 [3]
C
TC
C
A
T
G
U Jundm2 ii
TGA
A
G
C T
T A
C
G
150
J NFE2L1::MafG
21
0
150
25
G T
G
AC
G A
AC
T
GT
hg18 cFos K562 [3]
AT G C
C CCTCG
T CC G T T GG
C
A
C
A
T
T
G
T CC A
T
A
GT
A
A
C
T
G
T
C NFYA
A
TG C
C
C
C
A
CACGTG
G C
T
TC
AC T
C
A
A
G T TG A
150
U Cbf1 b
G T
G
AC
G A
AC
T
GT
hg18 cFos K562 [3]
AT G C
C CCTCG
C
A
C
A
T
T
G
T CC A
CCAAT
AG C G
AG
A
G
C
T
C NFYA
A
T
G
C A
A
C
T
150
J NFYA
0
150
G T
G
AC
G
A
AC
T
GT
hg18 cFos K562 [3]
AT G C
C CCTCG
C
A
C
A
T
T
G
T CC A
CTGTCA
AC
A
GG
C
G T
GG TA
C
C
C NFYA
AT
CA
C
A
A
A
TC
G
G G
150
U Pknox2
0
150
G T
G
AC
G A
AC
T
GT
hg18 cFos K562 [3]
AT G C
C CCTCG
C
A
C
A
T
T
G
T CC A
GG G
A C TG C
A G
A TT
G G C
C
C NFYA
GA
A
T
T
C
T
G
GT
CT
TT
C C
A
C
G
C
150
U Sp4 ii
0
150
G T
G
AC
G A
AC
T
GT
hg18 cFos K562 [3]
AT G C ATGC AAT T
C CCTCG
C
A
C
A
T
T A
G
T CC A
C NFYA
C Octamer b
150
0
150
G T
G
AC
G A
AC
hg18 cFos K562 [3]
AT G C
C CCTCG T
GT
C
A
C
A
T
T
G
T CC A
C NFYA
A
TGACGTCA
GG T
C
C
C
A
T
T
TA
A
A
T
CC A T
G
G G
150
U Jundm2 i
0
150
A
TGA TCA
G
TG
GA
C
AC
hg18 cJun K562 [3]
G
C
TC
C
A
U Jundm2 ii
T
G
A TG
GGAA
A
CC
A
A G T
T
AT
J SPIB
13
T
150
0
150
+6, Opp. 8.62e-21
150
0
150
-17, Opp. 6.71e-20
150
0
150
+2, Same 6.55e-18
150
0
150
-4, Opp. 1.59e-06
150
0
150
-4, Opp. 3.69e-05
10
0
150
53
CT
150
7
10
T CC G T T GG
6.6e-03
24
7
T CC G T T GG
-5, Same.
24
24
T CC G T T GG
150
36
24
T CC G T T GG
0
25
36
T CC G T T GG
150
150
0
150
-9, Same 5.88e-04
53
0
150
150
0
150
+1, Opp. 3.49e-16
,./ 021 3 465 7 8:9 ;
27
A
TGA TCA G
G
TG
GA CT
C
AC
hg18 cJun K562 [3]
A
C
C
TC
A
T
U Jundm2 ii
TGA TCA G
C
G
TG
GA CT
G
C
C A
TC
A
C T
G
U Jundm2 ii
150
27
0
150
17
A
TGA TCA G
G
TG
GA CT
C
AC
hg18 cJun K562 [3]
C
C
TC
A
T
G
U Jundm2 ii
CACGTGA
T
C
G
A
CG
T
TA
G
A
C
T
T
150
U Bhlhb2 i
A
TGA TCA G
G
TG
GA
C
AC
hg18 cJun K562 [3]
C
C
TC
A
T
G
TCA
CG
G
AATGT CG
T
T
T
G C
A
T
A
C
C
150
U Jundm2 ii
J Pax2
0
150
A
TGA TCA G
G
TG
GA
C
AC
hg18 Jund Gm12878 [3]
C
C
TC
A
T
G
CGAAAC
A
TT T
C
C
G
A
C
U Jundm2 ii
A
T
T
G A
A
150
U Irf4 i
0
150
A
TGA TCA
G
TG
GA
C
AC
hg18 Jund Gm12878 [3]
G
C
C
TC
A
T
G
GGAA
A TG
A
CC
A
A G T
U Jundm2 ii
T
AT
T
J SPIB i
150
0
150
C A
TTAC
G
C
hg18 cMyc K562 [3]
J Mycn
J bZIP910
150
0
150
CCGGAAGT
A
G
TG
hg18 GABP Jurkat [8]
A
AC
T
A
CGCA
GA
CT
AG
U Gabpa i
T
AA T
GC T
C
T G
150
U Fhl1
0
150
CCGGAAGT
A
G
TG
hg18 GABP Jurkat [8]
A
AC
T
U Gabpa i
A
CGCCCCC
C A
C A T
T
A T
T
ATC
U Sp4 i
14
A
G
150
0
150
-1, Opp. 3.68e-05
150
0
150
-5, Opp. 2.78e-03
150
0
150
+1, Same. 2.02e-16
150
0
150
+1, Same. 3.76e-08
150
0
150
-1, Same 6.30e-05
39
0
150
47
A C
150
12
39
A C
5.78e-08
27
12
CACGTG TGACGT
-1, Same.
28
27
CT
150
29
28
CT
0
17
29
CT
150
150
0
150
+1, Same 7.95e-28
47
0
150
150
0
150
+1, Same 1.43e-21
= ? @BA C DFE G HJI K
18
CCGGAAGT
A
G
AC
T
TG
A C
hg18 GABP Jurkat [8]
A
A
TGACGT
C A
G
U Gabpa i
J bZIP910
150
18
0
150
33
CCGGAAGT
A
G
AC
T
TG
A C
hg18 GABP Jurkat [8]
A
A
U Gabpa i
GGAA
C
CA G A T
G A T
C
150
J Eip74EF
CCGGAAGT
A
G
AC
T
TG
hg18 GABP Jurkat [8]
A
A
CG
TC
G
A
CGGA
G
GT
C
TC
CG
T
A
T A CC
G
A
C
G
150
U Gabpa i
U Hal9
0
150
CCGGAAGT
A
G
AC
T
TG
hg18 GABP Jurkat [8]
A
A
GG TTCC T
G
CT TG A TCA
T
A
C
U Gabpa i
AAA T A
G
C
J REL
150
0
150
A T
TA AA T A T A
TT
G
C
G
G C
C
T
A
C
A
C T
T
U Srf i
G T
A
C G T
A
hg18 SRF Jurkat [8]
TCC
A
T C
G
G
150
J ETS1
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [5]
A
T
G
T
G A
A
T
G AGC C
C
C Stat3
CCAT
G A
T
T
J YY1
150
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [5]
A
T
G
T
G A
A
G AGC T
C
C
C Stat3
CACGTG
G A
TA
G C
T
J USF1
150
0
150
T C GGAA
G T A
hg18 STAT1 HeLaStim [5]
T GCT
A
A
T
G
T
G A
A
C Stat3
G AGC
TGA
A
T
G
C
C
C
T A
C T
G
J NFE2L1::MafG
15
150
0
150
+14, Same 2.54e-09
150
0
150
-1, Opp. 9.60e-04
150
0
150
+1, Opp. 1.16e-03
150
0
150
-7, Opp. 3.99e-04
150
0
150
+1, Opp. 9.70e-10
36
0
150
47
C
150
68
36
C
6.71e-15
12
68
C
+2, Opp.
19
12
CC TATA GG
150
24
19
A C
0
33
24
A C
150
150
0
150
-1, Same 2.85e-09
47
0
150
150
0
150
+1, Same 5.47e-09
LNM O PRQ S TVU W XZY [
26
T C GGAA
C
G T A
hg18 STAT1
T GCT
A
HeLaStim [5]
A
T
G
T
G A
A
G AGC T
C
C
A
A
G
CA A T T G
T C G
A
C Stat3
GATCTAC
G
C
C
G
T T
T
A
A
A
AG
C
T G
T
C
G
150
U Gat3
26
0
150
46
T C GGAA
C
G T A
hg18 STAT1
T GCT
A
HeLaStim [5]
A
T
G
T
G A
A
T
G AGC C
GAA
G T
ACT
G
TG
A
C Stat3
ATCA T
G
TG
G
T
C
C
T
C
C
G
A
A
U Hdx
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [5]
A
T
G
T
G A
A
T
G AGC C
C
C
ACGT A
T
CT AGT
AA
C Stat3
T G
J TGA1A
150
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [5]
A
T
G
T
G A
A
G AGC T
C
C
C Stat3
CC GG
G
C
TGA
C
T
CCG G
CA
T
A
G
GT
AC T
G
150
U Tcfap2e i
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [5]
A
T
G
T
G A
A
G AGC T
C
C
CCCCCGGGGGG
G
AA AGGTC T T T TC T A A A AT TT G
GT
A
AC A
C
T AC
CA
150
C Stat3
U Zic3 i
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [5]
A
T
G
T
G A
A
T
G AGC C
C
C Stat3
A
TGA TCA G
C
G
TG
GA CT
C
C A
TC
A
C T
G
150
U Jundm2 ii
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [5]
A
T
G
T
G A
A
T
G AGC C
C
CC CGCCC C
A
G
AA T
C
T
TG
C Stat3
A
C
A
T
TA
T
150
U Klf7 i
0
150
T C GGAA
G T A
hg18 STAT1 HeLaStim [5]
T GCT
A
A
T
G
T
G A
A
C Stat3
G AGC T
C
C
C AG GGC
CA
C
GT G
G T AA AG T
C
T
A
C
AT
GG AT
T
A
AC
T GGC
CT AT AG
C CTCF
16
T
C
TG A
150
0
150
+7, Opp. 4.20e-07
150
0
150
-1, Same 6.91e-07
150
0
150
-1, Opp. 9.60e-06
150
0
150
-1, Opp. 1.05e-05
150
0
150
-2, Same 2.03e-05
47
0
150
43
C
150
36
47
C
1.83e-08
44
36
C
+2, Opp.
48
44
C
150
38
48
C
0
46
38
C
150
150
0
150
+1, Opp. 2.32e-05
43
0
150
150
0
150
-3, Opp. 8.20e-05
\^] _ `ba c dfe g hji k
98
T C GGAA
C
G T A
hg18 STAT1
T GCT
A
HeLaStim [6]
A
T
G
T
G A
A
T
G AGC C
CCAT
G A
T
T
C
C Stat3
J YY1
150
98
0
150
35
T C GGAA
C
G T A
hg18 STAT1
T GCT
A
HeLaStim [6]
A
T
G
T
G A
A
G AGC T
C
C
C Stat3
CACGTGA
T
C
G
A
CG
T
TA
G
A
C
T
T
150
U Bhlhb2 i
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [6]
A
T
G
T
G A
A
G AGC
TGA
A
T
G
C
C
C
C Stat3
C T
T A
G
150
J NFE2L1::MafG
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [6]
A
T
G
T
G A
A
T
G AGC C
GAA
G T
ACT
G
TG
A
C Stat3
ATCA T
G
TG
T
G
T
C
C
C
C
G
A
A
U Hdx
150
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [6]
A
T
G
T
G A
A
T C GGAA
T
C
C
T A
G AGC
C
T GCT
G
C Stat3
A
A
T
T
G AGC
G
T
G A
A
C
C
C Stat3
150
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [6]
A
T
G
T
G A
A
G AGC T
C
C
A
TGACGTCA
G
CC
C Stat3
T
T
TA
A
A
T
G
CCA A
GG
T
T
C
150
U Atf1 i
0
150
T C GGAA
G T A
hg18 STAT1
T GCT
A
HeLaStim [6]
A
T
G
T
G A
A
T G AGC C
C
C Stat3
A
TGA TCA G
C
G
TG
GA CT
C
C A
TC
A
C T
G
150
U Jundm2 ii
0
150
T C GGAA
G T A
hg18 STAT1 HeLaStim [6]
T GCT
A
A
T
G
T
G A
A
C Stat3
T
G AGC C
C
T AA T T
G T
A
A
GGAA
C A
C
G CC
C
C
A
TC AA TC C
C
G
GT T
A
G T
C G
150
U Sfpi1 ii
17
0
150
-1, Opp. 2.35e-16
150
0
150
+1, Same 1.03e-14
150
0
150
+7, Opp. 7.89e-12
150
0
150
+10, Same 9.44e-08
150
0
150
+1, Same 1.23e-07
31
0
150
35
C
150
21
31
C
1.52e-29
52
21
C
+1, Opp.
53
52
C
150
54
53
C
0
35
54
C
150
150
0
150
+2, Opp. 8.51e-05
35
0
150
150
0
150
-8, Opp. 1.55e-04
lnm o prq s tvu w xzy {
32
T C GGAA T GCT
C
G T A
hg18 STAT1
A
A
HeLaStim [6]
T
G AGC T
G
T
G A
A
C
C
C
ACGT A
T
CT AGT
AA
C Stat3
T G
J TGA1A
150
32
0
150
33
T C GGAA T GCT
C
G T A
hg18 STAT1
A
A
HeLaStim [6]
T
T
G AGC
G
T
G A
A
C
C
TC AGGAA
TT
G
C
TCA AC A AG G
C Stat3
T
T T TC T T T AA A C
C
G
G
C
T
C
150
U Bcl6b i
T C GGAA T GCT
G T A
hg18 STAT1
A
A
HeLaStim [6]
T
T
G AGC
G
T
G A
A
C
C
ATTCA
C
T
AG TTCAG C
C
C
G G
G
G
CT A
G A
TA
150
C Stat3
U Sox17 ii
0
150
T C GGAA T GCT
G T A
hg18 STAT1
A
A
HeLaUnstim [5]
T
T
G AGC
G
T
G A
A
C
C
GAT GAAT A
T GG
C
T CT
G
T
T
G
G
G
A C
A
A
150
C Stat3
J En1
0
150
T C GGAA T GCT
G T A
hg18 STAT1
A
A
HeLaUnstim [5]
T
G AGC T
G
T
G A
A
C
C
A
A
G
CA A T T G
T G C
A
GATCTAC
G
C
C
G
T T
A
T
A
C Stat3
U Gat3
Logo
Logo
A
C
AG
T G
T
C
G
150
0
150
TTT GCGC CCAT TTT GCGC GCGCGC G
ESC [1]
CC
G
Position
ESC [1]
A T
Position
CEQLOGO 03.12.09 11:44
J E2F1
J YY1
Logo
Logo
G
mm8 E2f1
T
G
CEQLOGO 03.12.09 11:44
CC
G
Position
G A
C
ATATATG AT
C
G TG CA T C AT A T
J E2F1
A G T T G A
T A
G
C
C G
C
Position
CEQLOGO 03.12.09 11:44
CEQLOGO 03.12.09 11:44
U Zfp161 i
150
0
150
0
150
AGGTCA
A
G
G A
mm8 Esrrb ESC [1]
GGG
C Esrrb
T
AGGTCA
A
C
G
G A
GGG T
C Esrrb
18
150
0
150
+11, Opp. 1.75e-04
150
0
150
+1, Opp. 6.45e-03
150
0
150
+3, Same 2.38e-03
150
0
150
+2, Opp. 3.76e-03
150
0
150
-1, Same 9.39e-04
24
0
150
101
C
150
27
24
150
1.63e-04
10
27
mm8 E2f1
-1, Same
18
10
C
150
31
18
C
0
33
31
C
150
150
0
150
+1, Opp. 5.68e-03
101
0
150
150
0
150
-4, Same 4.23e-56
|~}
47
AGGTCA
A
C
G
G A
mm8 Esrrb ESC [1]
GGG T
C Esrrb
CC G
T
GC
G
A
GT T
T AA
T
C
G
AT
TA
G
TC
G
T
G
C
C
A
A
C
150
U Tcfap2a ii
47
0
150
45
AGGTCA
A
C
G
G A
mm8 Esrrb ESC [1]
GGG T
CCCC
CC
G
T
T
T T ATAGG G T A TAG A AG
A
A
G
G
T
C
150
C Esrrb
U Bcl6b ii
CC CGCCC C
A
G
AA T
T
TG
mm8 Klf4 ESC [1]
A
C
A
T
TA
T
U Klf7 i
CCCCC
C
CA
C
A
G AG TT
A
A
A
T
AC T
T
150
U Zfp740 i
0
150
CC CGCCC C
A
G
AA T
T
TG
mm8 Klf4 ESC [1]
A
T
TA
T
CC GG
G
C
A
U Klf7 i
A T
T
A
G
C
TGA
C
C T
C
G
TCCGA GT C
A
GT
AC T
G
150
U Tcfap2c i
0
150
CC CGCCC C
A
G
AA T
T
TG
mm8 Klf4 ESC [1]
A
C
A
T
TA
T
U Klf7 i
GGGGA AT
G
T
J MZF1 1-4
150
0
150
CC CGCCC C
A
G
AA T
T
TG
mm8 Klf4 ESC [1]
A
C
A
T
TA
T
CCC GGGG
CC
CA A A T
TT
G
GG
T TC AGGT CT T A T CA AA T
G
GT
G G
A
AT
C
A
C
A
C
C
A
150
U Klf7 i
U Zic2 i
0
150
CC CGCCC C
A
G
AA T
T
TG
mm8 Klf4 ESC [1]
A
C
A
T
TA
T
A
T G
T
T
C
U Klf7 i
C
G
G
GGAA AA GA
AA AA AG AGGG
GG
CC TC TC
G T
C
T
C
T
C Klf4 a
150
0
150
mm8 NRSFcanon
C T GT CC G T C T G
ESC JohnsonRory
J REST
GG T TC AC
A
A
CG T
CA
G
T
AA
G
T
T
C
G
AC
G A
T CG C TC A
G A
T
C
A
GCGCGC
G
TAC
CG TA
A
C
G
T
T GC
A
C A
G
U E2F2 i
19
T
G
150
0
150
-7, Opp. 2.11e-03
150
0
150
+1, Same 4.35e-07
150
0
150
+1, Opp. 3.62e-05
150
0
150
+1, Opp. 7.28e-04
150
0
150
+1, Same 1.05e-03
34
0
150
8
CT
150
29
34
C
1.02e-04
35
29
C
-1, Opp.
32
35
C
150
36
32
C
0
45
36
C
150
150
0
150
+3, Opp. 9.91e-03
8
0
150
150
0
150
+1, Same 7.89e-03
12
A T
T
C
AA T
GA
mm8 Nanog ESC [1]
CA T T C
GC
G
GA
CC
TC
A G A
G A
G T
C Nanog Loh2
ACA
A AACA C T
TC
G
G TAG C
C
T
C
TT
AG
G
G
C
C G
U Foxk1 ii
150
12
0
150
16
C
CA
T
TT ATGCAAA GT
T TCGCA
A
G
G
C
AA
T
G
T GT T
CA
G
C
TG
ACAAT
A
T
GC
C
C
C
C
G
G
G
C C G A TT
C
mm8 Sox2 ESC [1]
A
T TG G
A
G
A
C Oct4
U Sry ii
150
T
ESC [1]
C
A
G
AC TCGCGA T TCT
AT
mm8 Tcfcp2l1
T
G
C
C A
AAT
C
AG T
T
GA A
A
TG
C Tcfcp2l1
C T
T
G
C
A
G
ACTCGCGA T TC T C
AT
A
AA T
C
AG T
T
GA A
A
T
G
C Tcfcp2l1
150
0
150
T
ESC [1]
C
A
G
AC TCGCGA T TCT
AT
mm8 Tcfcp2l1
T
G
C
C A
AAT
C
AG T
T
GA A
A
TG
C Tcfcp2l1
CTGG
T
G A
A TT
C
CAG
C
TA T
T
G
A
T
G
C
150
J Hand1::Tcfe2a
0
150
T
ESC [1]
C
A
G
AC TCGCGA T TCT
AT
mm8 Tcfcp2l1
T
G
C
C A
AAT
AG T
T
GA A
C A
TG
GGAA
A TG
A
CC
A
A G T
C Tcfcp2l1
T
AT
T
J SPIB
150
0
150
G
C T
mm8 Tcfcp2l1 ESC [1]
T
C
A
G
AC TCGCGA T TCT
AT
C A
AAT
C
AG T
T
GA A
A
TG
G A
GATTA
G
C
C A
C G
C
A
C
C Tcfcp2l1
GGGT
T
T
T ACG
C
G
C
A
T
C
U Tcf1 ii
150
0
150
T
ESC [1]
C
A
G
AC TCGCGA T TCT
AT
mm8 Tcfcp2l1
T
G
C
C A
AAT
C
AG T
T
GA A
A
TG
C Tcfcp2l1
CAGCTG
CAG T
A
G
G C
C
A
A
C
CG
T
TA
T
G
A
A
U Ascl2 i
150
0
150
T
ESC [1]
C
A
G
AC TCGCGA T TCT
AT
mm8 Tcfcp2l1
T
G
C
C A
AAT
AG T
T
GA A
C Tcfcp2l1
C A
TG
GT
CTA TA
A T
T
G C
G
G
A
G
U Hmbox1
20
A
T
T
G
G
C
150
0
150
-5, Same 1.33e-04
150
0
150
+5, Opp. 9.24e-14
150
0
150
-5, Opp. 1.02e-12
150
0
150
-1, Same 9.55e-09
150
0
150
-3, Same 3.16e-06
52
0
150
25
CGC CG
150
33
52
CGC CG
4.75e-03
58
33
CGC CG
-9, Opp.
70
58
CGC CG
150
72
70
CGC CG
0
16
72
CGC CG CGC CG
150
150
0
150
+2, Opp. 4.53e-06
25
0
150
150
0
150
-3, Same 7.07e-06
¢¡ £ ¤¦¥ § ¨ª© «
23
CGC CG T
ESC [1]
C
A
G
AC TCGCGA T TCT
AT
mm8 Tcfcp2l1
T
G
C
C A
AAT
AG T
T
GA A
C A
TG
GATCTA
TA
CG G
C Tcfcp2l1
A
TA
T TC
CG
CA A T
T
G CA
G
G C
150
U Gat4
23
0
150
44
CGC CG G
C T
mm8 Tcfcp2l1 ESC [1]
T
C
A
G
AC TCGCGA T TCT
AT
C A
AAT
C
AG T
T
GA A
A
TG
AAC G
GT
A
TCAT
CT
G
C
A
C Tcfcp2l1
J ovo
150
T
ESC [1]
C
A
G
AC TCGCGA T TCT
AT
mm8 Tcfcp2l1
T
G
C
C A
AAT
C
AG T
T
GA A
A
TG
C Tcfcp2l1
ACTG
C
A
G
T AGA AT TCG CA A A T TG
G C
T
G
CC T T
CT TG
C
C
A
CTG A A
G
G
C
150
U Zbtb3 ii
0
150
T
ESC [1]
C
A
G
AC TCGCGA T TCT
AT
mm8 Tcfcp2l1
T
G
C
C A
AAT
C
AG T
T
GA A
A
TG
CGCCC
TA
A T
AC
G G
C Tcfcp2l1
T
T
A T
U Klf7 ii
150
0
150
T
ESC [1]
C
A
G
AC TCGCGA T TCT
AT
mm8 Tcfcp2l1
T
G
C
C A
AAT
AG T
T
GA A
C A
TG
AACTG C
CC T T
A
G A
C Tcfcp2l1
C
A
A
T TG
C
A
A
AT
150
U Myb ii
0
150
G
C T
mm8 Tcfcp2l1 ESC [1]
T
C
A
G
AC TCGCGA T TCT
AT
C A
AAT
C
AG T
T
GA A
A
TG
A
A
GCT T
G
T
TCCGG
G
T TC
C
C Tcfcp2l1
T
AA
TC
A
AG
G
C
150
U Spdef i
0
150
TTAC C
mm8 nMyc ESC [1]
CGCGCG
CG T
C
C
T AAG
GA
G C
A
G
J Mycn
T
CGG
CT
A
T CG
C
A T GG A A
C
T G A
150
U Rsc30
0
150
mm9 Gata1
GATAA
G1EER4 [2]
U Gata6 i
A T
T
G
A C
T
C G
A T
CAGCTG
CAG T
A
G
G C C
A
A
CG
T
TA
A
U Ascl2 i
21
C T
G A
150
0
150
+1, Same 3.17e-05
150
0
150
-5, Same 2.22e-04
150
0
150
-5, Opp. 1.15e-03
150
0
150
-3, Opp. 4.85e-03
150
0
150
-3, Opp. 5.37e-03
21
0
150
35
C
150
29
21
CACGTG
1.57e-05
29
29
CGC CG
-2, Opp.
26
29
CGC CG
150
49
26
CGC CG
0
44
49
CGC CG
150
150
0
150
-1, Opp. 3.85e-03
35
0
150
150
0
150
-8, Same 1.32e-10
¬® ¯
34
mm9 Gata1
GATAA
G1EER4 [2]
U Gata6 i
A T
C
T
G
A C
T
C G
A T
CTGG
T
G A
A TT
C
CAG
C
TA T
T
G
A
T
G
C
150
J Hand1::Tcfe2a
34
0
150
24
mm9 Gata1
GATAA
G1EER4 [2]
U Gata6 i
A T
C
T
G
A C
T
C CAGCAGG
A
C
T
G
G
A T
A
A
G
G
TA
TC
TGT T
U Zic1 ii
22
T
150
150
0
150
-5, Same 4.73e-08
24
0
150
150
0
150
-3, Opp. 5.78e-04
Supplementary Table 4. Motif database. Summary name, full name, and Sequence logos for all 645 motifs employed in our anlayses. “Summary Name” indicates a short name for the motif employed in the main article. “J” indicates the motif was derived from the JASPAR [20] database. “U” indicates the motif was derived from the Uniprobe [21] database. “C” indicates the motif is a custom-generated motif. Custom generated motifs were created by running MEME [22] on publicly available ChIP-seq datasets (“C CTCF”, “C Esrrb”, “C Klf4”, “C Nfe2”, “C Oct4”, “C Srebp”, “C Stat3”, “C Tcfcp2l1”, “C Zfx”, and “C NFYA”), or by converting consensus sequences taken from the literature into position weight matrices using the iupac2meme tool available in the MEME Suite of tools (http://meme.nbcr.net). Summary Name
Full Name
Seqlogo
C AG GGC
CA
C
GT G
G T AA AG T
C
C CTCF
CTCF
C E-Box
E-Box From JASPAR
T
A
C
AT
GG AT
A
A
T CT
AC
T GGC
T AG
T
C
TG A
CAGGTG GG CA TG AAGGTCA GAT GGGAAT T A
C ETS
ETS factors like fli1
C Ebox
Ebox
C Esrrb
Esrrb
C Gata1
Gata1 Merika et al
C
G
G A
T A
C Ikaros
Ikaros
23
GGG T
CC C CCC G GGG G G AAC G TGCTGA TCA TGCTGA TCA CA T T C CA T T C C ATTA TGCT AGTCA A
A
C KLF-A
KLF-A
T A
G C
C
A
G
C
G
GGAA AA GA
AA A A AG A GGG
GG
T G
CC TC TC
T
T
C
C Klf4 a
KLF4 Shields and Yang 1998
Klf4
G T
T
C
C
T
C GG T T
A
G TA
C Klf4 b
C
CC
T A T TG
T
T
C
C
G
A
A
A
T C C Myb
C NF-E2 a
C NF-E2 b
Myb
NF-E2 Consensus
NF-E2 or AP-1
T C
G C
T C
T C
G C
T C
A
GC
GA
GA
C A
CC T
C Nanog Loh1
Nanog Loh et al
T
A
CC T
C Nanog Loh2
Nanog Loh
T
G A
A G A
G A
A G A
GC
GA
GA
TC
T
GA
C A
G T
TC
T
GA
G T
GGG G CAC C
C Nanog Mitsui
Nanog-Mitsui et al
G
T
AA T
G
C
C Nfe2
Nfe2
24
AC
C
G C
T CA
A
C
T
TC T
A
A
C
G
TTTT AAAA C Oct-Sox
Oct3 Sox2
C
T A
TT ATGCAAA
T TCGCA
A
C Oct4
T A
GT
CA
T
G
GCAT ACA G
G
C
AA
T
G
T GT T
CA
TG
T
G
C
C
C
G
A
Oct4
TT T
AT CGAT AT GCATAAT C
G
C
C
A
C Octamer a
Extended Octamer Loh et al
C
T
G
T
G
GGA
A T
G
C
C
TG
ATGC AAT G T G GA T G A G T T C GG A T A
C Octamer b
Octamer
CTC C
G
T
A
C Srebp
Srebp
A T
A CG C T TA
CG
T
G
G
C Stat3
Stat3
T
T
A AC
C
A
C
G
A
T
Tcfcp2l1
C G T
T G AGC
A
C
C
G
C A
C
A
AAT
G
A
C
AG T
T
GGCCT
A
Zfx
T
AC TCGCGA T TCT GA A
A
TG
GG
G
G CTC
G
C A
T
A TA
C A
G AG AGA G A
GA GT G G G C
C
A T T C AC A A
C Znf263
A
C
G A
C
T AG A
TC
G T
NFYA
25
G
AC
AT G C
C CCTCG G A
AC
T
GT
C
A
C
A
T
G
G
C
Znf263
T CC G T T GG
C NFYA
C
A
T
G
T
G A
T
A
G
T
T
C
CGC CG AT
C Zfx
A
A
C
C Tcfcp2l1
G
A
T GCT
C T A
G
A
T
T
G
T CC A
CC A G A
A
TT
G
J AG
MA0005 Agamous MADS
CCA
T
C
MA0001 AGL3 MADS
T
T
G
AT T
G
AATATA
G
TA
G G C
G
AG
J AGL3
TA
T TA T
T
G
T
T C G C A
AGAT
G
C
C
C
J ARR10
MA0121 ARR10 TRP-CLUSTER
T
A
TA AT
T
C
MA0007 Ar NUCLEAR
J Arnt
MA0004 Arnt bHLH
C
G
T
A
C
T
A GA
GT A
GG
C
J Ar
TT
A
AT ATT G A C GT C CACGTG GCGTG CA
G
MA0110 ATHB5 HOMEO-ZIP
T
A
G
CG
J ATHB-5
T
C
C
C
CC TT
C
T
TC CT A
A
T
G CC AA
G
A
A T
C
C
T
G CA A
G
G
A T
A
G
T
C
TTT
A
G
J Arnt::Ahr
MA0006 Arnt-Ahr bHLH
A
C AC
G
T G
C
MA0133 BRCA1 -
G
T
C T
J CREB1
CA
T
MA0018 CREB1 bZIP
T
T
GT A
C
MA0102 Cebpa bZIP
26
T
T
CGA
T
AG
J Cebpa
A
A
A
T
G
T
C
A
A
TGACG CAA
GCG
G
T
G
T
J BRCA1
C
A
GACG
A
G C
C A
T
C
G
T AT AT T
G A
A A
G
C
CG
C CCG G C C
J Cf2 II
MA0015 CF2-II ZN-FINGER
A
TGCAAT
G T
MA0019 Ddit3-Cebpa bZIP
J Dof2
MA0020 Dof2 ZN-FINGER
T
C
C
C
C
T CAGG
A
CT
C
J Ddit3::Cebpa
A
C
TCG
A
G
T
AAAG AAAG TTT GCGC TCC
C A
T G
CG TC A
G
J Dof3
MA0021 Dof3 ZN-FINGER
G
CC
J E2F1
MA0024 E2F1 E2F TDP
G
T
ACA T
G
TG
J ELF5
MA0136 ELF5 ETS
T
G A
C
C
C
GAA
CG
C
AA
J ELK1
G A
C
T
T TG
G
AG T
MA0028 ELK1 ETS
CCGGAA AGGTC G CC
GT
A
TAC
G T C
J ELK4
MA0076 ELK4 ETS
CA
AC
CC G TT
C
GG
A A
J ESR1
MA0112 ESR1 NUCLEAR
T
A
GG
CG
TAGAT
G GA A C
TA
T
CA
G
C
TCC
C T
A
T
A
T C
G
A
J ETS1
MA0098 ETS1 ETS
27
G T
A
C G T
GGAA ACGTGG
C
CA G A T
J Eip74EF
MA0026 Eip74EF ETS
AT
G A T
C
C G
T
T
A
J EmBP-1
MA0128 EMBP1 bZIP
CC
GAT GAAT A
T GG
J En1
G
G
G
A
GA A GATAA
A
J Evi1
MA0029 Evi1 ZN-FINGER
J FOXC1
MA0032 FOXC1 FORKHEAD
J FOXD1
MA0031 FOXD1 FORKHEAD
C
A C GA T
A
T
A
J FOXL1
MA0033 FOXL1 FORKHEAD
A
G
A
T
T
AA T
G
AG
GA
C
A
ATA
C
G CT
T
C G
C
G TT AG
A
G
C
T
T
A
G
G C
G
MA0042 FOXI1 FORKHEAD
T G
G T CA
C
TA C
T
G
J FOXI1
C
C
GTA GTAAACA GTA ACA TTTT T C A
MA0030 FOXF2 FORKHEAD
G
A
C
A
CT G
T
T GC
GCC
A
T
TGA T A
G A
C
J Fos
T
T
A C
A CT
AT
G C
J FOXF2
C
T CT
G
MA0027 En1 HOMEO
MA0099 Fos bZIP
28
G
CA
CC
CCTA
T
C
A
A
TA T TT T T
J Foxa2
MA0047 Foxa2 FORKHEAD
ATAT
G A T
J Foxd3
MA0041 Foxd3 FORKHEAD
J Foxq1
MA0040 Foxq1 FORKHEAD
G C A
CC
TGT T TTT
C
C
C
AC
GGT C
G
T AC T C
C G G
A
G
A
C A
GTTTA CGGAAG GAT AT T
T
T
AA
G
AC
G
C T
GG CA
A
MA0062 GABPA ETS
J GATA2
MA0036 GATA2 ZN-FINGER
J GATA3
MA0037 GATA3 ZN-FINGER
T
GA
GCG
C
C
J GABPA
C
ACG G ATA
A
T
A T
G
C
C
G
GAT
A G T A T
G
T
G
C G
AAC G C
C T
MA0034 GAMYB TRP-CLUSTER
J Gata1
MA0035 Gata1 ZN-FINGER
J Gfi
MA0038 Gfi ZN-FINGER
J HAT5
MA0008 Athb-1 HOMEO-ZIP
C
C
AAA
G
G
AC
J Gamyb
C
T
A
A
G
T
GAT AATC AATTATT C
G
T A
AC
A
T
C
G
CACA
AA
C T
T
G
C
A
29
TG
AC
G
G
T
C
T
G
GA
TT CG AA
GA
G T
J HLF
A ACT
G
MA0043 HLF bZIP
T
T
GTTG
A
G G
C
CGC
T
CTC
T GG
A
C
G
T
TC T
ACG C TC AC
J HMG-1
MA0044 HMG-1 HMG
A A T
G
J HMG-I/Y
A AA
GGG
TC
G
G
C
A
TT
A
AA
A
MA0046 HNF1A HOMEO
A
C
T
C
T
G
A GC
T
T C
A T
A
AT
G
C
A
G
G
C
T T GGC
G
G A TG A
T
T
C
TC
G
MA0092 Hand1-Tcfe2a bHLH
A TT
C
CAG T
G
A
G
T
C
CT AAA GA A GA A A G GA A
T
C T
A A
MA0109 RUSH1-alfa ZN-FINGER
G A
A
MA0050 IRF1 TRP-CLUSTER
C
G
CA T
MA0051 IRF2 TRP-CLUSTER
T
G
A T
G
T C
G
CGT
A
AA
C A
T C
G CC A T
G
MA0039 Klf4 ZN-FINGER
30
A
T
G
AA
C TA TA
G
G
TA
G
C
C
T
G
G
AAG
AGG GGGAA
T
A
CGC
C
GA
G T
CTCTCCC
J Klf4
C
TC TA
T A AGG AC
CTGG
T
C
TA T
J IRF2
A
G
MA0114 HNF4A NUCLEAR
A
J IRF1
C
A
GA T
GT
G
A
G
J Hltf
A
C
G CAAAG
GT T
C C
J Hand1::Tcfe2a
AA
C G A A CGT CGT G
T
C
GTTAAT TT
T A AA T
J HNF4A
G
MA0045 HMG-IY HMG
G J HNF1A
T G
T
A
T C
C
TAATT A AT A AT T A CACGTG CTATTT TAG ACGTCCG AAAG CACGTGG GGGGA A
A
T
TC
J Lhx3 a
MA0134 Lhx3 HOMEO
CGG
AT
A
TG
T
C AC
C
A
GC T
J Lhx3 b
MA0135 Lhx3 HOMEO
A
TT
G
T TC GA
C
A
G
C A
CT
J MAX
MA0058 MAX bHLH-ZIP
T
A
J MEF2A
MA0052 MEF2A MADS
AT
MA0131 MIZF ZN-FINGER
J MNB1A
MA0053 MNB1A ZN-FINGER
AT
A
AGT
C
ATCTGT T
A
G
C
J MIZF
AA
C C
A
G
C T A
A
A
T
G
G
C
GCA
J MYC::MAX
MA0059 MYC-MAX bHLH-ZIP
J MZF1 1-4
MA0056 MZF1 1-4 ZN-FINGER
T C A
A
T AC
T A TC
AT
G
T
AGGGG
T G
T
AC
J MZF1 5-13
MA0057 MZF1 5-13 ZN-FINGER
A T
MA0118 Macho-1 ZN-FINGER
31
G
A
GG G
G
J Macho-1
A
G A TG
CT
T
G T
C
T
T
C
T
C
T G
A
C
A
G
G
CTGA
CTCCG
T TT G AG ATAA
J Mafb
MA0117 Mafb bZIP
C GTTG
GG A A T
C
J Myb
MA0100 Myb TRP-CLUSTER
J Mycn
MA0104 Mycn bHLH-ZIP
A
G
AA
CTG
A
C A
T
CACGTG CA C G G GGG T CC ATGA TTA GTAA GGGG CCCC CCAAT CAGCTG TTAC C
C
AG G T CT
A A GA
AGA
CG
G
J Myf
MA0055 Myf bHLH
G
A
GA
T
T
CA
J NF-kappaB
MA0061 NF-kappaB REL
J NFE2L1::MafG
MA0089 TCF11-MafG bZIP
C
G
A C TG AT
A
G
A
C T
T A
C
G
T
J NFIL3
MA0025 NFIL3 bZIP
C
C
T
A
GT
A
T
GG
ATT
A
J NFKB1
MA0105 NFKB1 REL
GACT GG
C
AG C G
AG
A
G
C
T
J NFYA
MA0060 NFYA CAAT-BOX
G
C
A
A
T
C
CT
J NHLH1
MA0048 NHLH1 bHLH
32
G
C
A
A
T
CG
G AA
T G A
T
CG T G
C
AAA
T
T AA
A
TACTTA
T G C
TAAG
C
J NKX3-1
MA0124 NKX3-1 HOMEO
G TCA AG TCA A TGA CTTTG AG
A AG
CG TT
C
J NR1H2::RXRA
MA0115 NR1H2-RXRA NUCLEAR
T
CCAACC
A
J NR3C1
G
T
T
T G A
AC
G
A GT C
GGAAC T AT
G C
C
AA
T
AA CG T
A
MA0017 NR2F1 NUCLEAR
G
C
C
GAG
J NR2F1
C
T G
T
T
C TG T CC T A A G A
GA T TG GC A GA CT A
G
C
G
A
T
MA0113 NR3C1 NUCLEAR
AA AGTG TAATT AAAG ATCAATCA T
T
T
GTG
AC
AT
CA
G
J Nkx2-5
MA0063 Nkx2-5 HOMEO
J Nkx3-2
MA0122 Bapx1 HOMEO
C
TA
A
G
GG
C
CT
A T
G
J Nobox
MA0125 Nobox HOMEO
A
GT
G A
G
T
C
C
A
CC
T
G
T
A
C T
G
A
J PBF
MA0064 PBF ZN-FINGER
GC CA
J PBX1
MA0070 PBX1 HOMEO
A
G
J PEND
MA0127 PEND bZIP
33
T
GTG AG CC A ACA
G
T
G
A
T
TTCTTAT
C
T
C
A
T CG
CTG
A
G
G
G
T
C
G
C T A
J PPARG
MA0066 PPARG NUCLEAR
T A GT C A T A C A T
A
G
T
C
T
T
A
MA0065 PPARG-RXRA NUCLEAR
G
C
TCA
CG
CG
T
T
G C
T A
T
A
C
MA0067 Pax2 PAIRED
G
A
AA A T A
T A GC T T TA
C
MA0068 Pax4 PAIRED-HOMEO
G
G
C
GA
GCG
C
C
T CC A
A
A T
G
C
CA
GT T
T ACC
G
GG
C
TA
AA
C
C
A
T
G
A
C
T
CG
C
A
G
G
MA0014 Pax5 PAIRED
MA0069 Pax6 PAIRED
A
T
T
A C C C C CT CA C A TA T
TTA
T
A GT
G
CAGTGA A
T G
AC
G A T
C
A
T
T
T
G
T
T
G
A
TCCG
G
G
G
AT
A
A
C
T
G
C
G
GT
G
A
G
T A
G
A CA
TAG TAT
TCCC
A
C
T
A
GG C
TG
C
CC C
G
G
T AT
C
A
CCA T
G
C
G CC AC A
J Pax6
G
G
AATGT
J Pax5
C
AT
T CA G
G
G
J Pax4
CC A
T
G
T CA
C
J Pax2
T
G TC A A G TC A
GAGA
C
J PPARG::RXRA
T
T
CC
T AG A A
A
T
G
G
GG C
CACACG
A T
A
TAAT AATTA T
C
G
T
G
G
C
A
J Pdx1
MA0132 Pdx1 HOMEO
J Prrx2
MA0075 Prrx2 HOMEO
J REL
MA0101 REL REL
G C
G
T
GG TTCC T
G
CT TG A TCA
A
T
C
TT
MA0107 RELA REL
34
AAA T A
G
C
GGA TTTCC
G
C
J RELA
G
GA
G
A
C
C
C T G T CC G T C T G AGGTCA A TAGGTCA C CC C A A C A CC C TG GGT GGTCA G GTTC GG C
CG T
T T AC
CT A
J REST
MA0138 REST ZN-FINGER
CA
A
T A TA
G
G A
T
AA
T
G T
G
C
AC
T G C TCC A
G A
T
C
G
CA AT
G
G
G C
C
J RORA 1
MA0071 RORA 1 NUCLEAR
A T
T
AT
T
A
GGC
J RORA 2
MA0072 RORA 2 NUCLEAR
G
G
C T
A C CA AC
A A A C CC A
A
T
J RREB1
MA0073 RREB1 ZN-FINGER
T
A
J RUNX1
MA0002 RUNX1 RUNT
TC
C
J RXRA::VDR
MA0074 RXRA-VDR NUCLEAR
TGC
C
T
G
T
T
T
T
C
A
G A
A
G
A TC
MA0077 SOX9 HMG
CGG
J SPI1
MA0080 SPI1 ETS
T
G
T A
TT G T AC
TA
C A
MA0079 SP1 ZN-FINGER
AA
C T
GG G T GGAA GGAA GG
CT
J SP1
G
GC
A
T
CC C C G
J SOX9
TA
CCG
CAAT
A
A T
T A
T
T
G
AA
C
A
AA T A
GA
T
T
AT
G C C
CC
C
A A AC A AG
G
C A
G
C
A TA
A
T
C
C T
A TG
T
A
CC T
J SPIB
MA0081 SPIB ETS
35
T
A
A G
AT
T
CC TATA GG ACAA
GC A
T
AT
A
G G A
C
J SRF
MA0083 SRF MADS
T
T
A
A
C
A
T
AA
T
AA T
T
A
TT
G
G C
J SRY
MA0084 SRY HMG
MA0137 STAT1 Stat
G G
A GA AC ATTGT AACAAT GA A
GA
C
J STAT1
G
A
T
T AC
C
G
CC
GA
G
C G
C T
GT
A TC
J Sox17
MA0078 Sox17 HMG
J Sox5
MA0087 Sox5 HMG
C
T G G T
C
AGGGTA CAGC
GCAT T
J Spz1
A
TT
GA
GTG GAA TAGGTGT AA A CA CTG GA
T
C J Su(H)
GGC TG A
G A
MA0111 Spz1 bHLH-ZIP
MA0085 Su H IPT TIG
CC A
T G A
C
G
JT
MA0009 T T-BOX
A
T
MA0091 TAL1-TCF3 bHLH
A
T
A
36
T
T
T
C
T
C A
G TC
C
ATAAA
G
MA0108 TBP TATA-box
T
G
GA
G
C
J TBP
C
T
C
G
J TAL1::TCF3
G
CT
C
TC
A
T
A T
G
G A
G
C
T
T
CAT CC GCC C T
A
G
T
G
A
J TEAD1
MA0090 TEAD1 TEA
TC AG G T C
A
G
GAG
A C
C
T
TT
C T
G
J TFAP2A
MA0003 TFAP2A AP2
J TGA1A
MA0129 TGA1a bZIP
C
AC
G G C
C TG CA GC AA G ACATG C GGGCATG CACGTG T
ACGT A
CT AGT
AA
T G
CCA
TGGGT T C
T G
A
A
T
C
A
J TLX1::NFIC
MA0119 TLX1-NFIC HOMEO CAAT
C
G A
J TP53
MA0106 TP53 P53
J USF1
MA0093 USF1 bHLH-ZIP
G CT
AAG
T
T
T T AA
AGT A A
T
C
T CG AA
G A
TA
G C
T
TAAT
TG C
C
A
G
T
G
J Ubx
MA0094 Ubx HOMEO
J YY1
MA0095 YY1 ZN-FINGER
J ZEB1
MA0103 ZEB1 ZN-FINGER
CCAT
G A
T
T
ACCT
C
TG
G
G
G
G T
A
T
A
C
CCAC
T
A
A C C G
J ZNF354C
MA0130 ZNF354C ZN-FINGER
37
G
C AG
GCGCACA CTTGA GTGTGCA A
C
J Zfp423
CG GC TGACGT G TGACGTG C A ACA CTA AAC A T AAA A GGG TTT GGG TTCC GT
C
ACC
CCTC TG
CG
MA0123 ABI4 AP2
T
TGG
G A
A
J abi4
T
C
T
A
MA0116 Roaz ZN-FINGER
AA
C A
G
J bZIP910
MA0096 bZIP910 bZIP
A
T A
J bZIP911
MA0097 bZIP911 bZIP
GTC
G
C
TA
T A A TG A T G
G CC T AG
J br Z1
MA0010 Broad-complex 1 ZN-FINGER
J br Z2
MA0011 Broad-complex 2 ZN-FINGER
T
T
A
T
AC
G
C A
T
T
MA0012 Broad-complex 3 ZN-FINGER
TATGAAG
C A
J br Z4
MA0013 Broad-complex 4 ZN-FINGER
G
T
C
T
MA0022 dl 1 REL
G
T
T C
J dl 2
MA0023 Dl 2 REL
38
C
A
T
T
T
G
C
A A
GCT T T T
G
C
G
A
T
CT TTGGA
J dl 1
AA
T G
G
J br Z3
G
GA
ATG
AC
G
A
T
T T
TC
C
C
AT
A
AA T
G C
A
G
GG
T G
C
A T
A
A
T
T AA
CC
CC
CT
T
G C A
G
AA
C
A
CAT
G
G AC
C
A
G
T
J hb
T
MA0049 hb ZN-FINGER
T
AAAA
CTG
T
TG
G
GA
T
C
AC
G
A
MA0120 id1 ZN-FINGER
T
A
AAC GTTT T
MA0054 MYB
C
T
C
A
C
AA
A TG
G G
C
J myb.Ph3
T
TCCA
GG
C
T
G
C
T
AA
A
GC
T C TG C TC T
GG CC
J id1
A
CC
A
C
J ovo
MA0126 ovo ZN-FINGER
AAC G
J sna
MA0086 sna ZN-FINGER
CAGGTG
GT
A T
CA CT T G
C
A
AA
T
G T
A T
J squamosa
GA
CA AATATGA
C
A TGTT T
TA
C
A T
C
GGGGTCA
A
C
T
G
C AC
CG
MA0082 SQUA MADS
C
CG
J usp
MA0016 usp NUCLEAR
G
T
T
TC
G
J znf143
MA0088 Staf ZN-FINGER
U Aft1
GR09 Aft1
A
TC
A
GC A
TTT
G A
C A
T
A
A
A T
39
A
C T
G
C
G
C TGC
C
T
G T A TC A GA C G
C
G
A
G
C
A
T
T
TG A
TA T A
T C
A AG
C
G
C
A
T
Cell08 Alx3 3418
TCA
G
C
G
CA TC C
A
G T
TGCACCC
G A
G
C
U Alx3
G
A CT A T
TC C
TC
GA
T
CA
T
T A
A C
GCT AT
G
T
C
A
G A
G
T
CG A
CC
GA T
U Alx4
A
C
TAATTA
C
G
T
A
T
Cell08 Alx4 1744
A
G
G
T AT A
T A T AA G
CC
AG
T
GA
U Arid3a i
Arid3a pwm primary
U Arid3a ii
Arid3a pwm secondary
G T AC A
A TC
G T
C GT TC C
AT
CA
T
C G
G C G G G C AT A
T
A
AT
A TA T
G C A
TT
U Arid5a i
Arid5a pwm primary
AT
A
T
A T
C
ATACG
A
G CG
T
Arid5a pwm secondary
G
T
T
A
T
C
T A
G
A
G
CT
TC
G C
A
A
G
GR09 Aro80
T
A CG A
GT T
Cell08 Arx 1738
T
U Ascl2 ii
Ascl2 pwm secondary
A
TA
CCC
CCGG GR09 Asg1
40
C
CC GA
A
T
A T
T
A T
C G
C T
G
A
A
CCC T
T ATG A
GC
G
C
A
G
GAAG
A
T
T
C
GG
C A T
CG
T
G TG T
A
ATA
CAGCTG
C
G
T
G
GT
C
A
Ascl2 pwm primary
C
C
G
A
G
G C
U Ascl2 i
CG
TA T AA
CC
C
CAG
U Asg1
G
C A
CTA T
C
U Arx
T
G
C
A G
U Aro80
A
G
CG TCGCG AA
C
U Arid5a ii
G
CA
A
C
C
TT
AA
G
G G
T
G GT
CCGG
T A T A TGGCA T
C
CT
A T CGA G
T
G
A
C
A
A
T
C
A
TGACGTCA
G
CC
U Atf1 i
Atf1 pwm primary
A
T
TA
T
A
A
AA T
A
G
T
C
G
C
CACTTA
C
A AG
GT
C
T
A
G
Cell08 Bapx1 2343
TT
AA
A
T
G
T
T
A
Cell08 Barhl1 2590
A
A
T
C
C
T
G
G
A
A T TA
CA
C
T
T
A
C TG
A
G
G
GC T AC C
U Barhl1
T
G
T
C
AA
CC T
T
A
G
A
Cell08 Barx1 2877
AAT T
C
C
G
Cell08 Barx2 3447
AATT
TT
G
GC
C T
GT
G
GR09 Bas1
U Bbx i
Bbx pwm primary
C
T
C
A
TA
C
A T
C
T
T CG
T
AC
G
G
A
C
T G
A
A
C
T
A
T
A
A CG T
A
GA
C
C
T
AT
G
T
A
TA T T T
T G C
G
C
C
T
C
G
G
C
G
C
C
C
A
G
G
GTTAACA
G CA T
AGCG T A AC
C
GT
C
41
G
TA
GC C
TTC GAA
G
T
C
Bbx pwm secondary
AT A
C GAGTCA
A AG
AA A
G
G
U Bbx ii
T
C
TG
G
A G CA G A
U Bas1
G C
C
C
C
A
A
G
G
CG
G
T AT
A
G
CT
U Barx2
C
G
C
TC
G G
U Barx1
T
T
A
C
Cell08 Barhl2 3868
T
G
GC T GT
TTT
G
A
G
A CA A T T A A
AG AC
C
U Barhl2
T C
Atf1 pwm secondary
C
U Bapx1
T
CT ACG TG T
U Atf1 ii
G
A
TGACG
G
CA T T TGG CG ACCA T
T
CCA
GG
T
C T
G G
C
TT
TC AGGAA G
Bcl6b pwm primary
T
G
C
C
CCCC
CC T
C
C
G
U Bcl6b i
T
T T TC T T TA A A
T CA ACA AG G
G
T
T
T A TAGG G T AT AG A AG
A
T
C
U Bcl6b ii
Bcl6b pwm secondary
U Bhlhb2 i
Bhlhb2 pwm primary
A
G
G
CACGTGA
T
C
G A
A
C
C CG G
T A T GA A
T
GC
CC
A
A G
GAG
T A
T
G
U Bhlhb2 ii
C
Bhlhb2 pwm secondary
T
C
G
AG T
T
U Bsx
A
Cell08 Bsx 3483
A
U Cart1 a
AATT C
TA
C GG A
T
U Cbf1 a
GR09 Cbf1
CT T
T
C
T
T
C
NBT06 Cbf1
42
T
A
C A
T
G
A
C
A
T
T
G
CA C G T G T
A
TA
CCG T
C
T
G
G C
C
AA
C
T
GTAA AA
AA
Cell08 Cdx1 2245
A
C
A
A
GT
GT
TG
C
U Cdx1
G
G
C
C
G
TA
A
A
C
T
TC
G
C
G
T
AA
C
T
G
TT
C
G
A
AGG
TAATTA
AG A
U Cbf1 b
G
CACGTG
G
A
T
TAATTAA
C
G
A
A
C
Cell08 Cart1 1275
C
T
C
U Cart1 b
T
C
C
Cell08 Cart1 0997
T
G
G
G
C
A
T
T
A
G
G
TC
A
T
C TCC
C
T
G
C
CG
T
TA
G
TT
TC
ACT
C
T T
AG
GA
A T
T
TG
C
C
G
A
C
A T AAA
G
TA GAC C A T
U Cdx2
Cell08 Cdx2 4272
C
CAC T T A
GT T A
U Ceh-22
NBT06 Ceh-22
G
U Cep3
G GC TC A
T
C
A
T
A
A
CC
T CC G
A T
A
CA
T
C
C
GR09 Cep3
T A
C
A
G
C
T
C
PNAS08 Cgd2 3490
G T
Cell08 Cphx 3484
T
T
AATC T
AG
C
C
T
C
A
G
C
G
AG
C
A
T
G
G
T
TC
C
G
T
C T
A
A
GC
A
G T
T
T
TC
C
GG
A
T
G CG
A
Cell08 Crx 3485
G
C G
T
C
T C T GA T A A
G
T
A
C
G
A
C
C
U Crx
C
A
C
U Cphx
T
G
GT
G
A
GR09 Cha4
G
AA
GT
A
GCATGC T C GC TGAT ATCA GGAT A ATGTGTCA
C
U Cha4
T
A
A
C T U Cgd2
A
T
GG
T TC
G
T
AT
G
C
GT C
C
G
G
T
CG A
G
T
TCGGAA
T GC
A
T
A
T TC
A T GG
A
G
C
T
G
C C
CA
G C AT T
GG
C
T
A
T
A
T
A
T
AT
G
U Cup9
GR09 Cup9
U Cutl1
Cell08 Cutl1 3494
AAC
C
A T
Cell08 Dbx1 3486
43
A
GT
A TT
A TTA
AT
A
C
G
A
C
AT A
ATT
A AG CC GCC T
T CCGGG G
T
G
AC
CG
C
T GAAC
G
U Dbx1
C
G
TA T TA
G
C
C
T
AT AT A
TG
A C GT
A
C
C
G C
G C
A
AT
TA
C
TA CG C
TCGA
U Dbx2
Cell08 Dbx2 3487
U Dlx1
Cell08 Dlx1 1741
G
AA
G A
T
AT T
TA
GG
A
G
G
A
T
A
A T
U Dlx2
Cell08 Dlx2 2273
A
AA T T A TAATTA TA T A AATT GGATTA G
CT
Cell08 Dlx4 3488
C
A
GCC
G
A
TCT
G T
T
T
A
U Dobox5
Cell08 Dobox5 3493
G A
C
T
C
CCT T
GT
U Duxl
Cell08 Duxl 1286
44
A
C
T
T
TT
C A
T
A
T
C
GA A
A
T
A
C G
C
T
GG A
C
G
G
GCT
T
T
C G TTA T
A
T
A
C G T AG A
AT
GG
C
C
GA
C
Cell08 Dobox4 3956
T
G
AG TACCC
T AT T
U Dobox4
C
A GGATTAA A CA TCAA
T
AG G
T G
G
GA
TG
A
C G
G
C
AA
GT
C A T
G
C
G
C
C C
Cell08 Dmbx1 2277
T
A
C
AA
U Dmbx1
A
G
C
GG
Cell08 Dlx5 3419
C
T
CC T
U Dlx5
A
A
A
A
T
A
GT
C
A
G
G
GCA
T
U Dlx4
C
T A AT C
A
TC
Cell08 Dlx3 1030
T
A
TCG C T
G C
T
G
U Dlx3
C
G
T
C
G C
T
T A AT T A
C
G CC GT T
T
G
A
G
GT
C
T
T
TG
C
GCGCGC
A
G
AC TG
CT A
T GC
CA
C
A
G
U E2F2 i
T
E2F2 pwm primary
G
T
CG
C
AAA
G
U E2F2 ii
E2F2 pwm secondary
U E2F3 i
E2F3 pwm primary
TG AC
CG
T
E2F3 pwm secondary
T
A T
A
G
GGG CGGA
C
G
A
C
G
GR09 Ecm22
A
GC TA T C
T
CG C
G
A
C
A
G
Egr1 pwm primary
A
A
A
G
GC T
C
CC
A TA T
T
G
CG CCC C
C U Egr1 i
C
GTGC
AT
C
C T
U Ecm22
T
C
A
GG CCA
TAC
A
A
A
T
T
C
TC
A
T
G
A
A
T
G
T
G
GC TC
C
U E2F3 ii
C
A
GCGCGC
AG
G
A
GTG T
AT
T
CT A
A
A
G
GG CCA
C
T
T
T
T
G
A
A
TTT
CGG A
C
GG
GA TG GA GA
AG TC
A
A
T
U Egr1 ii
Egr1 pwm secondary
C G A
C
Ehf pwm primary
U Ehf ii
Ehf pwm secondary
AG T
A
G
A T
C
Elf3 pwm primary
45
C
GT
TA
A
T
A T
A
G
GT CG TT
AC
G
GGAA
GGA
C
C
A
A
C
A
A
T
U Elf3 i
A
C
C
G C
GGAA
AAT
T
T
G
G
GA
C
TTCC A
A
T
A
G
A
G
G
C
TT T
A
C
C
A T
C
U Ehf i
T
T
CA
C
A
T
A
G
GT A
CA
C
T
A C
G
G
A
A
G
TC
G
T
T
A
U Elf3 ii
AA
AAA TAAT
CA T T T T
G C
A T
CC T
G
T
A
C
A T
C A GCG A
A
C
G
T
T AA T A
C
G
A G
U Emx2
Cell08 Emx2 3420
U En1
Cell08 En1 3123
C
G
GCT A
GC T
TA
T
C
A
TG
A AC
GG TC
C
C
C
T
G
TG
Cell08 En2 0952
A
GA TT
TA
G
AA
CC
CT
C
T TG
AC
T
C
Eomes pwm primary
T
G
GAC
T
A
CA CA
G
T
G
G
TG
T
A
AT
C
G
G GC
CA
G
ATT A TA T A GGTGTGA
AA
CC GT
U Eomes i
T A
A
G G G
G
Elf3 pwm secondary
C
U En2
C
T TA CC CCC CCC C
GG
G
AGGTGT G C
A
C
GA TT
C
U Eomes ii
Eomes pwm secondary
A
AAGGTCA AGGGGTCA T AA T TA T AA T TA T
G
G G
U Esrra ii
Esrra pwm secondary
A
C
G
A
T
G
T
G A
T
A
Esrra pwm primary
C
A
C
T
C U Esrra i
TT
G
C
G
C
C
AT
C
A
G
A
T
T
A
GT
C
G
C
G
A
C
U Esx1
Cell08 Esx1 3124
C
A T
AG
G
U Evx1
Cell08 Evx1 3952
46
G
A
C
C
C
T
C
TC
A
A
C G
T
T
G
T
G
C
G
A
TC
T GC
C
GA
G
T
TA AT A GACGCA GTAAACAA GTAAACAA GTAAA A GC
T
A
T
C
GG
U Evx2
Cell08 Evx2 2645
U Fkh1
GR09 Fkh1
A
AA
C A T G T
U Fkh2
GR09 Fkh2
A
AC G
G G
T
C
G
A
C
C
AA T T
G
A
U Foxa2 i
Foxa2 pwm primary
U Foxa2 ii
Foxa2 pwm secondary
AA T
C
A T
CG C
T
C
T
A T
CG G
CT A
A
TT
CG G C
A
TAAC TT
G
T
T
C
ACCC
AA
G
T G
G
C
T
A
C
GC T
T
A AT T TT
G
CC
T
C
C
AG
GR09 Fhl1
C
T GGG GGT T
C
T
A
CT
U Fhl1
G
C
CC A AG
AA
G CTG G CT A TC TT G G ACG
C
G C
CT
C
Foxj1 pwm primary
AT
C
C
A
U Foxj1 i
T
TAAACA A
G A
C
T
C
G
C
T
T TT
G
G C
A AACA C
TC
T GTGCAG
G G
T
CAC
G
T
U Foxj1 ii
T
T
C
T
C
A
Foxj3 pwm primary
A
G T
Foxj3 pwm secondary
47
C
T
A T CC
T
AG
C T
T
T
C
G
A T
CC G
G
CA AACA
C
C
U Foxj3 ii
C
TAAACAA
GA U Foxj3 i
G
T
G C
A
Foxj1 pwm secondary
T
A T
A T
C
G
A
T
T AA A
GA CA
ATT
A
G
GGA
A
C
C C
U Foxk1 i
Foxk1 pwm primary
C
Foxk1 pwm secondary
T
G
A
Foxl1 pwm primary
A T
T A
AT T
A
G
U Foxl1 ii
T
T
Foxl1 pwm secondary
T
C
U Gabpa ii
Gabpa pwm secondary
T
T
TCC
AC
AG
G GA
T
T
A
G
G
T
G
G
A
T
G
G
GC T
A
CG G
A
G
C
C
G
T T
48
AC T
A
CA A T T
GR09 Gat4
G
A
C
C
C T GG
U Gat4
A
CG C G CTTATC AGATCTAC TAGATCTA
GR09 Gal4
GR09 Gat3
T
G
T
U Gat3
A
G
CC C C TGA T AA T
G C
A
C
GR09 Gat1
A TC
AC
T
A
GG
U Gat1
A
G
C
T
A
CC T
U Gal4
T
G T C C
G
TG
Gabpa pwm primary
C
G
CCGGAAGT
A
G
A C
U Gabpa i
T
A
TT
CG
AACA
CG
CC T
A
C
C
C G
C
CAAT T
G
G
TT
AG
G
G
TAA CAA
GC
C
G
T
C
AATGA
A T TTA
C G
C
C
G
C
TC
G T AG C
U Foxl1 i
A
TT
CG
A AACA
ACA
G C
U Foxk1 ii
T
T
A
T
A
A
AG
C
T G
T
C
G
T TC
TA
CG
CA A T
T
CA
G
G
C G
A
GATAAG
A T
GG TT
U Gata3 i
Gata3 pwm primary
A T
T
C
A
C
GAT
T
U Gata5 i
Gata5 pwm primary
T
TA
G
GATAA
C
A
T
AT
Gata5 pwm secondary
Gata6 pwm secondary
GATAA T
G
A C
T
G TA C
TC
AT
G AG T
TA
CGCGA
GC GA
C
A
T
C
G A
Gcm1 pwm primary
C
A
A
G
G C
G
A
T
G
C T
G
G
T
G
T
C G
G
T
A
T
G
T
G
CCC
A
CA
A
TG
GT
AA
AC
C
49
GA
A
T
Gcm1 pwm secondary
CT
A
C
C
C
U Gcm1 ii
CA GC
CC
T
U Gcm1 i
T
G
G
G
T
Cell08 Gbx2 3110
G
T
CT T AG T A
GC
GT
C
C
U Gbx2
C
A
AA T A CTAATTAG CCCGCAT ATAGGGG CT
A AC
G
CG T T
Cell08 Gbx1 2883
G
CA TG
G C
U Gbx1
A
C
G
A T
U Gata6 ii
T
A
AT
C
Gata6 pwm primary
A
AC
TT CGA
G G AC
T G
U Gata6 i
G
CG
T
AGATATC
GCT C
U Gata5 ii
G
T
CA G
G A T
CA
AC
G C
G C G
Gata3 pwm secondary
ATC
TC
C
CT TA
U Gata3 ii
A
GGT
C
A
A
CC G
T
G
GA
AC
G
T
C
C
C
CT
T
TG
TGA TCA ACCCCC G
A
G
U Gcn4
GR09 Gcn4
C
T
C
T
A
C
G
C
T
A
Glis2 pwm primary
U Glis2 ii
Glis2 pwm secondary
G
A
TTA
TC
CG
U Glis2 i
T
C
A
G
T
A
TA T T A
AA
G
C
T
G T
C
AAA
T T TC
GGAGG
A
CTGA T ACCGT T
ACCCC
T
U Gln3
C
T GT A
GR09 Gln3
T
AA T
G
Gm397 pwm primary
U Gm397 ii
Gm397 pwm secondary
A
A
C
C
C
A TC T
G
G
T G
T
CG
C A
A
G
A TA
T
C
Gmeb1 pwm primary
CC
CG
C A
T
T
G
C A T GT
G
G
AA
T
C
C
CT CT
C G GC T AT
T GG
AA
C
TCGA T CGA A
G
G A
T A
Gmeb1 pwm secondary
TAATCC T AA T TA T
T
CT
G
C
AC A A
C T CA T
Cell08 Gsc 2327
G A T C
U Gsh2
GT T
G C
G
A
AA
U Gsc
T AC
TCCA
A TG
GG
G T
U Gmeb1 ii
T
C
G
G A A A T
C
TG A
GCACACAC
C
U Gmeb1 i
A
G
GTGCACA
C G
U Gm397 i
T TATC
G
T
A
G
C
G
AC TCC
T
C
G
A
C
T GG
A
G C
G C G
Cell08 Gsh2 3990
50
C
T
T
A
GC T
G
A
C T
TA
G A
GC
TT
CA
TG
A
G
A
G T
C
A
A T
G
U Gsm1
GR09 Gsm1
GR09 Gzf3
U Hal9
GR09 Hal9
T
C
AG
CCT
T
GA
A
T
AT
A
G
G A
CG A
T
A
G
TT
A
G
T
G
T
CCC
TT
U Hbp1 ii
Hbp1 pwm secondary
U Hdx
Cell08 Hdx 3845
ATTGT
A
GAA ACT
T
TG
A
Hic1 pwm primary
T
Hic1 pwm secondary
U Hlx1
Cell08 Hlx1 2350
T
A
C
A
C
A
CT
C
G
A
G
A
T AA T
C TG
A
G
C
T T A T TA A
GGAAG
CA
AC
A
AT
A
CT
T
G
G
T
TGCCC
G A
U Hic1 ii
T
G
G
C
G
TGCCA C
G
U Hic1 i
ATCA
GT
G
C T
CC
G
G G
G
G
G
AA
C
G G
CT
A
G
C
TT TA TG CGA A CA A GA
C
GC A
T
C
A
G
T A CC
G
T AATGAA C
C
CGGA
C
TC
A
Hbp1 pwm primary
A
GT
C
G
GT
C
U Hbp1 i
T
CC A
T
TC
G
CG
C
C G
G
G C
U Gzf3
C GATA G
A CT CGGA
TT
GT
GACT TCCC
G G
A
G
G
TAATTA
CC GC G T
C
A
U Hlxb9
Cell08 Hlxb9 3422
51
C
GTG
CGA
G
G
CT
T
A
C
T
U Hmbox1
Cell08 Hmbox1 2674
G
T
G
T
Cell08 Hmx1 3423
U Hmx2
Cell08 Hmx2 3424
A
A
A
A
GT C
G
T
CT
TC
Cell08 Hmx3 3490
T
A
T
GC
CT T T
A
GC
TA C TGT A
A
A
AA
C
C
A
TC
U Homez
Cell08 Homez 1063
GC
G
C
A
A
T
A
T
A
C C
G C
U Hoxa1
Cell08 Hoxa1 3425
T
GCTCA A
C T
C
C
U Hoxa10
Cell08 Hoxa10 2318
A T
U Hoxa11
Cell08 Hoxa11 2218
52
A
A
G
C
G
A TA AA A
T
A
TT
T T T AG CA
C
CG
G
C
A
A
T
A T
C A
G
TC
TC T A A
C
T
G
T
A T TC
GG
G GA
A
CG
A C
G
G
CCGT
T CC
A
T
T
AT
CC
G
G
G
A
A
A
G
G
T AGC
C GG AAT
A
G
T C
G
TC A T
A
GC
A
G
AA TC
T
G
T
G
AT
G
T
C
A
C
CG
T G
G
T
G
T
G
GT A
CGC
G
C
G
T
C
Hnf4a pwm secondary
T
G TCA AAAGTCCA ATCGTTT TA T A T
U Hnf4a ii
T
AAA
C GG G C
G C
A
GG G
A
Hnf4a pwm primary
T
C
A
CA A T A
GC
CA
U Hnf4a i
A
TG
G
T CTG
CAAT AA
G
GA CT
U Hmx3
GC
T
A GG
A
GC C C
A
G
CAATTAA
AG
A GC CT
U Hmx1
GT
CTA TA
A
G C
A T
C G
T
T
CTCGTAAA GCT A
U Hoxa13
Cell08 Hoxa13 3126
U Hoxa2
Cell08 Hoxa2 3079
U Hoxa3
Cell08 Hoxa3 2783
A GG AC
G T
A
C
TT
C
C
G
A
A
T
T
TA AT A
CC
A
AT
G
TA A T TA
CC
T
G
G
CA
A
G
T
C
Hoxa3 pwm primary
Hoxa3 pwm secondary
U Hoxa4
Cell08 Hoxa4 3426
T
A
C A
C
G
GCA G
T C A TC T
U Hoxa5
Cell08 Hoxa5 3415
U Hoxa6
Cell08 Hoxa6 1040
U Hoxa7 a
Cell08 Hoxa7 2668
C
T
T
T
C
A
G
A
G T
GC A
53
T
CT
G A
A
AT T
A
A
A
GA C T GA
T
A
G
C
C
C A
A
T
G
G
G
T
C
CTG
G
CC
TA A T A T
A
CT A A T
GA T
AG
CT C AC
G
Cell08 Hoxa7 3750
A
G C
G
G
T
AT
C
U Hoxa7 b
C
TT
GA CC
CC A AC T AGT
T
C
TA AT A
G
T TTG
CA
GG
TA T A
T CT
G C
AC
GGG
TA AT T A
C
G
G
TA AT T A
CC
A AGG
GCA T
C
A
C
C
T
CC
G
A
G
G
T
G
C
TC A G A CT T GG
T
T TC
A C T GC A
A
A
G
GGC
A T TA
C
AA A AG
GC
AC
CG
T AA T T A
CC
C
T
U Hoxa3 ii
C
G
G
T
C
A
T
A
C
CA CA G
G
C
C
GT T C T
GG
C G
C
T
U Hoxa3 i
T TA
G G
GT
A
C
T
A
C
T
T
A GGG
GTC C G A
C
A
G
T
C
A
A
GT
C
U Hoxa9
ATAA A
GCC T
G TA G
CAC T
A
AT
Cell08 Hoxa9 2622
A
T TA TA
C TG
T G A
Cell08 Hoxb13 3479
TT
T
G T
A
Cell08 Hoxb3 1720
T
C
GC
G
AA
A
C
T
Cell08 Hoxb4 2627
U Hoxb5
Cell08 Hoxb5 3122
U Hoxb6
Cell08 Hoxb6 3428
T
G
A
TT
G
C
C
T AA T A
CC
TA AT A T
C
A
A
G
A
CC T A
T
U Hoxb7
Cell08 Hoxb7 3953
A T
U Hoxb8
T
C
T
A
T
Cell08 Hoxb9 3413
AT
54
T
C
GGA T
TA
A
T
G
TG
GT
A
CCA G
AC
TA
TC
C
G TCA
T
G
G
T
TT
T
G
TCGTAAA
G
Cell08 Hoxc10 2779
A
G
CC
U Hoxc10
T
A T AAAA
C
A
A
A
C
AT A
C T
U Hoxb9
A
CG
A
G
G
C T
T
A
T
G
AG C TA
G
A
TC
GA G
C
A
T AA T
TC
Cell08 Hoxb8 3780
T
A
GCA T A
C
AG
TA TAC
A
G
T G C
T
C
C
T GC
C
CA
TA A T TA
C
T
G
GG
GC
T AT
G
GGT
CC
AT A TG G
CC
C
GGG
G
AG
C T
A
T
TAATTA
G
C
C
U Hoxb4
T
A
G
C
TC
TG A AA CCC
G
C
U Hoxb3
AT
GG
C CC T G
G
ATAAAA
CCTA U Hoxb13
TT
A
A
T
T
T AA GTCGTAAA CTC TAAA TA T A GTCG A
AA
GT A TG
A
A
G
CC
C C
U Hoxc11
Cell08 Hoxc11 3718
AG
GA
A
C
CC
C
T
T
U Hoxc12
Cell08 Hoxc12 3480
A T
T
T
T
C
A
U Hoxc13
Cell08 Hoxc13 3127
A
C A
A
T
T
T
AA
A
T
C
A
U Hoxc4
Cell08 Hoxc4 3491
U Hoxc5
Cell08 Hoxc5 2630
U Hoxc6
Cell08 Hoxc6 3954
T
C
T
A
GCCC
C A
T
T
T
TC T
G
T TA
CC
T
G
G
G
T A
A A
T
TC
A
T
A
GC T
GG
T
AA
GA T
GC
A
T
T
G C
U Hoxd10
Cell08 Hoxd10 2368
55
G
CA
A
AT
T
C
CT
G
GA T G
G
TA
C
CGA
A A AA
TCT
T
C
TG
A
A
T
T A TA
AC GTCC
C
C
T
TC
C
A
AT A A
A
Cell08 Hoxd1 3448
T
A
AG A
A
U Hoxd1
G
C
GTC T
GAC
Cell08 Hoxc9 2367
A
C
T
G
T
C
U Hoxc9
T
A
AGT
T AA T T A
CC
Cell08 Hoxc8 3429
T
G
G
U Hoxc8
T
C GA
TA
G C
T
G
AT
GGC
G
T
AA C
A
C
T
G
TAATTA
GCT
C
A
T
GC
T
T AA T A
AA T
GG C
A
T
GGC
G
A
C
C
T
A
CC
GGCGC T
T
G
A
A
G
G
A C
T
T
GC
TCA T
TC T AA GTCGTAAA ATAAAA TAATTA G GA A
C
C
U Hoxd11
Cell08 Hoxd11 3873
U Hoxd12
Cell08 Hoxd12 3481
A
C
A
T
A
T
CTA
C
T
T
G
A
U Hoxd13
Cell08 Hoxd13 2356
TG
T
GT
C
A
T
U Hoxd3
Cell08 Hoxd3 1742
TA
A CC T AG T
GT
AC
T
C GC
U Hoxd8
Cell08 Hoxd8 2644
U IRC900814 i
IRC900814 pwm primary
T
T A
GA
T
AA TCGT G
T
T
T
U Ipf1
Cell08 Ipf1 3815
T
A
U Irf3 i
T
C
C
GC
GGCT
AA T
T
A
CT
AG
C
GA
C
TT
G
G
C A
C
A
T
G
C
A
CT
A
C
G
Irf3 pwm primary
AA GG
AG ATT A T
C
G
CCT
T
T CG
T AA C GTG G T G
C C
G
C
U Irf3 ii
T
T TGC
AG
C
T
G
A T
G
AA A A C
G A
G
GT A
TAATTA
G C
T
C
T
A
CC
C
T
AA
G
C
C
GG A
T TA
G
A
C
T
C
C TC
T
C
IRC900814 pwm secondary
T
C
G
AG
GGC
U IRC900814 ii
GG
TCAACA
A A TCA T T AG G
G
C
T
G
GG
G
GT
A
T
T
ACGACAAA
C A
C
T
AT AAT
G C
G
C
T
CC
T AG CA A A GC
T
T
T
CT
G
T
A
A
C
A
C
Irf3 pwm secondary
56
AT
CGAAAC
A
C
TTT C
G
T
A
A
C
U Irf4 i
Irf4 pwm primary
T
A
TCTCG
T AC
AAA C
G
C
G G A
G
U Irf4 ii
T
C
Irf4 pwm secondary
TA T
A
C
U Irf5 i
Irf5 pwm primary
A
T
GAGA
AT
G
T
T
A
Irf6 pwm secondary
AA
T
T
AA T
A A
T
A
G
GG C
Cell08 Irx2 0900
T
A
A C A T GT A T
C
T
Cell08 Irx3 0920
T
U Irx3 b
Cell08 Irx3 2226
T
T
A
T
U Irx4
Cell08 Irx4 2242
57
G
T
C
T
T
A
T
A
T
A
A
C
T
AA
A T
G G
G
C
T
T
T
AA
C
G
G
C
ACATGT
T T TA AA
C
G C
G
C
G
G
G
A
T G
C
C
A
TA
T
A A
C
ACATGTA
C
A
A
A
G C
G
G
TA
TA
G
CA
CT
G
A
ACATGTA
G
U Irx3 a
AA
TT
A G
G
U Irx2
T
GT
C
AGG T
G C A
G
C
A
G
C
TC CG
C A T
CT A
A
C T
T
T
TC
U Irf6 ii
T
CGAAAC
A
G C
Irf6 pwm primary
GC
TAG C
G
Irf5 pwm secondary
U Irf6 i
T
G
A
C
U Irf5 ii
C
T
A
C
T
G C
T
GAAAC
AC
C A TGT
G
A
GT
C
A
A A TG T AG
C
T
G
AT
C
C
AAA
CT T
T GG
G
C
T
A
ACATGT T
G
U Irx5
Cell08 Irx5 2385
T
C
T
A
A
TA T
C
C
U Irx6
ACATGTA T
C
Cell08 Irx6 2623
A
T
T A AA
G
T
U Isgf3g i
A
C
C
G
Isgf3g pwm primary
A
AA
T
U Isgf3g ii
A
A
C
C
A
C
A
T
A G G
ATCTCACA C
A
GG T
Jundm2 pwm primary
A
A T
T
C
T
TA
C
TC
C
AC
C
A
G
AA T
C
T
TG
Klf7 pwm primary
A T
A
Klf7 pwm secondary
58
G
A
T
CC A T
G
G G
A T
C
A
T
G
C T
TA
CGCCC
TA
AC
G G
A
G
A
G
TG
GA CT
Jundm2 pwm secondary
C
G
C
A
TT
AATT G TGACGTCA TGA TCA CC C CCC C
C
A
G
C A
A
Cell08 Isl2 3430
Cell08 Isx 3445
TTA
C A
G G
G
T
U Klf7 ii
TT
A G CT
T
G
A
U Klf7 i
G
C
CT
U Jundm2 ii
A
A
C
A CC
C
U Jundm2 i
C T
G
T
C T TG
T
T
G
U Isx
G C
Isgf3g pwm secondary
C
U Isl2
A
T
TA
CA
C
C
T
A G C
GGT AG
G C
T
G
T
C
A T TGGT T
A A
G
G
G
T
A T
G
C
GAAAC A
AA C T
T
T
G
C
G C
GGT A T A C
A
G
G
G
AT
T A A AC
T
A T
T
T
T
AG C
C
C
A
A
A
G
U Lbx2
T
CC
AA T T A T
Cell08 Lbx2 3869
G
C
A
U Lef1 ii
Lef1 pwm secondary
A
A
T
U Lhx1
Cell08 Lhx1 2240
T
A
T
CT A
AA T T T
T GC
C
G
C
T
G
A AC
Cell08 Lhx3 3431
A
C T
U Lhx4
Cell08 Lhx4 1719
U Lhx5
Cell08 Lhx5 2279
A
C
T
A
G
G
C
GC T
C
T
CG AC A
TC
G
T
U Lhx6 a
Cell08 Lhx6 2272
59
C
CG
A
T
T
G
CCGT GA A GCA C T T
T
G
AC
A
AT
GGT A
CC
A
C G
G
G
T
T
T A TAG
CC
T
GT A
G
G
AT T TA A T TA A T AA T TA A
T
A
A
T
G
GA
CGCG
C
A
G
A
A
G G
AC TC
CG
U Lhx3
A
AT
C
T
T
G
TC
C
CC
TC
A GT T AC
G C
GGA TC
T A
G A A AC
Cell08 Lhx2 0953
T
T
C
G GT
U Lhx2
G
T
A
AA
C
G
G
T
G
C
AC
G T
C
A
C
A
CA
T
AC GCG
GA
G
C
T
G
A
CG T TA A T TA A T AA T T A TTAATTAA T
G
T
T G AGTG A
C
C
T
AAT
ATC T
GR09 Leu3
A
A
C
U Leu3
C
G
G
Lef1 pwm primary
T
CTTTGATC
C
C TT TG
U Lef1 i
A
GG
A
G C
C
A
T
T
A
C
G G
A
CGGT
T
GGC T
C
T
A
A
A T
GC G
C
TC
AA
A
A
C
GT
U Lhx6 b
AT
T A TAG
TCG
G
CG
G
Cell08 Lhx6 3432
AT
C
CGA T
CTA TAGC A
CG
G T
U Lhx8
Cell08 Lhx8 2247
U Lhx9
Cell08 Lhx9 3492
T AC A
CG G
C
A
T
U Lmx1a
T
A
TT
A AC G
U Lmx1b
Cell08 Lmx1b 3433
U Lys14
GR09 Lys14
C A T
A
T
GT
A
TT A TA
G
GA T GCA C
C
U Mafb i
Mafb pwm primary
C G
C
A
T
AA
GT T A T
T AG T
TA
C G
C
T A
A
A
G
G
A
A
TG
C
C
GT
A
CT
C G
AT
GG
G
C
G C
G
G
Cell08 Lmx1a 2238
T TG C
AA
C CA
G
T AC T
C
C
T
TGGT
G
C
AC
A
A
T
A
A
AT T AA T A T T AA T T AA AAATTCCG TGCTGAC
TT
T
A
T
C
T A TA
A TC
CGC CC G G
CG
T
G
C
G
G
C
T
T
T
G T
C
A
A
C
T
T
AG
T
A GA
T
T
A
C
G
A
G
T
C
GCA AAA
TT
A
TGT T T
GGC
T TA
CCT ACG CG G C
G T
U Mafb ii
Mafb pwm secondary
U Mafk i
Mafk pwm primary
C
AA A
A TT T G
G
T
G
G C
C
T
A
AATT T CA
U Mafk ii
Mafk pwm secondary
60
T
CA
C
G
A
G A
G CCC
T A GG
G
CA T
A
T
A
G
G
G
T TGCT
G
TC
T
C
C
AAAA TGCA
AG
G
CT T
G
TGCTGAC
A TC A
C G
C
C
G
AAA
TT
C
ACAAT G
A
A T
A C G
G C T
U Matalpha2
GR09 Matalpha2
U Max i
Max pwm primary
T
CACGTG
A
C CG G A T
TA
AG
T
T
T
T
Max pwm secondary
A T
ACGCGT
G A
AT
T
T
G
C
U Mbp1
GR09 Mbp1
TT
CC
T GA A
C A
A
C
G
U Mcm1
GT
CA
GG
T
G
T
T
A T AT
GGA AT
CC
T
AG A
C GCG
AA
G
CC G
AT
T
T
C
A CTGTCAA C
G G
C T
Cell08 Meis1 2335
A
T
T TA
G
A
C
C
AT TGTGGCG A GAACA GCG G TA T A
G T
A
C
C
Cell08 Meox1 2310
G
C
G
G
C
T
A
T
T
U Mga1
GR09 Mga1
C G
A
A
A
C
GTC A
TGT C
G
G
G
TA
C
A T
AAT
A T GGC TAT
GG
G
GR09 Mig1
61
C
TT
T
A
GR09 Met32
G
CA T G
C
A
G
U Met32
A T
CC C G
A
G C T
U Mig1
A
A
C
G
G
G T
T
C
T
AT
C
A
GCC
A G
AA T
C
A
G
AT
G
A
U Meox1
T TA
ACC
GR09 Mcm1
G
U Meis1
T
A
C
G
C
G
C
CT CG C
G
A
A
T
G
G
CT
CA G
G C
U Max ii
T
A
T AC
CC G
T
A
GTGA A
T
T
T
A
C G
C C GCA C C GCA A CTGTCA CTGTCA TA A T TA CATA AA T T A CGTGTGCA TA
CG
GT A
TA
T
A
U Mig2
GR09 Mig2
C
GR09 Mig3
A
GT A G A CCC
G
C
GA
U Mig3
T
T
T
AC
CT T
AC
A
G
AC GC
GT
A
T
GT
A
A
T
CC
G
T
U Mrg1
Cell08 Mrg1 2246
T
T
A
A
U Mrg2
Cell08 Mrg2 2302
U Msx1
Cell08 Msx1 3031
C
A
AC
G
G
G T
T
T
G
C
T
T AC
G
C
A
C
C
A CT
U Msx2
Cell08 Msx2 3449
C
T
T
A
GA
U Msx3
Cell08 Msx3 3206
U Mtf1 i
Mtf1 pwm primary
U Mtf1 ii
Mtf1 pwm secondary
T
AACCT
T
A
T
C
TA
T
A
A
A
A
G T
A
AC
C
T
A
G
T
T
T
AAA
A
G
T
A
G G G
T
C
G
C
CCGTT
AA
GG
G
T TA
62
G
TT C T AGC TCCA
CT
Myb pwm primary
C
C
A
A
G C
U Myb i
T
A
GC G G
CT
G
A
T
G
C
C
T
A C
C
G
A
A
G
GA
C
A
CC T T
A
C
GC T G T
GGG T
G
C
G
A
G
A
T
TA
A
A
TT
CT
C
G
G
GC
C
C
C
A
G
CG
T
T
GA A
G
C
A
G
C
T
GT A
G
A
CG T
AACTG C AACCGTT AACTG C CA TG
CC T T
A
U Myb ii
Myb pwm secondary
A
GG T
Mybl1 pwm primary
U Mybl1 ii
Mybl1 pwm secondary
TT
A
A
A T
CAG
C
T
AT
G
A
G
C
AA G C
T
C
T
U Myf6 i
Myf6 pwm primary
T
A
T
T C AC
CAG
AC T A
CG T
U Myf6 ii
G
CC A
C
GT CG
T
CC
T
T
C AC A A A A
GCA
GA T
A
T
TG
A
G
GR09 Ndt80
T
TG
GA
G
TA
T
T A TA TA
G
A
T A TA TA TG
C
ACT
C
TA
C
C
G
CTA
C G
G C
C
U Nhp6a
AA T AGGA T
A
Myf6 pwm secondary
C
U Ndt80
T
G
C
A
G
ACTGACGGG
G
T
C
G
GG
A
C
A
C
T
AT
CG
G
CC
A
T TG
A
A
T
U Mybl1 i
C
C
A
G
G
GR09 Nhp6a
T
AAT
TA
T
TAT ATA
AT A
TA
TA TAT A T AG
C T CC GC GGG CC C GC A
G
U Nhp6b
T
TG
T
C
G
Cell08 Nkx1-1 3856
AC T
Cell08 Nkx1-2 3214
63
T
C
GT
C
U Nkx1-2
C
A
G
AA T A
CCC
G
CA T AC A G A
G
U Nkx1-1
CG
G G T
C C C
GR09 Nhp6b
A
TA
T GGCG
G
AA T TA
A
C T
GGT
CT A G
A
G
C
T
A
C
T A
G
C
C
G
A T
A
CT G T
C
A
CACTTGA
C
A AG G
G
CT
U Nkx2-2
TT
A
Cell08 Nkx2-2 2823
TC
A
U Nkx2-3
Cell08 Nkx2-3 3435
U Nkx2-4
Cell08 Nkx2-4 3074
A
GC
G
CC A
G A
A
Cell08 Nkx2-5 3436
T
GT
T
A
T TT
A CA T
GA C A
U Nkx2-9
G
G
AA
T AC
A TT T
A
G
CG
C
TT
T
G
AA
C
C
C
GA
GC CG
C
T
U Nkx3-1
Cell08 Nkx3-1 2923
A
G A
T
U Nkx3-1 i
Nkx3-1 pwm primary
U Nkx3-1 ii
Nkx3-1 pwm secondary
T
A
TT
C
G
G
G
CTGA
C
G
TA
T
CTC
G
A
G C
ACTTA
CC
A
G C
G
C A ACC
G
A A T A T T AA
GG
A
C
AGTACTT A
G T
Cell08 Nkx2-9 3082
T
A AT
TGACC
GT
C
A
G
G
C
C
GCC A
GC
C
G
A
Cell08 Nkx2-6 3437
A
C
T TA
A
T
G
G
G
G T
G
C
G
CT
A
CA TC
A
G
G T
AC T A
TT
G
T
U Nkx2-6
A
A
CAG
C
G
T CCACT A A CCACT A
G C
U Nkx2-5
CG
C
T T
A
G
CC
GC
G
AG
G
A
GT
CT
AA TA T T
T TG
C TC
CA
A
A T
CTG C
GTAC
A
A
TT
GG
CC
TCG A
CT AA T TAG
TA
AC
AC
G
G G
G
C
U Nkx6-1
Cell08 Nkx6-1 2825
64
AT
AT T T A
CT T
T
A
GG
C T
TG
TC
C A
T
G A
G
A T
C
AT
U Nkx6-3
T AA T T A
TAC
Cell08 Nkx6-3 3446
T
GG
C
C
G
G
A
G
A
T
A
GGTCA GGGTCA AGGGTCC TA CCG GGGATTA GGGAT A GGATTA GGGATTAA T GGAT AA T AAA
GG
T
G
U Nr2f2 i
Nr2f2 pwm primary
G
T
TG
C
C C T
GA
G
G
T
T
U Nr2f2 ii
Nr2f2 pwm secondary
C A T
U Nrg1
GR09 Nrg1
A
AT
G
TA
A
A
T
C
G
T
U Oaf1
GR09 Oaf1
U Obox1
Cell08 Obox1 3970
G
T
T
T
G
GA A
A
G
A
T
T
AC
T
U Obox5 a
Cell08 Obox5 2284
A
A
TA TA A
A
A
A T
U Obox5 b
Cell08 Obox5 3963
T
65
G
G
AC
T
T
T
T TA A
GT
AG
GA T
A
T
G
G
T
AC TA
C
G
G
CC T
C
TGT G
C
C
G
G
A
TC
A
G
T
TA
GT
C
G
ATT
Cell08 Obox3 3439
T
C
A
GAA
C
U Obox3
G
G
T
T
C
Cell08 Obox2 3438
T
C
A
AA T
CC
U Obox2
T
C
G
AAA
G
CC T
A
C
C
G
G
C
G
TT
TT
T
C
AA
C
A
A
C
G
G
G
AA
A
GT
C
U Obox6
A
G
A
T
C
A T
NBT06 Oct-1
A
C
A
CT
T
C
TA
C
Cell08 Og2x 3719
G
T
TA
T
C
GA
C
Osr1 pwm primary
G
CTAC
G A
T
A
T
G
CTA
TAG
CTA
T
C
G
G A
T
C
G A
T
C C
G
Osr1 pwm secondary
C GTAGC
AA
G
C T
G
U Osr2 i
A T
G
CAGTAGC
A
C
U Osr1 ii
T
A
G
G
G
C
T A
TG
AA T T A
TC
G
T A
T
T TGCA A
C
CA
T
G
U Osr1 i
AA T
A
C
C
U Og2x
T
Cell08 Obox6 3440
T
U Oct-1
G
G
CG
G
GGAT A
C A
TC
T G
Osr2 pwm primary
G
C T AC
G
A
G
T
TA
TCGC AT C
C
T
A
T
A
A
T
G T AG
CTA T G A
CC
A
G
U Osr2 ii
Osr2 pwm secondary
A
T T A T TA A
GC
C
U Otp
Cell08 Otp 3496
G
A
C
T
U Otx1
AA
Cell08 Otx1 2325
C
A
Cell08 Otx2 3441
66
AT
TCT A T GA
C
G
G
GGATTAA A
C
U Otx2
T
A C
A
A
G
A
GA C
G T
G G
GGATTA
GG C
T
GC
C
T
GC
C
A
A
TT
G A
CATGCA GGTGCAC TA T A
TG
CA
U PF14
PNAS08 PF14 0633
G
T
G
A
AA GCG TG
C A
U PFF0200c
T
C
PNAS08 PFF0200c
T A
C
A T
G
Cell08 Pax4 3989
T
T
T AC
CGC G
GA
A T
U Pax6
C
A
T
AAT T
G
C
GR09 Pbf1
C
GA TT
TCATCG
C
G
T
G
C
A
CT
C A TG
T TG
CATCG
C
GR09 Pbf2
A
A TG
C
A
A
TGT A
ATCAA
C
CTCCAG T
T AGT
G
G
A
T
G
T
A
A
G A
C T
GR09 Phd1
67
GG A
T
AA
A
CG
A
G T
T
CA
A T
G
G
A
A
C
C
GC
A
T
TGCAT A
G
C
A
T
A G
G
C
G
C
T GC
A
T
GC T C
G
C
G
G
TTC GAA
AAT
G CC
T
TA
C T
C
G
TC G G
AA
C
GG
GT
U Phd1
C
G
G
T
A
GR09 Pdr1
TT
AA
C
TA
G
U Pdr1
A
TGGG
G C
TC
Cell08 Pbx1 3203
A
GT C
C
A
G
U Pbx1
G
AATTA
C
U Pbf2
C
C
TAG
T
AA
U Pbf1
T
A
T A
A
C TCG
Cell08 Pax7 3783
AC
G
Cell08 Pax6 3838
U Pax7
T
G
G
C
T
A
C
G
C
A
G
C
G
U Pax4
T
GA A
TTA
A
C GA T
T G
G
G
C
T
T A A
C
A
G
T A
A C
C
C
GG C
G
G
T
A T
AT T
U Pho2
T AA T TA
A T TA AT
C
G
G
A
CA
C
T
CACGTG
G
C
GR09 Pho4
C
TA A T TA
T AC
G
A
T
Cell08 Phox2a 3947
G
T
G
C GAC
G
U Phox2b
Cell08 Phox2b 3948
G
G
G
T
C T
A
A
GGATTA
G
A
GAA T
Cell08 Pitx1 2312
U Pitx2
Cell08 Pitx2 2274
T
A
T A
T
Cell08 Pitx3 3497
G AT A A CTGTCA CTGTCA C
GG T
G
A
C
T
C G
T AA
T
T
T
T
A
Cell08 Pknox1 2364
A
AC
T
A
A
G
TA
C
Cell08 Pknox2 3077
T
A
A
C
A
GC
C
G
G C A GT
G
AC
GG
C
GG C
A
A
C
CG
G
U Pknox2
TG
C
G
G
GCA
T
TG
C
C T CA
U Pknox1
C
TT
C
A
C
U Pitx3
A
GGATTAA
G A
A
T
A
A
U Plagl1 i
Plagl1 pwm primary
68
GC
T
A
T
TA
CC G G
AT
CA
TC
G
G G
GG CG CC
C
T
TGA
C
TC
U Pitx1
T
G
T
T AA T T AA
AAC
C T
T
GAC
C
C
G
T
TA
G
A
U Phox2a
C
G
T
G
TC
GR09 Pho2
CA
U Pho4
G
TG GA
C
G
C
A
T
C
AT T
A
G
GGGGTAC
G
G
C
AA TT
C
U Plagl1 ii
Plagl1 pwm secondary
U Pou1f1
Cell08 Pou1f1 3818
U Pou2f1
Cell08 Pou2f1 3081
T
AA
A
C
G
G
T
A
T
A
Cell08 Pou2f3 3986
U Pou3f1
Cell08 Pou3f1 3819
T
A
G
GT
A
TGAC C
C
TA
A
GTGGA T
C
T
T
CG
C
G
A
ATGCAAAT ATGCAAAT TT
C
C
TT
G
T
AT
T
G
U Pou2f3
T
T
G C
C G
C
C
Cell08 Pou2f2 3748
A
T AA T T A
CA
U Pou2f2
T
T
T T AA T T A
GC T A T C
A GA T
C
A
AA
GC
T
T
T
T
T
T TA A T TA A
A
G
T
A
G
A
G C
G
C
AA T
U Pou3f2
Cell08 Pou3f2 2824
A T
A
C
T
G
G
U Pou3f3
Cell08 Pou3f3 3235
U Pou3f4
Cell08 Pou3f4 3773
TA
A
C
ATT
G G
T TA
G A
Cell08 Pou4f3 2791
69
A
A
T
TT
A
A
G
T
A
A
A
T
G
G
C
C
T AA T T A
AT
GT
T
G A
AC
G C
C C
G
C
T
A
C
AT A T A
CT
U Pou4f3
A
A
C
A
TGCATA
AA T
GC C
C
T
AC C T
G G
T
T
C
A
CT
G
A
C
G
C
A
T
G G
T
T AA T T A
C
TC
GT
G C
T
GCG
A TC A A T TGA TC
C
T
T
A
GTC
C T
T TC A
G A
A
C A
TAAT AG TAATGAG T TA A T AA TA T A TA T A GT
A T
C
U Pou6f1 a
Cell08 Pou6f1 1731
A
T
A
A
U Pou6f1 b
Cell08 Pou6f1 3733
U Prop1
Cell08 Prop1 3949
T
C
G
TC
A
T
U Put3
GR09 Put3
A
T
TC
T
AG
T
C
A
A
G
NBT06 Rap1
U Rara i
Rara pwm primary
C
GCAA C
T
T
T
AG A
A
G
C
T
T
A
C
C
T
C
CT
C
TA
G
C
C
AG
A
TA
G
T
C T
GA
T
G
GGGTCA
CG TC
T
A
C
A
TG
CC
GG
TTA A
T
C
G
TA
70
G
T
G TCA
A
Rara pwm secondary
T
A A AG T
GG
T
G
GCT
CC C GT T G
AAA G
G
U Rara ii
CCG
A
GG
A
G
C
C
A
CC ACACCC
TA CG T
T A AC T TA
G
U Rap1 b
C
GGTGTAC
G GR09 Rap1
G
TC GG
A T
GG CA
T
T
C
AC
G
GA
A
T
U Rap1 a
A
GC
G A
C
T
G
T
T
G
C
C
A G
C
T
C A
A
T GC
G
C
C
A
G
Cell08 Prrx2 3072
T
T
G
A
C
G
U Prrx2
C
A
T
AC
A GT
Cell08 Prrx1 3442
A
G
GT
U Prrx1
T
G
A CC
TT
G
C
C
T
A
T
T
C
T
G A CC
T
T
TT
A
G
T
G
GT
C
AT GCGGA A
TG A CC T
C
A
G
G
AA
G C
U Rax
Cell08 Rax 3443
C T
T AG
C
TC
GA T
A
T
G
T
C
G
U Rdr1
GR09 Rdr1
U Rds1
GR09 Rds1
G
TA
A
TC
A
C
G
C
G
G C
G
C
C
T
C GC G A CCGA C TAGCAAC
TG CA
G
C
A
C
G
CG
G
G
G AT
A
C
C
C
G
C
A
C
A
A T
GGT T TC
T
C
C G C
T
G
G
C
G
U Rds2
GR09 Rds2
U Rfx3 i
Rfx3 pwm primary
T
C A
CG C
G
A
T
CT
C G
G
T
Rfx3 pwm secondary
A
C TGGATT C GA A
T CC
A
G
C
T
T
A
A GT
C
G
G
A
G
G
G A AG
C
A TG
C T
Rfx4 pwm primary
TG
C TAGCAAC
C
U Rfx4 i
A
C
A
A
T
T
T
T
TG
GC A
U Rfx3 ii
G
G
G
C
C
T
A
A T
C T GTTAC A
G A
A
G C T
G
A
A
U Rfx4 ii
Rfx4 pwm secondary
U Rfxdc2 i
Rfxdc2 pwm primary
G
C TAGCA G
CG
A
T
C
G
A
Rfxdc2 pwm secondary
71
T
AC
G
A
T
A
G AC T
C
C
G
C
G
TGA ATGT
C
TT A
U Rfxdc2 ii
T
G
C
A
T
G
C
T
G
A
A
CGGA AA AA
C T
A
T
U Rgt1
GR09 Rgt1
T
G
T
T
T
Cell08 Rhox11 2205
A
T
A
C
T
G
A CC A
C
A T
C
T
GR09 Rpn4
T GC A
A
A
TA
T
AC
GT
A C
T
T
A
GR09 Rtg3
T
A T
C
C
T
C
G
C
T
A
CACGTG A
G
G
TA
G
AT
C
T
T
C
A
A
T A
G
G T
A
C
C
TCG
A TGG A A
C
T G
C
CA
C
T
T
G
TC
A
T
T
TA
CG
C
G
T
A
C
TGACCCC
CA
U Rxra i
C
G C
A
CGG
CT
G
AT
G C
T
C
GA
G C
A
GGA
A
CGCG
CG
GG GC TA
CC
G
T
T A AG
G
U Rtg3
G
TA
A
CGCGCG
CG GR09 Rsc30
T
T
A
GR09 Rsc3
U Rsc30
A
A GGG
G
C
G
T
T
T
T
C
C G
G
GC A
C
T
CA
U Rsc3
AT
GC
GT
CGCCACCC
C
A
C
C
G T
T
CCGG
C
C
A
TT
TT G
AA T AA
G G C
U Rpn4
C
G
C
T AA T TA
A
A
TT
C
G
T
G
Cell08 Rhox6 4251
GR09 Rph1
T
A
AC
G
U Rph1
T
G
T
AA G
U Rhox6
T
A
A
GCTGTAA
C
U Rhox11 b
A
AC
A
G
C
G
Cell08 Rhox11 1765
TT
TC
GCTGT A
AA
A
U Rhox11 a
G
C
A G C
T
CT
G
G
C
C
G
Rxra pwm primary
72
A
TT
G
GA
C
T
U Rxra ii
C
A
TA
GA G
A
A
G
GR09 Sfl1
A
A
G T
A
A
TG
C
G
A
T
T
GCT G
C
G
A
AG A
G
GR09 Sfp1
T
Sfpi1 pwm primary
T AA T T A
G T
GGAA T G
A
T
C
T
C
A
A
G
GGAA
TC AA TC
C A
C
G CC
C
C
C
C
GT T
A
G
A
G T
C G
Sfpi1 pwm secondary
T
TAATTA
A
C
C
Cell08 Shox2 2641
T
T
C T
G
G
G C TA
A
C
C
G
T
A
T
G
T
A
TCCGGA
C C T A G
C
GR09 Sip4
U Six1
Cell08 Six1 0935
U Six2
Cell08 Six2 2307
C
A
T
T
A
A TGA T GA
C
A
C
G
A
T
TA
TA
T
C
Cell08 Six3 1732
73
T
GG
T
C
C
A
GC T
C GG
T C
ATCA GGGTATCA GGGTATCA
GGT
G
G A AC
C
C
T
A
GG
A
GG
A
GG
GC AC T
G A
U Six3
T
ACCA TC
CA G C
C
T T AG
U Sip4
A T
C
G
C
AA A T T T T
C T GG
AAGA
U Shox2
A T
G
C
A
GGCCA
U Sfpi1 ii
T
GT C T A T TC CT
C
TG
C
T
U Sfpi1 i
G C
A
AA A
GCC T G
U Sfp1
C
CA
Rxra pwm secondary
C
U Sfl1
C
C
T
C
C
G
T
AG T
G G A T TATGTA
C
AGA
GA T
GT T
C A
T
T A C
T
G A
C
C
GT
C T
A
G
C
G
C
A
T
T
A
T
A
C G
T A
G C
T
G A C
T
G C A
A T
TGACACC T
C C
T
C
A
G
A
G
U Six4
Cell08 Six4 2860
A T
U Six6
Cell08 Six6 2267
U Six6 i
Six6 pwm primary
T
GGTA CA
G
T
A
A
CC
GG
T
A
A
T
T TG C
C
CA
A
TATCA
C
TG
U Six6 ii
CA
T
G
U Skn7
GR09 Skn7
U Smad3 i
Smad3 pwm primary
G
C
C
A
T
C
C
GCC
TG
T A GC
GA T
G
C
C
T
CC A
C
T
G
G
C
T
Six6 pwm secondary
G A
TA
CG
G C CAC
C
T
T
AT A T
G
G
C A
G
GG
TA
T
A
A
TT
CC
A
GGG
C
T
T
A
A
A
TC
A
A T GC T T A C GT G
AG
A
C
GT
G
G
C
A
AGAC
CC
A
T TC
G
G
C
G
A
T
CGCC
CC
C TG T
A
C
C
GAGATAT
A
U Smad3 ii
Smad3 pwm secondary
A CC
T
T T AC
GG C
U Smp1
A
A
C
G
T
G
T
T
AT
A TAAA
CC T AGG
T AT A T
G
G
G C
G
C
AT
C
G
A
A T
G T
T
C
C
C
G
ACAAAG
G
T AAA
AG
TCT
Sox11 pwm primary
TT
G
C
74
T
AAT
A
G C
C
T
Sox11 pwm secondary
G
C
C
AA GT
G
U Sox11 ii
T
G
GR09 Smp1
G
U Sox11 i
G
T
AT
G
C A
G
TA T
C A
C
G
U Sox12 i
Sox12 pwm primary
ATTGTT T
A
T
A
A CCC
A
AA
T
C
A
G
G
A AAA
G
G
AG C
A
G
C GCCT TGTC A AG GC TT G
T
C
U Sox12 ii
C C C TG T T
G
T
Sox12 pwm secondary
A T
A AAT
AC
GG
T GA
T
C
C
U Sox13 i
A
T
TT
GA
Sox13 pwm primary
A
TA
T
T T TA
A AC C
G
CG
A
G
C
G
C
GGGTGGG
T T TA ACT T
C A
A
U Sox13 ii
T
C
AC
C
G
C
Sox13 pwm secondary
A
ATTATAAT AGCTT
T TA
C
CG
G
U Sox14 i
Sox14 pwm primary
U Sox14 ii
Sox14 pwm secondary
ACAAT
AC
G G A
A
GG
C C
T
G
T
G
A
T
C
ACAAT
A
TT
AC
Sox15 pwm primary
AA
T
T
A
G
A
T ACGGC
A
G
G
T T AC T T T A A G G
C C T
A
G
U Sox15 ii
Sox15 pwm secondary
U Sox17 i
Sox17 pwm primary
C C
A
TT
C
G
AAC
AG
GT TC
T
A
C
TG ATT
GCC C
T
A
GG TT
A
G
C
CA TG
U Sox15 i
A
A TCT A A
C
C G
AA T
GT
T
T
A
T A A TA
GC G G
A
C
C
C
G
ATTCA
C
T
AG T TCAG C C
G
G G
C A T
G A
U Sox17 ii
Sox17 pwm secondary
75
C G
TA
A
ATTGTT
C TT
U Sox18 i
Sox18 pwm primary
U Sox18 ii
Sox18 pwm secondary
U Sox1 i
Sox1 pwm primary
T
AAA
A
C
A AC
C
C
G
G
T
AT
TGA
G
TCA
CGTG CACG TA T GTG
A
AC
C
C G
ATT A T C
A
A
T TAAGT TA
C
CC
C C G C A G
T A A
G
G G
C
T
TTGTT
A
CTGCC CGGC A ACTA
U Sox1 ii
Sox1 pwm secondary
CG
A
C
G
G G G C
T
A
T
ATTATAAT TA
T AGCT TAA TA
G
C
C G G
C
G
U Sox21 i
Sox21 pwm primary
U Sox21 ii
Sox21 pwm secondary
G C
C
ATTGT
A
A
C A C
G
G T
C
T
U Sox30 i
Sox30 pwm primary
U Sox30 ii
Sox30 pwm secondary
G
ACAAT
A
G
T
C
A
T
C
TA
AT AT AT
CACCGGTG GT ACC
TG
A
GC TG
CA
G
G
C
ACAAAG
A
G
TAA
G
C
Sox4 pwm primary
C
T
ATTGT
A
G
G
Sox4 pwm secondary
76
G
T
AAC
C A
TT
U Sox4 ii
C A
G
G
T
G
U Sox4 i
G
G
A TA
T
TA
CC
TC
G CAC GT
T TC
CG
C
A
C
G
A AAT
AC
GG A T
T C
C
U Sox5 i
Sox5 pwm primary
C
T
A
TAATT
A
TAGCTAC
C
G
GT AGCGA C
U Sox5 ii
Sox5 pwm secondary
U Sox7 i
Sox7 pwm primary
A
ACA T
AG
G
T TT
C
GT
A
G A T GC
U Sox7 ii
T
C
G
C
GC G
T
AA T
A
T
A
AA
C
T
T
G
G
G
TG
CC G
C
C A
ATTGT
T
T
U Sox8 i
Sox8 pwm primary
U Sox8 ii
Sox8 pwm secondary
AA
ATTCA T
G
A
C
T
C
A
T
T
G
C
A
G CG
C T
A
AA
C
AA
G
T
G
C
C
G
CGCCCCC
77
T
GG G
ATC A
G
A C TG C
C
Sp4 pwm secondary
A T
A G
A TT
G G
U Sp4 ii
T
A
Sp4 pwm primary
C
T
G
G
C C A T
TA
CC
G
TG C AC
C
G
G
T
T
G
TTT
A ACA A
Sp100 pwm secondary
G
C T
C
Sp100 pwm primary
T
T
T
G
CT
C
C
G
A
C
A
C
A
CG A
T
AAA
G G
A
G
TG
TGGA
A
C G C G
T
C
CTCAC
C
U Sp4 i
C
A
G
A
A G
U Sp100 ii
T
C
Sox7 pwm secondary
C
U Sp100 i
A T
T
T
C
CC G
T
A
A
T
A T T GT
CTCT A
TA
CG A
GA
AT
T
G
A
G
G
C
T
AG
T
A
C T
GA
T
T
G
GT
T
C
T TA
C C
C
C
G
A
A
GCT T
G
T
TCCGG
G
TT
C
U Spdef i
Spdef pwm primary
A
A
C
T
T
G
U Spdef ii
Spdef pwm secondary
U Spt15
GR09 Spt15
A T
G
CC
C
AA
A T A T A TA
T
CGG
T
GT T TA
C
A TG
G
AT
A
C
G
TCCTA
A TG
G
C
G C
C
C
GTG C A
T
A
T
A
GR09 Srd1
A
G
C
A
T
C G
A T
TA AA T A T A
TT
G
U Srf ii
Srf pwm secondary
U Sry i
Sry pwm primary
U Sry ii
Sry pwm secondary
G C
C
G
AAA
T
C
A
CC TATA GG Srf pwm primary
G
C
GATCTAC A
U Srf i
T
TA
G
A
G
U Srd1
T
AA
TC
A
AG
C
A
C
T
T
A
G
C
AAAA
A
AGCCCTCCC
GT
GGTCT T T
T
G G G
CT T
C
ATTATAAT T
AAG CT T
A
ACAAT
A
GC
T G AGTG
A
C
G C
G
C
C
G AT T
C
G T
U Stb3
C
A
A
G
A
AAT
AAT
C
T TCT T
C
T
A
GGG
GR09 Stb3
T T T TCA
AA
G
CC
C
G
A
G
GG
CT
TG
AA
G
C
G
GC CC CTA
GA A
C T
U Stp2
GR09 Stp2
78
T
T
A
GG
T
G T
C
AC G
GTGAC
C
A
A
A
GT
T
A
U Stp4
T
C
T
G
A
A
C
G CC
T
A
GGCTG A
CC
GT
A
G
A
T
G
GR09 Stp4
AAATTAATTT T
T AT AA
A
AACTCCGA
GT T
GR09 Sut2
T
A
GR09 Tbf1
T
A
G
TA
T A TA T
A
C
CT C T
T
C G
Tbp pwm primary
GT
A
G
TT G
A AAAC CT
G
C
G
C
A T
T C T GT
G
C
G
A
G
C
C
A
A
A
G
Tbp pwm secondary
CG ATC G
C
G
C A T
GR09 Tbs1
TA
U Tcf1 i
Tcf1 pwm primary
T
T
G A
C A
T
T
T
T
A
A
CG A
C
TG T
G
TA A
C
G
GG
A
T
AG
C
C
T
GATTA
G
G
T
T
G
T
C A
C G
C
C
C
A
CA
C
A
G
G
G
AA A
GT C
A
C
T
A
G
A
G
T
G
79
A
A
C
Tcf1 pwm secondary
C
C
A
GT C
T
G
G
T A AC T T A AC
GT
T
Cell08 Tcf1 2666
A
G C
G
U Tcf1
T
CG
T
C
U Tcf1 ii
G
G
C
A TA TA TA TA
CGGA T
U Tbs1
T
C
T
A
C
U Tbp ii
G
AACCCTAA
G
A
G
T
C
C
U Tbp i
GA
G
T
CT
U Tbf1
T A
C
GR09 Sum1
C
U Sut2
T
G
G
U Sum1
A
CC
GGGT
T
T ACG
C A
C
C
TAAC
GT TA A T
A
CC
U Tcf2
Cell08 Tcf2 0913
T
T
Tcf3 pwm primary
U Tcf3 ii
Tcf3 pwm secondary
T
C
G
G
TA
A
AGG
TCAC C
G
TG
T
T
T
AAA
AC
G
T
C
C
T
T
TG T
G
T AAA
AC G
G AC T
G C
Tcf7 pwm secondary
T
T CTG C C G C
C
U Tcf7 ii
T
T
G
A
Tcf7 pwm primary
C
C
T AAA
AAT
T
G C
C
C
G
AA AA T
G
U Tcf7 i
G
CT A
AC G
G AC
G
U Tcf3 i
T
T
A
G
AT
T
G
T
A AGG A
CCC
G
T
T
T
TATTA AAA
AT
AGG
TCC
G CCAC
CT T
CG G CT
CT TGAT
TC
TT CG
C
G
G
A
A
U Tcf7l2 i
T
G G
Tcf7l2 pwm primary
A T
CT
C
AT
T
AGA
TCAAT
Tcf7l2 pwm secondary
A CG
T
T
U Tcfap2a ii
Tcfap2a pwm secondary
C
G
CC G
T AA
T
C G
A
C
T
G
G
AT
TA
T
G
TC
G
CC GG
G CT AGA CA
C
C
AA
80
AT
C C
A
T
A
G
GC
G
A
Tcfap2b pwm primary
C
C
T
GT T
T
G
TGA
TCCGA
C
U Tcfap2b i
T
CC GG
G
Tcfap2a pwm primary
T
A
C
A
C U Tcfap2a i
T
G AGTG A
C
C
U Tcf7l2 ii
C
A
GT
T
CG GC
G
C
A
G
C
T
G T
C
TT
GCC
T
AC
U Tcfap2b ii
GGC
C GAA
AA GAC AG T
C
TC T
TG
T
T
TA
A
AG TT
G
C G
Tcfap2b pwm secondary
C GG
G
A T
T
A
G
U Tcfap2c i
Tcfap2c pwm primary
U Tcfap2c ii
Tcfap2c pwm secondary
C
TGA
C
C T
C
G
TCCGA GTC
A
GT
AC T
G
GCC GGC
A
CAAG
AA TT
C
A
G
Tcfap2e pwm primary
U Tcfap2e ii
Tcfap2e pwm secondary
U Tcfe2a i
Tcfe2a pwm primary
G
A TTT T
C
AGG
C
CC GG
G
C
TGA
CCG
C
U Tcfap2e i
T T TA
CT AG
G
G
T
C
CA
T
A
G
GT AC
G
T
AAAAAA
GT TGGTC AGGCCCT
A
G
C
T
T
CT TG G C
CAGGTG CAGATG T CG A T A A C ACATTC TGACAG A
G
C
CC
C
T
G
C
A
A
GT
TG
A
CC
G
T
A
C
U Tcfe2a ii
Tcfe2a pwm secondary
T GT
A
C
C
A
G
G
A
G
C
C
C TG C
U Tea1
GR09 Tea1
T
AT
GA
U Tec1
GR09 Tec1
A
A
A
A T T
TG
A
G
G
C
U Tgif1
Cell08 Tgif1 2342
81
C
C
T
T AT
C
G
C T
C
G
G
TT
CC
G
C
G
GT
C
G
A TC
G
A
C T
TC
A
A
A
A
A T
CT
T
GG
A
G
T
C
A
A
T
T
G
T
Cell08 Tgif2 3451
A T
C
U Titf1
Cell08 Titf1 1722
U Tlx2
Cell08 Tlx2 3498
T A
A
TT
ATA T
CC
G
A
U Ume6
GR09 Ume6
U Uncx4
Cell08 Uncx4
GCA
G
C
G
T
A
CAT T
C
C
C
T
CG
T
U Vax2
Cell08 Vax2 3500
C
A AC
GGC
AC
GT
T A
T
C
A
TA A T TA
CC
T
U Vsx1
Cell08 Vsx1 1728
82
T
T
T
C
G
A
C
T
G
G
G
T
C
A
C
G
A
T
C
GT
A
C
G
A T
C
GT T CG T
G
CA
A
A
A
GG
T T GCC
A
C
C
G A
G
G
TA T A
G CC
AA
GC AC
G
T
A
C
C
C
GG
C G
CG
C
T
T
TA AT A
CC
TG
T
ATG A
G
C
TC
GT
A
C
G
C
G
G
A
AGG
AC
Cell08 Vax1 3499
T
C
T
A
T
T
G
U Vax1
G
GC A
C
TGA
C
GR09 Usv1
TT
AA
G C
G
C
T A
AC
G
U Usv1
T
A
C
G
G
T
GGC C
GC G A T T A T TA A CCCCTGAA A
C
T
C
C
C GT
C
T
T
T
A
T A TG
CA G CT
GA
G
GR09 Tye7
A
TT
AA
G G
CG
T
A
G
G
TTA
A
C
GTCC
AA ATA
G
C
C
C
A
CA TC C
C
G G
CACGTGA
T
G
C
U Tye7
C
A
C
G
A
C
TT GA C T
C T GA
A
CT T A
CCA
GGG C
A
G
T
TA
C
GT
C
C
G
U Tgif2
A CTGTCAA G
A
AT C
A
GT A
G
G
T
T
C A
G
C G T
T
TCGA
CT
C
C
G
A
U Xbp1
GR09 Xbp1
GA
A
T
G
G
T A
AC
GG
G
C
A
C A
T
TTACGTAA
G
C A
TA
G C
C
G
U Yap1
GR09 Yap1
G
GCA
TC T T AG T C
C
A
A
A
C
G
U Yap6
T
G
C
A
T
GT
T
C
AT
G
GR09 Ybr239c
G
T A T CA
T
G C
A
A
U Ydr520c
GR09 Ydr520c
U Yer130c
GR09 Yer130c
G
AAT
G
T GT
C
A
C
GR09 Ygr067c
A
U Yll054c
GR09 Yll054c
A
G
A
G
G
G A
T
T
G
83
T
G T
C
T
A
A T
C
CCC C
G
C
A GA
AC
CG
C
C
GT
A
GR09 Yml081w
AA
G
A
T
T
C
CGGA
C
A
T
T
C C
A
T
T C
A
G
A
C
C C C
CG
TC
CT
G
GA
C
GGT A T
T
GR09 Ykl222c
TA
GT
GT CT G
A
A
GC
U Ykl222c
T
GCC
C GA
T
A
A
G
C
C
A
AG
C
A
TA
C T
C
C CA T AG T
TGG
C
T AG
A
GGGT GC A
A
CGGAGATA ATAGGGG GGG A CGGA AT
T
C
U Yml081w
A
CCG
CGGT
TTCCGGAAC
A G
U Ygr067c
C TA
G
A
GR09 Yap6
C
U Ybr239c
T
A
TTA GT A
G C
C
A
C
G
AT
A T
T
C
TCCGA TA T A GTAAATC C GT A A A TC
ATC TA
G
A T
G
U Ynr063w
GR09 Ynr063w
T
AC T
U Yox1
A
C
G C
T
T
G
GR09 Yox1
TA
A
GR09 Ypr013c
T
T
T
A
GR09 Ypr015c
A
GR09 Yrm1
A
A
A
C
C
G
G
C A G T
T
C A
C
T
T
T
A
CC T
G
CA T
C
G
A
G T
T
CT
A
G
A T
C
GG
C
C
TC
A
G
T
GT
C G T
A
G
CG T A AC
GA
G
CC A
T
CGGA ATAA A
G A
G
GT
CT
GR09 Yrr1
C
T
C G
T
C
A
G
GTTCTAGA
G T
U Zbtb12 i
Zbtb12 pwm primary
U Zbtb12 ii
Zbtb12 pwm secondary
CA
T
TCGA
T
C
A
C
A
TA
C T
CA
T
C
T
A
G G
G
T
A
C
GG
T
84
TC T
G
CACTGCA A
Zbtb3 pwm primary
A
TAGAAC
GGAGG
T
C
C
CA A A
C
U Zbtb3 i
CG
G
CA A
CG A A A T A C
A
A A T CG
C
T TA TA A GA T GG G C
G
T CCG
AAT T
G
T
A
T
C
C
CAT
G
G T
G
G
G
G T
A
U Yrr1
A
TC
T
T
U Yrm1
T
GA
C
C
A A
G
GR09 Ypr196w
C
T A
G
C
C
GG
C
U Ypr196w
A
T GA
G
G
TC
U Ypr015c
C
C
A
GA C
U Ypr013c
T
G
C
GC
G
T
T
C
ACTG
A
G
T AGAA T TCG CA A A T TG
C
C
A
U Zbtb3 ii
CCT T
CT TG
G C
G
C TGA A
G T
G
C
Zbtb3 pwm secondary
CCCCC GACCACC
C
AA
G A
A
TA T TA A TCCT
G
C
T
G
G
U Zbtb7b i
Zbtb7b pwm primary
U Zbtb7b ii
Zbtb7b pwm secondary
A
AC
C
GTC
G T
A
G
AC
C
TT T T TC A
T
G
G
Zfp105 pwm primary
T
G
T
C
Zfp105 pwm secondary
U Zfp128 i
Zfp128 pwm primary
A
A
CC G G
T
C CGGGG
A
G
U Zfp105 ii
G
TC A T A A
GC
CT
AGT
TC GTC
G C
U Zfp105 i
A
T
T
A
A
T
T
A
C
G
C
TAC
GGCG
T TC
G
C G
C
T
T
GT A A
T
A AA AA
CC A
T
T
CC GT A
G A
TA T A T A TA
G T
AGAGT
A
U Zfp128 ii
T
AGAG
C G
C
G
Zfp128 pwm secondary
A T
GCGCGC
G AC
G
U Zfp161 i
Zfp161 pwm primary
U Zfp161 ii
Zfp161 pwm secondary
A
C
T
A
AT
TTT
TA
CG A
A
A
G
T
C
G
GT T
G
T
C
G
AA TT
CG
ATGTAC AAT
AG C C
G
85
TA T
G
T
A
T
A A ACA
Zfp187 pwm primary
A
CGCGCA GC
GC C
T
C
G
G
TT A
C
U Zfp187 i
A
A
C
C
CT
CT
CTC TC G G
C
T
C
GT
A
G
T
G A
A
CCT GTCC
G C AA T
C
U Zfp187 ii
T
Zfp187 pwm secondary
TT
A
A
C
C
Zfp281 pwm primary
U Zfp281 ii
Zfp281 pwm secondary
A
A
GA
G T
A
A T
A
A
T
T
A
A
T
AT
TA A
CT G C
G
C
G
TGGGATG
G
A
G
A
T
A
C
G C
T
T
T
G
G
Zfp410 pwm primary
C
A
CCC C
T A
C
AC
U Zfp410 i
A
A A TG T
G
T AG
T
C
T
CC
A
G A TT T
GT
A
CCCCC
AT
GA
T
A
C
T
G TA TAT A
GT
G
U Zfp281 i
CA
G
TT
C
C
CC
C AA T
CT A
G
CCGCCCC TT
TA
G AG T
AG G T C G G A ATA
U Zfp410 ii
Zfp410 pwm secondary
AGTGCTC
A
C
T AG
U Zfp691 i
Zfp691 pwm primary
A
A
A
G
T
AT
G C
C
U Zfp691 ii
GACTCC
T
T TGG
G
T
C
G
G
Zfp691 pwm secondary
TA
CCCCC
C
CA
C
A
G AG
Zfp740 pwm primary
U Zfp740 ii
Zfp740 pwm secondary
AA
TT
T
T AC A A C
CCC
CC
A TT
GGG T
A
AC
A
A
TT
U Zfp740 i
AC
G G
A
C
C C
G
T
A
T
T
CG
T
A
G
A G GTC A CGG T AT TT
T
G
G
G A
CCCC GGGGG CG
C
G
A A AGGCCT T T TC TT
T
G
G
G
U Zic1 i
Zic1 pwm primary
86
T
A
ATA T
C A
A
C
AC
T
AA
C
C CAGCAGG
A T
A
G
Zic1 pwm secondary
TC
T
TT
U Zic2 i
T
G
GG
T CA AA T A
A
AT
C
C
A
C
A
C
Zic2 pwm primary
C CAGCAGG
A T
A
G
T
G
U Zic2 ii
T
T TC AGGTC T T A
G
GT
G G
TGT
CCC GGGG
CC
CAA A
TA
A
G
G
U Zic1 ii
Zic2 pwm secondary
TA
C
T
TG T
T
CCCCCGGGGGG
G
A A AGGTCT T T TC T A A AA T TT G
GT
U Zic3 i
A
A
A
TA
G
A
G T
G
T
Zic3 pwm secondary
A
TA
C
C
G
A GA
A
T
T
C
C T
G A
T
A
CT
T
CA
A
C
TGTG
C
A
G
G
GCACA AA C
AA
TGAA
C
C
Zscan4 pwm secondary
T
GTGCACA
T
T
A TG
T
A
G C
U Zscan4 ii
T
CCCC
ACA
G
NBT06 Zif268
Zscan4 pwm primary
TGT
CG CA G A
CT T
T
G C
U Zscan4 i
CA
C CAGCA G
A
U Zif268
C
T AC
Zic3 pwm primary
G
U Zic3 ii
C
T
T
G
A
T TC T C
A
G
G
References [1] Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., Loh, Y.-H., Yeo, H. C., Yeo, Z. X., Narang, V., Govindarajan, K. R., Leong, B., Shahab, A., Ruan, Y., Bourque, G., Sung, W.-K., Clarke, N. D., Wei, C.-L., and Ng, H.-H. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133(6), 1106–1117 (2008).
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[2] Cheng, Y., Wu, W., Kumar, S. A., Yu, D., Deng, W., Tripic, T., King, D. C., Chen, K.-B., Zhang, Y., Drautz, D., Giardine, B., Schuster, S. C., Miller, W., Chiaromonte, F., Zhang, Y., Blobel, G. A., Weiss, M. J., and Hardison, R. C. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res 19(12), 2172–2184 (2009). [3] ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146), 799–816 (2007). [4] Johnson, R., Teh, C. H.-L., Kunarso, G., Wong, K. Y., Srinivasan, G., Cooper, M. L., Volta, M., Chan, S. S.-L., Lipovich, L., Pollard, S. M., Karuturi, R. K. M., Wei, C.-l., Buckley, N. J., and Stanton, L. W. REST Regulates Distinct Transcriptional Networks in Embryonic and Neural Stem Cells. Plos Biology 6(10), 2205–2219 (2008). [5] Robertson, A. G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A. P., Wederell, E. D., Cullum, R., Euskirchen, G., Krzywinski, M., Birol, I., Snyder, M., Hoodless, P. A., Hirst, M., Marra, M. A., and Jones, S. J. M. Genome-wide relationship between histone h3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res 18(12), 1906–1917 (2008). [6] Rozowsky, J., Euskirchen, G., Auerbach, R. K., Zhang, Z. D., Gibson, T., Bjornson, R., Carriero, N., Snyder, M., and Gerstein, M. B. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnology 27(1), 66–75 (2009). [7] Seo, Y.-K., Chong, H. K., Infante, A. M., Im, S.-S., Xie, X., and Osborne, T. F. Genome-wide analysis of srebp-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif. Proc Natl Acad Sci U S A 106(33), 13765–13769 (2009). [8] Valouev, A., Johnson, D. S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R. M., and Sidow, A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5(9), 829–834 (2008). [9] Wilson, N. K., Miranda-Saavedra, D., Kinston, S., Bonadies, N., Foster, S. D., Calero-Nieto, F., Dawson, M. A., Donaldson, I. J., Dumon, S., Frampton, J., Janky, R., Sun, X.-H., Teichmann, S. A., Bannister, A. J., and Goettgens, B. The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. Blood 113(22), 5456–5465 (2009). [10] Williams, D., Cai, M., and Clore, G. Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1 center dot Sox2 center dot Hoxb1-DNA ternary transcription factor complex. Journal of Biological Chemistry 279(2), 1449–1457 (2004). [11] Mo, Y., Ho, W., Johnston, K., and Marmorstein, R. Crystal structure of a ternary SAP1/SRF/c-Fos SIRE DNA complex. Journal of Molecular Biology 314(3), 495–506 (2001). [12] Muhlethaler-Mottet, A., Di Berardino, W., Otten, L., and Mach, B. Activation of the MHC class ii transactivator CIITA by interferon-gamma requires cooperative interaction between Stat1 and USF-1. Immunity 8, 157–166 (1998). [13] Wei, P., Taniguchi, S., Sakai, Y., Imamura, M., Inoguchi, T., Nawata, H., Oda, S., Nakabeppu, Y., Nishimura, J., and Ikuyama, S. Expression of adipose differentiation-related protein
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(ADRP) is conjointly regulated by PU.1 and AP-1 in macrophages. Journal of Biochemistry 138(4), 399–412 (2005). [14] Wadman, I. A., Osada, H., Grtz, G. G., Agulnick, A. D., Westphal, H., Forster, A., and Rabbitts, T. H. The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins. EMBO J 16(11), 3145–3157 (1997). [15] Cai, D. H., Wang, D., Keefer, J., Yeamans, C., Hensley, K., and Friedman, A. D. C/EBP alpha: AP-1 leucine zipper heterodimers bind novel DNA elements, activate the PU.1 promoter and direct monocyte lineage commitment more potently than C/EBP alpha homodimers or AP-1. Oncogene 27(19), 2772–2779 (2008). [16] Horard, B., Castet, A., Bardet, P., Laudet, V., Cavailles, V., and Vanacker, J. Dimerization is required for transactivation by estrogen-receptor-related (ERR) orphan receptors: evidence from amphioxus ERR. Journal of Molecular Endocrinology 33(2), 493–509 (2004). [17] Rosmarin, A., Resendes, K., Yang, Z., McMillan, J., and Fleming, S. GA-binding protein transcription factor: a review of GABP as an integrator of intracellular signaling and proteinprotein interactions. Blood Cells Molecules and Diseases 32(1), 143–154 (2004). [18] Nateri, A., Spencer-Dene, B., and Behrens, A. Interaction of phosphorylated c-Jun with TCF4 regulates intestinal cancer development. Nature 437(7056), 281–285 (2005). [19] Schlisio, S., Halperin, T., Vidal, M., and Nevins, J. Interaction of YY1 with E2Fs, mediated by RYBP, provides a mechanism for specificity of E2F function. Embo Journal 21(21), 5775–5786 (2002). [20] Sandelin, A., Alkema, W., Engstr¨ om, P., Wasserman, W. W., and Lenhard, B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32(Database issue), D91–D94 (2004). [21] Newburger, D. E. and Bulyk, M. L. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 37(Sp. Iss. SI), D77–D82 (2009). [22] Bailey, T. L. and Elkan, C. The value of prior knowledge in discovering motifs with MEME. Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, Cambridge, United Kingdom, July 16-19, 1995 3, 21–29 (1995).
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