Graph Theoretical Prediction of Transcription Factor Binding Sites

Graph Theoretical Prediction of Transcription Factor Binding Sites

Timothy E. Reddy1, Charles DeLisi1,2, Boris E. Shakhnovich1,3

1Program in Bioinformatics and Systems Biology, Boston University, 24 Cummington St., Boston, MA 02215
2Department of Biomedical Engineering, 44 Cummington St., Boston, MA 02215
3Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Ave., Bauer 308, Cambridge, MA 02138

Publication along with Software and README.

Predictions of Transcription Factor Binding Specificity

Statistical Significance:
P < 0.001 P < 0.01 P < 0.1 P > 0.1

TFConditionPMotif Logo
ABF1YPD 0.63028
ACA1YPD 0.0038969
ACE2YPD 0.15257
ADR1SM 0.019975
ADR1YPD 0.25797
AFT2H2O2Hi 0.041069
AFT2H2O2Lo 0.015268
AFT2YPD 0.44394
ARG80SM 0.18294
ARG80YPD 0.34287
ARG81SM 0.27291
ARG81YPD 0.18157
ARO80SM 0.66345
ARO80YPD 0.48478
ARR1H2O2Hi 0.91773
ARR1YPD 0.10687
ASH1BUT14 0.045136
ASK10YPD 0.55404
AZF1YPD 0.52551
BAS1SM 0.056298
BAS1YPD 0.0038513
CAD1H2O2Hi 0.023837
CAD1SM 0.022546
CAD1YPD 0.011358
CBF1YPD 0.01077
CHA4SM 0.6301
CHA4YPD 0.13053
CIN5H2O2Hi 0.014857
CIN5YPD 0.064371
CST6YPD 0.91981
CUP9YPD 0.14829
DAL80RAPA 0.021126
DAL80YPD 0.40995
DAL81YPD 0.38868
DAT1YPD 0.010744
DIG1Alpha 0.066362
DIG1BUT14 0.30159
DIG1BUT90 0.064911
EDS1YPD 0.1957
FKH2H2O2Lo 0.0095441
FZF1YPD 0.11123
GAL3YPD 0.0049515
GAL4GAL 0.82538
GAL4RAFF 0.17199
GAL4YPD 0.024803
GAL80YPD 0.0065233
GAT1RAPA 0.35328
GAT1SM 0.11182
GAT1YPD 0.6786
GAT3YPD 0.071532
GCN4YPD 0.00097756
GCR1YPD 0.0058357
GCR2SM 0.62883
GCR2YPD 0.4576
GLN3RAPA 0.0095365
GLN3SM 0.42055
GLN3YPD 0.63177
GTS1YPD 0.96601
GZF3H2O2Hi 0.12033
GZF3RAPA 0.015598
GZF3YPD 0.80074
HAC1YPD 0.54572
HAL9YPD 0.46925
HAP1YPD 0.014215
HAP2RAPA 0.10661
HAP2YPD 0.75583
HAP3YPD 0.28595
HAP4H2O2Lo 0.18249
HAP4SM 0.9148
HAP4YPD 0.0071246
HAP5SM 0.21969
HAP5YPD 0.2883
HIR1YPD 0.23373
HIR2YPD 0.015426
HIR3YPD 0.61605
HMS1YPD 0.68587
HMS2YPD 0.23487
HOG1YPD 0.14469
HSF1H2O2Hi 0.038404
HSF1H2O2Lo 0.018193
HSF1HEAT 0.34988
HSF1YPD 0.66672
IFH1YPD 0.42699
IME1H2O2Hi 0.067195
IME4H2O2Hi 0.65275
IME4YPD 0.46314
INO2YPD 0.0051614
INO4YPD 0.0053942
IXR1YPD 0.65913
KSS1Alpha 0.0077669
KSS1YPD 0.77074
LEU3SM 0.012582
LEU3YPD 0.062552
MAC1H2O2Hi 0.060204
MAC1YPD 0.39757
MAL33H2O2Hi 0.01806
MATA1YPD 0.94676
MBP1H2O2Lo 0.0085446
MBP1YPD 0.0066679
MCM1YPD 0.014075
MDS3YPD 0.010363
MET18YPD 0.94729
MET28YPD 0.14207
MET31SM 0.78104
MET31YPD 0.048349
MET32SM 0.011297
MET32YPD 0.011171
MET4SM 0.021666
MET4YPD 0.043759
MGA1YPD 0.78985
MIG1YPD 0.085536
MIG2H2O2Hi 0.21043
MIG2YPD 0.596
MIG3YPD 0.33182
MOT3H2O2Hi 0.30446
MOT3H2O2Lo 0.08321
MOT3SM 0.078929
MOT3YPD 0.41683
MSN1YPD 0.1081
MSN2Acid 0.67583
MSN2H2O2Hi 0.08494
MSN2H2O2Lo 0.099221
MSN2RAPA 0.58079
MSN2YPD 0.02544
MSN4Acid 0.49133
MSN4H2O2Lo 0.0092178
MSN4RAPA 0.97724
MSN4YPD 0.087556
NDD1YPD 0.1718
NDT80YPD 0.61386
NRG1H2O2Lo 0.043428
NRG1YPD 0.11865
OAF1YPD 0.25236
OPI1YPD 0.0028067
PDC2YPD 0.024272
PDR1H2O2Lo 0.014185
PDR1YPD 0.1434
PDR3YPD 0.47055
PHD1YPD 0.016676
PHO2H2O2Hi 0.69807
PHO2SM 0.43797
PHO2YPD 0.17189
PHO4Pi- 0.031004
PHO4YPD 0.88362
PIP2YPD 0.27631
PPR1YPD 0.33307
PUT3H2O2Lo 0.42903
PUT3SM 0.051615
PUT3YPD 0.57591
RAP1YPD 0.07202
RCO1YPD 0.63615
RCS1H2O2Hi 0.005315
RCS1SM 0.5953
RCS1YPD 0.93433
RDS1H2O2Hi 0.14756
RDS1YPD 0.018787
REB1H2O2Hi 0.0012663
REB1YPD 0.0045754
RFX1YPD 0.039192
RGM1YPD 0.0084362
RGT1YPD 0.0043238
RIM101H2O2Hi 0.83011
RIM101YPD 0.67286
RLM1YPD 0.92215
RLR1YPD 0.14732
RME1YPD 0.98385
ROX1H2O2Hi 0.095286
ROX1H2O2Lo 0.22343
ROX1YPD 0.91594
RPH1H2O2Hi 0.10705
RPH1H2O2Lo 0.0014485
RPH1SM 0.89631
RPH1YPD 0.87241
RPN4H2O2Hi 0.25014
RPN4YPD 0.1038
RTG1RAPA 0.81786
RTG1SM 0.52866
RTG1YPD 0.17743
RTG3H2O2Lo 0.19442
RTG3RAPA 0.099556
RTG3SM 0.11216
RTG3YPD 0.056629
SFP1H2O2Hi 0.35438
SFP1H2O2Lo 0.24982
SFP1SM 0.00294
SFP1YPD 0.057616
SIG1H2O2Hi 0.12428
SIP4SM 0.0592
SIP4YPD 0.45264
SKN7HEAT 0.058276
SKN7YPD 0.024544
SKO1YPD 0.26433
SMK1YPD 0.0082248
SMP1YPD 0.10409
SNF1YPD 0.010242
SNT2YPD 0.0014685
SOK2BUT14 0.11908
SPT23YPD 0.13552
SPT2YPD 0.85218
SRD1YPD 0.14507
STB1YPD 0.017736
STB2YPD 0.23712
STB4YPD 0.076051
STB5YPD 0.062035
STE12Alpha 0.05108
STE12BUT14 0.18464
STE12BUT90 0.065184
STE12YPD 0.10492
STP1SM 0.19386
STP1YPD 0.060799
STP2YPD 0.10035
STP4YPD 0.23309
SUM1YPD 0.0026762
SUT1YPD 0.040446
SWI4YPD 0.024456
SWI5YPD 0.14161
SWI6YPD 0.010058
TEC1Alpha 0.017194
TEC1BUT14 0.008163
TEC1YPD 0.2153
THI2Thi- 0.38403
THI2YPD 0.013947
TYE7YPD 0.0047762
UGA3RAPA 0.026778
UGA3SM 0.13903
UGA3YPD 0.0066669
UME1H2O2Hi 0.060673
UME1YPD 0.43042
UME6H2O2Hi 0.001274
UME6YPD 0.0013019
UPC2YPD 0.13434
WAR1YPD 0.99442
WTM1YPD 0.15374
XBP1H2O2Lo 0.029787
YAP1H2O2Hi 0.98402
YAP1H2O2Lo 0.013916
YAP1YPD 0.010945
YAP3YPD 0.1654
YAP5H2O2Hi 0.058746
YAP5YPD 0.10486
YAP6H2O2Hi 0.049875
YAP6H2O2Lo 0.33397
YAP6YPD 0.3959
YAP7H2O2Hi 0.0029489
YDR026cYPD 0.0023719
YDR266cYPD 0.0047893
YDR520CYPD 0.0041438
YER051wYPD 0.0049481
YER130CYPD 0.12294
YER184CYPD 0.0068204
YFL044CYPD 0.29876
YHP1YPD 0.56056
YJL206CH2O2Hi 0.12111
YJL206CH2O2Lo 0.0016912
YJL206CYPD 0.98621
YKR064WYPD 0.0037818
YML081WYPD 0.063787
YOX1YPD 0.37468
YRR1YPD 0.7605
ZAP1YPD 0.14116
ZMS1YPD 0.0038768