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• Predicted nucleosome occupancy by the biophysical model with 158 TFs taken into account (wig)

• Predicted nucleosome occupancy by the biophysical model using binding energies from Kaplan et.al and WITHOUT TFs (wig)

• Predicted total occupancy of TFs (wig)
Total TF occupancy (sum over all TFs) predicted by the biophysical model with nucleosome sequence specificity and 158 TFs.

• Experimental nucleosome occupancy (ChIP-Chip Lee et al. 2007)
Experimental nucleosome occupancy based on the ChIP-Chip experiment by Lee et. al (2007). For each probe i along the genome (from a tiling array with 4 bp resolution) we obtain a signal xi corresponding to the log-ratio of signal from the nucleosome and background sample. We assume that the signal xi is proportional to the logarithm of the probability Pi that a nucleosome is bound to the corresponding segment in the genome, i.e. xi = λ * log(Pi) + c; where λ and c are unknown constants. We determine c and λ by demanding that the average coverage probability matches the experimentally observed average nucleosome coverage of 0.8, and that all coverage probabilities Pi must lie in the interval [0; 1].

• Predicted TF binding sites (gff)
TF binding sites in S.saccharomyces predicted by MotEvo algorithm (Arnold et al. 2012) using multiple alignments for 5 species (S.saccharomyces, S.paradoxus, S.mikatae, S.bayanus, S.kudriavzev).

• Motif Weight Matrices

Occupancy for every TF individually predicted by the biophysical model with nucleosome sequence specificity and 158 TFs.

Factor name Download link
CAT8 CAT8_predicted_occupancy.wig.gz
SWI5 SWI5_predicted_occupancy.wig.gz
HAP3 HAP3_predicted_occupancy.wig.gz
MIG2 MIG2_predicted_occupancy.wig.gz
NHP6B NHP6B_predicted_occupancy.wig.gz
UME6 UME6_predicted_occupancy.wig.gz
GZF3 GZF3_predicted_occupancy.wig.gz
SPT15 SPT15_predicted_occupancy.wig.gz
ROX1 ROX1_predicted_occupancy.wig.gz
PBF1 PBF1_predicted_occupancy.wig.gz
HCM1 HCM1_predicted_occupancy.wig.gz
REI1 REI1_predicted_occupancy.wig.gz
EDS1 EDS1_predicted_occupancy.wig.gz
HAC1 HAC1_predicted_occupancy.wig.gz
PDR1 PDR1_predicted_occupancy.wig.gz
ABF2 ABF2_predicted_occupancy.wig.gz
YDR026 YDR026c_predicted_occupancy.wig.gz
TYE7 TYE7_predicted_occupancy.wig.gz
YOX1 YOX1_predicted_occupancy.wig.gz
CUP2 CUP2_predicted_occupancy.wig.gz
STB1 STB1_predicted_occupancy.wig.gz
YAP6 YAP6_predicted_occupancy.wig.gz
TBS1 TBS1_predicted_occupancy.wig.gz
RSC3 RSC3_predicted_occupancy.wig.gz
AFT2 AFT2_predicted_occupancy.wig.gz
STP4 STP4_predicted_occupancy.wig.gz
GLN3 GLN3_predicted_occupancy.wig.gz
PHO4 PHO4_predicted_occupancy.wig.gz
CUP9 CUP9_predicted_occupancy.wig.gz
USV1 USV1_predicted_occupancy.wig.gz
SKN7 SKN7_predicted_occupancy.wig.gz
ASG1 ASG1_predicted_occupancy.wig.gz
ARO80 ARO80_predicted_occupancy.wig.gz
CRZ1 CRZ1_predicted_occupancy.wig.gz
CIN5 CIN5_predicted_occupancy.wig.gz
HAP1 HAP1_predicted_occupancy.wig.gz
GAT3 GAT3_predicted_occupancy.wig.gz
TEA1 TEA1_predicted_occupancy.wig.gz
NHP6A NHP6A_predicted_occupancy.wig.gz
STP2 STP2_predicted_occupancy.wig.gz
RFX1 RFX1_predicted_occupancy.wig.gz
RGT1 RGT1_predicted_occupancy.wig.gz
SUT2 SUT2_predicted_occupancy.wig.gz
SKO1 SKO1_predicted_occupancy.wig.gz
ZMS1 ZMS1_predicted_occupancy.wig.gz
PUT3 PUT3_predicted_occupancy.wig.gz
FKH1 FKH1_predicted_occupancy.wig.gz
YAP3 YAP3_predicted_occupancy.wig.gz
CEP3 CEP3_predicted_occupancy.wig.gz
YPR015C YPR015C_predicted_occupancy.wig.gz
UPC2 UPC2_predicted_occupancy.wig.gz
ECM23 ECM23_predicted_occupancy.wig.gz
DAL82 DAL82_predicted_occupancy.wig.gz
MBP1 MBP1_predicted_occupancy.wig.gz
STB3 STB3_predicted_occupancy.wig.gz
MGA1 MGA1_predicted_occupancy.wig.gz
SFL1 SFL1_predicted_occupancy.wig.gz
YLL054C YLL054C_predicted_occupancy.wig.gz
PHD1 PHD1_predicted_occupancy.wig.gz
YRM1 YRM1_predicted_occupancy.wig.gz
GCR1 GCR1_predicted_occupancy.wig.gz
YER184C YER184C_predicted_occupancy.wig.gz
HAP5 HAP5_predicted_occupancy.wig.gz
YNR063W YNR063W_predicted_occupancy.wig.gz
TEC1 TEC1_predicted_occupancy.wig.gz
RDR1 RDR1_predicted_occupancy.wig.gz
MSN2 MSN2_predicted_occupancy.wig.gz
INO2 INO2_predicted_occupancy.wig.gz
STB4 STB4_predicted_occupancy.wig.gz
MIG1 MIG1_predicted_occupancy.wig.gz
MIG3 MIG3_predicted_occupancy.wig.gz
XBP1 XBP1_predicted_occupancy.wig.gz
RLM1 RLM1_predicted_occupancy.wig.gz
CHA4 CHA4_predicted_occupancy.wig.gz
LYS14 LYS14_predicted_occupancy.wig.gz
LEU3 LEU3_predicted_occupancy.wig.gz
GAL4 GAL4_predicted_occupancy.wig.gz
RPH1 RPH1_predicted_occupancy.wig.gz
AZF1 AZF1_predicted_occupancy.wig.gz
SRD1 SRD1_predicted_occupancy.wig.gz
HAL9 HAL9_predicted_occupancy.wig.gz
MAC1 MAC1_predicted_occupancy.wig.gz
AFT1 AFT1_predicted_occupancy.wig.gz
YER130C YER130C_predicted_occupancy.wig.gz
FKH2 FKH2_predicted_occupancy.wig.gz
ABF1 ABF1_predicted_occupancy.wig.gz
YML081W YML081W_predicted_occupancy.wig.gz
STE12 STE12_predicted_occupancy.wig.gz
STP3 STP3_predicted_occupancy.wig.gz
INO4 INO4_predicted_occupancy.wig.gz
YPR022C YPR022C_predicted_occupancy.wig.gz
MET31 MET31_predicted_occupancy.wig.gz
SWI6 SWI6_predicted_occupancy.wig.gz
YLR278C YLR278C_predicted_occupancy.wig.gz
MCM1 MCM1_predicted_occupancy.wig.gz
NRG1 NRG1_predicted_occupancy.wig.gz
GAL80 GAL80_predicted_occupancy.wig.gz
ADR1 ADR1_predicted_occupancy.wig.gz
RSC30 RSC30_predicted_occupancy.wig.gz
SWI4 SWI4_predicted_occupancy.wig.gz
RIM101 RIM101_predicted_occupancy.wig.gz
CAD1 CAD1_predicted_occupancy.wig.gz
PHO2 PHO2_predicted_occupancy.wig.gz
RTG3 RTG3_predicted_occupancy.wig.gz
FZF1 FZF1_predicted_occupancy.wig.gz
HSF1 HSF1_predicted_occupancy.wig.gz
CST6 CST6_predicted_occupancy.wig.gz
RAP1 RAP1_predicted_occupancy.wig.gz
SMP1 SMP1_predicted_occupancy.wig.gz
SFP1 SFP1_predicted_occupancy.wig.gz
GSM1 GSM1_predicted_occupancy.wig.gz
TBF1 TBF1_predicted_occupancy.wig.gz
RGM1 RGM1_predicted_occupancy.wig.gz
OAF1 OAF1_predicted_occupancy.wig.gz
TOS8 TOS8_predicted_occupancy.wig.gz
YKL222C YKL222C_predicted_occupancy.wig.gz
YRR1 YRR1_predicted_occupancy.wig.gz
YPR196W YPR196W_predicted_occupancy.wig.gz
RDS2 RDS2_predicted_occupancy.wig.gz
HAP4 HAP4_predicted_occupancy.wig.gz
THI2 THI2_predicted_occupancy.wig.gz
NHP10 NHP10_predicted_occupancy.wig.gz
SUM1 SUM1_predicted_occupancy.wig.gz
PBF2 PBF2_predicted_occupancy.wig.gz
DAL80 DAL80_predicted_occupancy.wig.gz
SOK2 SOK2_predicted_occupancy.wig.gz
SIP4 SIP4_predicted_occupancy.wig.gz
GAT1 GAT1_predicted_occupancy.wig.gz
PDR3 PDR3_predicted_occupancy.wig.gz
MET32 MET32_predicted_occupancy.wig.gz
SNT2 SNT2_predicted_occupancy.wig.gz
GIS1 GIS1_predicted_occupancy.wig.gz
GCN4 GCN4_predicted_occupancy.wig.gz
STB5 STB5_predicted_occupancy.wig.gz
HAP2 HAP2_predicted_occupancy.wig.gz
MATALPHA2 MATALPHA2_predicted_occupancy.wig.gz
UGA3 UGA3_predicted_occupancy.wig.gz
SIG1 SIG1_predicted_occupancy.wig.gz
YAP1 YAP1_predicted_occupancy.wig.gz
HMRA2 HMRA2_predicted_occupancy.wig.gz
RPN4 RPN4_predicted_occupancy.wig.gz
ACE2 ACE2_predicted_occupancy.wig.gz
YBR239C YBR239C_predicted_occupancy.wig.gz
YAP7 YAP7_predicted_occupancy.wig.gz
FHL1 FHL1_predicted_occupancy.wig.gz
GAT4 GAT4_predicted_occupancy.wig.gz
MSN4 MSN4_predicted_occupancy.wig.gz
PDR8 PDR8_predicted_occupancy.wig.gz
RDS1 RDS1_predicted_occupancy.wig.gz
YGR067C YGR067C_predicted_occupancy.wig.gz
NDT80 NDT80_predicted_occupancy.wig.gz
ORC1 ORC1_predicted_occupancy.wig.gz
YDR520C YDR520C_predicted_occupancy.wig.gz
ECM22 ECM22_predicted_occupancy.wig.gz
BAS1 BAS1_predicted_occupancy.wig.gz
CBF1 CBF1_predicted_occupancy.wig.gz
REB1 REB1_predicted_occupancy.wig.gz
YPR013C YPR013C_predicted_occupancy.wig.gz