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