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Table 1 Sensitivity of TFA profiles to errors in connectivity from ChIP-chip assay. Connectivity errors were simulated by randomly inserting and deleting connections in the connectivity graph generated from the ChIP-chip assay. gNCA was performed on the perturbed connectivity, and the resultant TFAs were compared to those from un-perturbed connectivity via the correlation coefficient. This procedure was performed on each of the 4 subnetworks 100 times. The average correlation coefficients for transcription factors in the 4 subnetworks are presented here. A low correlation coefficient (<0.5) suggests sensitivity to network connectivity error.

From: Inferring yeast cell cycle regulators and interactions using transcription factor activities

Subnetwork 1 Mean Correlation Coefficient Subnetwork 2 Mean Correlation Coefficient Subnetwork 3 Mean Correlation Coefficient Subnetwork 4 Mean Correlation Coefficient
ABF1 0.941 ABF1 0.951 ABF1 0.94 ACE2 0.912
ACE2 0.953 ACE2 0.857 ACE2 0.897 ARO80 0.657
ARO80 0.645 ARG81 0.286 CHA4 0.362 CIN5 0.601
CAD1 0.511 CAD1 0.659 CIN5 0.59 DIG1 0.718
CBF1 0.401 CHA4 0.448 CRZ1 0.313 FHL1 0.992
CIN5 0.651 DAL81 0.581 FHL1 0.993 FKH2 0.669
DIG1 0.686 FHL1 0.99 FKH2 0.657 GAT3 0.493
FHL1 0.992 FKH2 0.635 GAL4 0.492 GCN4 0.601
FKH1 0.614 GAT3 0.457 GAT3 0.511 GCR1 0.321
FKH2 0.535 GCR2 0.425 GCR1 0.306 GLN3 0.402
GAT3 0.446 GRF10(Pho2) 0.565 GCR2 0.446 GTS1 0.227
HAP4 0.706 HIR1 0.732 HAP4 0.769 HAP2 0.375
HIR1 0.472 HIR2 0.357 HIR1 0.465 HAP3 0.47
IXR1 0.511 IME4 0.357 HSF1 0.981 HAP4 0.856
MBP1 0.946 INO4 0.419 IME4 0.442 HIR1 0.32
MCM1 0.558 LEU3 0.575 MBP1 0.979 IXR1 0.475
MET31 0.436 MAC1 0.723 MCM1 0.572 LEU3 0.518
MET4 0.381 MBP1 0.985 MET31 0.435 MBP1 0.951
MIG1 0.336 MCM1 0.701 MIG1 0.354 MCM1 0.705
MSN4 0.444 MET31 0.507 NDD1 0.965 MIG1 0.33
MTH1 0.463 MOT3 0.413 NRG1 0.421 MSS11 0.404
NDD1 0.958 NDD1 0.971 PDR1 0.366 NDD1 0.962
NRG1 0.495 PHD1 0.541 PHD1 0.583 NRG1 0.563
PDR1 0.334 PHO4 0.599 RAP1 0.917 PDR1 0.372
PHD1 0.569 RAP1 0.856 RCS1 0.48 PHD1 0.64
RAP1 0.917 RME1 0.407 REB1 0.576 RAP1 0.897
REB1 0.643 RTG1 0.413 RME1 0.415 RCS1 0.424
RFX1 0.493 RTS2 0.302 RPH1 0.294 RLM1 0.553
RLM1 0.519 SFP1 0.564 SFP1 0.582 RME1 0.389
RME1 0.367 SKN7 0.536 SKN7 0.669 SKN7 0.609
SKN7 0.545 STE12 0.518 SMP1 0.619 SMP1 0.642
SMP1 0.614 STP2 0.322 SWI4 0.553 STB1 0.576
STE12 0.79 SWI4 0.592 SWI5 0.987 STE12 0.738
SWI4 0.747 SWI5 0.963 SWI6 0.61 SUM1 0.823
SWI5 0.991 SWI6 0.648 UGA3 0.392 SWI4 0.843
SWI6 0.606 UGA3 0.383 YAP5 0.512 SWI5 0.991
YAP5 0.863 YAP1 0.565 YAP6 0.404 SWI6 0.589
YAP6 0.56 YAP5 0.657 YFL044C 0.578 YAP5 0.572
YFL044C 0.583 YFL044C 0.546 ZAP1 0.442 YAP6 0.595
YJL206C 0.396 ZAP1 0.527 ZMS1 0.295 YJL206C 0.455