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.

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