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Table 5 Performance comparison with other protein complex prediction methods

From: A method for predicting protein complex in dynamic PPI networks

PPI data

Methods

#Complexes

P

R

F

Sn

PPV

Acc

Gavin data

Our method

447

0.662

0.434

0.524

0.413

0.617

0.505

CSO

174

0.645

0.302

0.411

0.476

0.534

0.503

Cluster ONE

243

0.502

0.324

0.393

0.46

0.597

0.524

COACH

326

0.525

0.331

0.406

0.44

0.547

0.49

CMC

120

0.608

0.218

0.321

0.371

0.606

0.474

HUNTER

69

0.87

0.206

0.333

0.386

0.508

0.443

MCODE

66

0.727

0.142

0.238

0.277

0.513

0.377

Krogan data

Our method

816

0.464

0.591

0.52

0.448

0.677

0.551

CSO

190

0.726

0.331

0.455

0.411

0.642

0.514

Cluster ONE

240

0.579

0.328

0.419

0.398

0.681

0.521

COACH

345

0.617

0.343

0.441

0.432

0.544

0.485

CMC

111

0.748

0.235

0.358

0.381

0.589

0.474

HUNTER

74

0.865

0.199

0.323

0.374

0.569

0.462

MCODE

76

0.724

0.157

0.258

0.255

0.583

0.385

MIPS data

Our method

1145

0.274

0.576

0.372

0.382

0.61

0.483

CSO

192

0.495

0.289

0.365

0.286

0.568

0.403

Cluster ONE

256

0.359

0.23

0.281

0.243

0.668

0.403

COACH

448

0.301

0.289

0.295

0.336

0.311

0.323

CMC

168

0.429

0.211

0.283

0.389

0.318

0.352

HUNTER

52

0.654

0.11

0.189

0.296

0.286

0.291

MCODE

85

0.447

0.115

0.183

0.19

0.503

0.309

STRING data

Our method

1240

0.324

0.586

0.417

0.836

0.404

0.581

Cluster ONE

893

0.151

0.245

0.187

0.846

0.459

0.623

COACH

1645

0.186

0.292

0.227

0.955

0.12

0.338

HUNTER

5

0.5

0.01

0.019

0.104

0.298

0.176

MCODE

393

0.092

0.09

0.091

0.675

0.242

0.405

  1. #Complexes refers to the number of predicted complexes. F: F-score, P: precision, R: recall. The highest score of each approach is shown in bold