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Table 1 Benchmark results using solely the unweighted PPI network with respect to the CYC2008 gold standard

From: Detecting overlapping protein complexes based on a generative model with functional and topological properties

 

Algorithm

Coverage

# Complexes

FRAC

MMR

ACC

PR

 

GMFTP

1168

179

0.868

0.591

0.765

0.593

 

AP

1363

207

0.697

0.785

0.497

0.444

 

CFinder

1161

114

0.653

0.439

0.693

0.440

 

ClusterONE

1293

203

0.847

0.571

0.775

0.564

 

Linkcomm

1126

407

0.903

0.646

0.744

0.456

Collins

MCL

1178

187

0.840

0.537

0.779

0.529

 

MCODE

853

115

0.743

0.496

0.730

0.593

 

MINE

1101

138

0.771

0.499

0.756

0.547

 

SPICi

958

124

0.708

0.448

0.728

0.570

 

SR-MCL

1304

337

0.875

0.625

0.755

0.481

 

GMFTP

1464

271

0.841

0.489

0.742

0.457

 

AP

1815

274

0.667

0.659

0.346

0.310

 

CFinder

1158

137

0.638

0.378

0.701

0.424

 

ClusterONE

1624

294

0.783

0.449

0.725

0.391

 

Linkcomm

1381

604

0.870

0.548

0.703

0.372

Gavin

MCL

1301

240

0.696

0.421

0.713

0.422

 

MCODE

899

155

0.710

0.438

0.685

0.492

 

MINE

1242

212

0.804

0.454

0.710

0.436

 

SPICi

1008

184

0.746

0.434

0.697

0.478

 

SR-MCL

1750

735

0.819

0.539

0.701

0.327

 

GMFTP

1244

270

0.756

0.474

0.722

0.491

 

AP

2506

391

0.575

0.433

0.242

0.182

 

CFinder

1143

115

0.433

0.281

0.555

0.268

 

ClusterONE

2044

539

0.720

0.431

0.708

0.326

 

Linkcomm

962

425

0.701

0.460

0.675

0.428

Krogan core

MCL

1933

388

0.671

0.377

0.691

0.299

 

MCODE

640

95

0.463

0.268

0.583

0.406

 

MINE

937

157

0.616

0.359

0.664

0.450

 

SPICi

1249

224

0.628

0.356

0.689

0.409

 

SR-MCL

2585

1833

0.884

0.575

0.686

0.197

 

GMFTP

1197

265

0.652

0.398

0.692

0.469

 

AP

3522

461

0.461

0.232

0.117

0.096

 

CFinder

914

88

0.287

0.172

0.543

0.277

 

ClusterONE

1114

239

0.481

0.296

0.633

0.407

 

Linkcomm

1925

998

0.652

0.424

0.687

0.317

Krogan extended

MCL

2973

531

0.503

0.254

0.636

0.190

 

MCODE

619

84

0.343

0.188

0.506

0.345

 

MINE

902

162

0.564

0.316

0.650

0.451

 

SPICi

1584

295

0.525

0.258

0.645

0.311

 

SR-MCL

3637

2644

0.702

0.431

0.617

0.154

 

GMFTP

1705

376

0.580

0.296

0.639

0.329

 

AP

4662

517

0.441

0.219

0.091

0.086

 

CFinder

635

75

0.263

0.119

0.453

0.297

 

ClusterONE

1402

346

0.429

0.227

0.554

0.280

 

Linkcomm

3396

1829

0.630

0.386

0.629

0.203

DIP

MCL

4007

609

0.451

0.234

0.628

0.173

 

MCODE

540

95

0.210

0.108

0.402

0.211

 

MINE

1135

260

0.536

0.268

0.585

0.333

 

SPICi

2103

403

0.455

0.228

0.583

0.245

 

SR-MCL

4825

3222

0.674

0.376

0.583

0.141

 

GMFTP

2456

434

0.687

0.377

0.723

0.378

 

AP

5632

206

0.316

0.064

0.027

0.044

 

CFinder

1729

110

0.220

0.127

0.512

0.186

 

ClusterONE

2580

473

0.610

0.318

0.683

0.325

 

Linkcomm

4119

4446

0.678

0.459

0.701

0.243

BioGRID

MCL

3652

335

0.314

0.158

0.520

0.126

 

MCODE

1087

136

0.297

0.154

0.514

0.294

 

MINE

2414

409

0.576

0.308

0.663

0.304

 

SPICi

2756

501

0.483

0.261

0.652

0.281

 

SR-MCL

5593

1097

0.496

0.273

0.594

0.143