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Table 6 Performance comparision on Krogan-core, DIP and combined6 datasets

From: A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations

Data set

Algorithm

Number

CYC2008

SGD

   

JaccardI

JaccardS

Jaccard

JaccardI

JaccardS

Jaccard

Krogan-Core

MCODE

78

0.4492 3rd

0.2163

0.292

0.4001 1 st

0.2192

0.2832

 

MCL

374

0.2507

0.342

0.2893

0.2195

0.3236

0.2616

 

CFinder

1396 3rd

0.2913

0.3437

0.3154

0.2311

0.3263

0.2705

 

DPClus

497

0.2816

0.4142 3rd

0.3352

0.2443

0.3897 3rd

0.3003

 

IPCA

579

0.4744 2nd

0.4016

0.435 2nd

0.3403

0.3671

0.3532 2nd

 

CMC

2136 1 st

0.1065

0.1403

0.1211

0.091

0.1346

0.1086

 

COACH

348

0.4206

0.3971

0.4085

0.325

0.3575

0.3405

 

HC-PIN

167

0.3543

0.2891

0.3184

0.3152

0.292

0.3032

 

SPICi

227

0.3453

0.3383

0.3417

0.2991

0.3165

0.3075

 

ClusterONE

243

0.426

0.3568

0.3884 3rd

0.3556 3rd

0.3244

0.3393 3rd

 

WPNCA

374

0.3889

0.3646

0.3764

0.2673

0.3239

0.2929

 

CALM

1411 2nd

0.2728

0.4495 1 st

0.3395

0.2377

0.4299 1 st

0.3061

 

ClusterEPs

540

0.3185

0.3034

0.3108

0.2927

0.3034

0.2980

 

SE-DMTG

371

0.5124 1 st

0.432 2nd

0.4688 1 st

0.3973 2nd

0.4044 2nd

0.4008 1 st

DIP

MCODE

53

0.188

0.1099

0.1387

0.184

0.1098

0.1375

 

MCL

609

0.142

0.33

0.1986

0.1241

0.3031

0.1761

 

CFinder

2147 2nd

0.1654

0.346

0.2238

0.1544

0.3437

0.2131

 

DPClus

909

0.1786

0.3991

0.2468

0.1602

0.3695

0.2235

 

IPCA

1242 3rd

0.2283

0.4062 3rd

0.2923

0.1986

0.3938

0.2641

 

CMC

1192

0.2086

0.4344 2nd

0.2818

0.1894

0.4081 3rd

0.2587

 

COACH

329

0.2986 3rd

0.3878

0.3374

0.2509

0.3659

0.2977

 

HC-PIN

21

0.0097

0.0075

0.0085

0.0142

0.0077

0.01

 

SPICi

402

0.2213

0.3303

0.265

0.1944

0.3175

0.2412

 

ClusterONE

341

0.2752

0.2909

0.2828

0.2556 3rd

0.2918

0.2725

 

WPNCA

654

0.2889

0.4059

0.3376 3rd

0.2458

0.3922

0.3022 3rd

 

CALM

2447 1 st

0.1031

0.3773

0.1619

0.0931

0.3519

0.1473

 

ClusterEPs

728

0.2992 2nd

0.3941

0.3402 2nd

0.2963 1 st

0.4107 2nd

0.3442 2nd

 

SE-DMTG

758

0.3266 1 st

0.4717 1 st

0.386 1 st

0.2842 2nd

0.4504 1 st

0.3485 1 st

combined6

MCODE

63

0.2309

0.1661

0.1932

0.2089

0.1625

0.1828

 

MCL

508

0.2182

0.3799

0.2772

0.1854

0.3456

0.2414

 

CFinder

5140 1 st

0.1829

0.4858

0.2658

0.1621

0.4506 3rd

0.2384

 

DPClus

658

0.2548

0.4742

0.3315

0.2227

0.4261

0.2925

 

IPCA

2160 2nd

0.3850 2nd

0.5025 3rd

0.4360 2nd

0.3136 2nd

0.4556 2nd

0.3715 2nd

 

CMC

892

0.2573

0.5006

0.3399

0.2188

0.4442

0.2932

 

COACH

682

0.2872

0.5082 2nd

0.3670 3rd

0.221

0.4458

0.2955

 

HC-PIN

176

0.2606

0.2481

0.2542

0.2225

0.2139

0.2181

 

SPICi

348

0.3033 3rd

0.4307

0.3560

0.2614 3rd

0.382

0.3104 3rd

 

ClusterONE

648

0.2292

0.4387

0.3011

0.1944

0.3971

0.261

 

WPNCA

898

0.2252

0.4339

0.2965

0.181

0.3943

0.2482

 

CALM

2064 3rd

0.2229

0.476

0.3036

0.1894

0.4255

0.2621

 

ClusterEPs

907

0.2542

0.3206

0.2836

0.2533

0.3381

0.2896

 

SE-DMTG

490

0.4679 1 st

0.5208 1 st

0.493 1 st

0.3520 1 st

0.471 1 st

0.4029 1 st

  1. CYC2008 and SGD are used as standard complexes.
  2. NOTE: The highest value in each row is shown in bold