Skip to main content

Table 2 Prediction performances as measured by AUC values of ROC curves.

From: Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior

MHC

Data Size

SMM

SMMPMBEC

NetMHC

H-2_Db

303

0.909

0.901

0.933

H-2_Dd

85

0.813

0.837

0.925

H-2_Kb

223

0.811

0.833

0.850

H-2_Kd

176

0.928

0.931

0.939

H-2_Kk

164

0.772

0.793

0.790

H-2_Ld

102

0.932

0.942

0.977

HLA_A-0101

1157

0.977

0.977

0.982

HLA_A-0201

3089

0.946

0.946

0.957

HLA_A-0202

1447

0.898

0.899

0.900

HLA_A-0203

1443

0.916

0.916

0.921

HLA_A-0206

1437

0.913

0.916

0.927

HLA_A-0301

2094

0.927

0.928

0.937

HLA_A-1101

1985

0.938

0.939

0.951

HLA_A-2301

104

0.793

0.840

0.852

HLA_A-2402

197

0.803

0.801

0.825

HLA_A-2403

254

0.919

0.932

0.918

HLA_A-2601

672

0.916

0.924

0.956

HLA_A-2902

160

0.912

0.916

0.935

HLA_A-3001

669

0.935

0.941

0.947

HLA_A-3002

92

0.878

0.830

0.744

HLA_A-3101

1869

0.925

0.925

0.928

HLA_A-3301

1140

0.923

0.925

0.915

HLA_A-6801

1141

0.885

0.885

0.883

HLA_A-6802

1434

0.899

0.899

0.899

HLA_A-6901

833

0.867

0.880

0.880

HLA_B-0702

1262

0.959

0.960

0.965

HLA_B-0801

708

0.932

0.956

0.955

HLA_B-1501

978

0.937

0.940

0.941

HLA_B-1801

118

0.881

0.880

0.838

HLA_B-2705

969

0.936

0.941

0.938

HLA_B-3501

736

0.883

0.889

0.875

HLA_B-4002

118

0.832

0.843

0.754

HLA_B-4402

119

0.731

0.739

0.778

HLA_B-4403

119

0.757

0.753

0.763

HLA_B-4501

114

0.825

0.866

0.862

HLA_B-5101

244

0.876

0.895

0.886

HLA_B-5301

254

0.889

0.885

0.899

HLA_B-5401

255

0.923

0.935

0.903

HLA_B-5701

59

0.826

0.843

0.826

HLA_B-5801

988

0.942

0.945

0.961

Mamu_A-01

525

0.855

0.854

0.861

Mamu_A-02

283

0.765

0.783

0.809

Mamu_A-11

468

0.883

0.894

0.894

Mamu_B-01

205

0.949

0.956

0.967

Mamu_B-17

300

0.934

0.943

0.954

Patr_B-0101

132

0.964

0.975

0.969

average AUC

 

0.887

0.894

0.897

t-test|SMM

 

NA

0.001

0.057

t-test|NetMHC

 

0.057

0.470

NA

  1. For each MHC-specific binding data set, 5-fold cross validation was carried out using one of the four methods listed. Area-Under-Curve (AUCs) from the 5-fold cross validations are presented here. Also shown are p-values of average AUC values calculated using Student's t-test (2-tail, paired) with respect to the SMM and NetMHC prediction methods.