Table 4

Five-fold cross-validation performance of the pan-specific NetMHCIIpan-2.0 method compared to the allele-specific NN-align and TEPITOPE methods on the quantitative benchmark data set

NN-align

NetMHCIIpan-2.0

TEPITOPE


Allele

#

# bind

PCC

AUC

PCC

AUC

AUC


DRB1*0101

7685

4382

0.675

0.825

0.711

0.846

0.727

DRB1*0301

2505

649

0.690

0.855

0.709

0.864

0.718

DRB1*0302

148

44

0.272

0.659

0.525

0.757

DRB1*0401

3116

1039

0.643

0.833

0.670

0.848

0.762

DRB1*0404

577

336

0.565

0.766

0.630

0.818

0.747

DRB1*0405

1582

627

0.710

0.869

0.698

0.858

0.780

DRB1*0701

1745

849

0.718

0.855

0.740

0.864

0.777

DRB1*0802

1520

431

0.518

0.778

0.526

0.780

0.645

DRB1*0806

118

91

0.744

0.902

0.796

0.924

0.884

DRB1*0813

1370

455

0.729

0.878

0.746

0.885

0.750

DRB1*0819

116

54

0.370

0.706

0.608

0.808

DRB1*0901

1520

622

0.597

0.810

0.634

0.818

DRB1*1101

1794

778

0.756

0.873

0.777

0.883

0.793

DRB1*1201

117

81

0.699

0.860

0.764

0.892

DRB1*1202

117

79

0.695

0.866

0.769

0.900

DRB1*1302

1580

493

0.630

0.819

0.634

0.825

0.596

DRB1*1402

118

78

0.623

0.825

0.694

0.860

DRB1*1404

30

16

0.466

0.661

0.613

0.737

DRB1*1412

116

63

0.680

0.857

0.757

0.894

DRB1*1501

1769

709

0.641

0.815

0.653

0.819

0.731

DRB3*0101

1501

281

0.673

0.843

0.690

0.850

DRB3*0301

160

70

0.604

0.826

0.736

0.853

DRB4*0101

1521

485

0.701

0.854

0.675

0.837

DRB5*0101

3106

1280

0.735

0.865

0.765

0.882

0.760


Ave

33931

13992

0.631

0.821

0.688

0.846

Ave*

0.673

0.841

0.697

0.854

0.744

Ave**

0.580

0.797

0.679

0.837


# gives the number of peptide binding data for each allele, #bind gives the number of peptides with a binding affinity stronger than 500 nM. NN-align is the method described by Nielsen et al. [5], NetMHCIIpan-2.0 is the method described here, and TEPITOPE is the method described by Sturniolo et al. [1]. Ave gives the per allele average, Ave* gives the per allele average of the 13 alleles characterized by the TEPITOPE method, and Ave** gives the per allele average of the 11 allele not characterized by the TEPITOPE method. In bold is highlighted the best performing method for each of the 24 alleles. AUC values were calculated using a binding threshold of 500 nM. Only AUC values are included for the TEPITOPE method since prediction values for this method are not linearly related to the binding affinity.

Nielsen et al. Immunome Research 2010 6:9   doi:10.1186/1745-7580-6-9

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