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Table 2 LOO benchmark comparison of MHC2SKpan with four well-known pan-specific methods on NielsenSet2. MRTA, Tepan, Pan1.0, Pan2.0 and MKpan are the abbreviations for MultiRTA, TEPITOPEpan, MetaMHCIIpan-1.0, MetaMHCIIpan-2.0 and MHC2SKpan, respectively. For each allele, we display the largest value in boldface.

From: MHC2SKpan: a novel kernel based approach for pan-specific MHC class II peptide binding prediction

  

AUC

PCC

allele

count

MRTA

Tepan

Pan1.0

Pan2.0

MKpan

MRTA

Tepan

Pan1.0

Pan2.0

MKpan

DRB1*01:01

5166

0.801

0.726

0.778

0.794

0.802

0.619

0.447

0.571

0.627

0.628

DRB1*03:01

1020

0.751

0.663

0.746

0.792

0.778

0.438

0.277

0.465

0.560

0.543

DRB1*04:01

1024

0.763

0.724

0.775

0.802

0.801

0.534

0.423

0.591

0.652

0.657

DRB1*04:04

663

0.835

0.783

0.852

0.869

0.862

0.623

0.504

0.693

0.731

0.714

DRB1*04:05

630

0.808

0.760

0.808

0.823

0.828

0.566

0.456

0.594

0.626

0.631

DRB1*07:01

853

0.817

0.759

0.825

0.886

0.889

0.620

0.499

0.655

0.753

0.761

DRB1*08:02

420

0.786

0.773

0.841

0.869

0.851

0.523

0.452

0.637

0.70

0.679

DRB1*09:01

530

0.674

0.615

0.653

0.684

0.674

0.380

0.259

0.406

0.474

0.471

DRB1*11:01

950

0.819

0.726

0.799

0.875

0.894

0.603

0.450

0.580

0.721

0.761

DRB1*13:02

498

0.698

0.661

0.658

0.648

0.639

0.365

0.326

0.323

0.337

0.341

DRB1*15:01

934

0.729

0.694

0.738

0.769

0.763

0.513

0.437

0.533

0.598

0.597

DRB3*01:01

549

0.813

0.675

0.716

0.733

0.70

0.603

0.332

0.449

0.474

0.423

DRB4*01:01

446

0.746

0.694

0.724

0.762

0.764

0.508

0.370

0.448

0.515

0.529

DRB5*01:01

924

0.788

0.680

0.831

0.879

0.883

0.543

0.421

0.627

0.722

0.737

average

14607

0.773

0.710

0.767

0.799

0.795

0.531

0.404

0.541

0.606

0.605