Table 4

Cross validation prediction performances of all methods on complete and similarity reduced datasets measured with AUC.

Allelic variant

ARB

SMM-align

PROPRED

combinatorial library

NN-align

Consensus

Consensus-best32


ALL

SR1

ALL

SR1

ALL

SR1

ALL

SR1

ALL

SR1

ALL

SR1

ALL

SR1


HLA-DPA1*0103-DPB1*0201

0.823

0.745

0.921

0.767

0.840

0.724

    0.943

0.793

0.932

0.809

0.935

0.796


HLA-DPA1*01-DPB1*0401

0.847

0.746

0.930

0.767

0.833

0.704

    0.947

0.802

0.938

0.803

0.941

0.794


HLA-DPA1*0201-DPB1*0101

0.824

0.743

0.909

0.786

0.849

0.723

    0.944

0.818

0.927

0.818

0.932

0.819


HLA-DPA1*0201-DPB1*0501

0.859

0.709

0.923

0.728

0.867

0.729

    0.956

0.787

0.942

0.781

0.946

0.782


HLA-DPA1*0301-DPB1*0402

0.821

0.771

0.932

0.818

0.864

0.756

    0.949

0.828

0.938

0.841

0.941

0.830


HLA-DQA1*0101-DQB1*0501

0.871

0.741

0.930

0.783

0.809

0.728

    0.945

0.805

0.933

0.809

0.942

0.811


HLA-DQA1*0102-DQB1*0602

0.777

0.708

0.838

0.734

0.765

0.752

    0.880

0.762

0.851

0.778

0.859

0.779


HLA-DQA1*0301-DQB1*0302

0.748

0.637

0.807

0.663

0.698

0.616

    0.851

0.693

0.823

0.690

0.837

0.692


HLA-DQA1*0401-DQB1*0402

0.845

0.643

0.896

0.761

0.681

0.637

    0.922

0.742

0.908

0.749

0.916

0.762


HLA-DQA1*0501-DQB1*0201

0.855

0.700

0.901

0.736

0.586

0.620

    0.932

0.777

0.917

0.774

0.923

0.779


HLA-DQA1*0501-DQB1*0301

0.844

0.756

0.910

0.801

0.802

0.745

    0.927

0.811

0.917

0.814

0.919

0.816


HLA-DRB1*0101

0.770

0.710

0.798

0.756

0.720

0.692

0.739

0.697

    0.843

0.763

0.810

0.759

0.820

0.769


HLA-DRB1*0301

0.753

0.728

0.852

0.808

0.699

0.669

    0.887

0.829

0.862

0.823

0.873

0.835


HLA-DRB1*0401

0.731

0.668

0.781

0.721

0.737

0.711

    0.813

0.734

0.799

0.735

0.804

0.738


HLA-DRB1*0404

0.707

0.681

0.816

0.789

0.769

0.753

0.823

0.803

0.826

0.800

    0.831

0.809


HLA-DRB1*0405

0.771

0.716

0.822

0.767

0.767

0.742

    0.870

0.794

0.847

0.797

0.851

0.797


HLA-DRB1*0701

0.767

0.736

0.834

0.796

0.773

0.750

0.762

0.729

    0.869

0.811

0.851

0.806

0.858

0.808


HLA-DRB1*0802

0.702

0.649

0.741

0.689

0.647

0.641

    0.796

0.698

0.772

0.708

0.778

0.710


HLA-DRB1*0901

0.747

0.654

0.765

0.696

0.572

0.553

    0.810

0.713

0.801

0.716

0.796

0.716


HLA-DRB1*1101

0.800

0.777

0.864

0.829

0.804

0.779

    0.900

0.847

0.880

0.850

0.885

0.854


HLA-DRB1*1302

0.727

0.667

0.797

0.754

0.600

0.577

    0.814

0.732

0.796

0.742

0.811

0.757


HLA-DRB1*1501

0.763

0.696

0.796

0.741

0.743

0.703

    0.852

0.756

0.820

0.756

0.827

0.758


HLA-DRB3*0101

0.709

0.678

0.819

0.780

0.655

0.655

    0.856

0.798

0.834

0.787

0.844

0.799


HLA-DRB4*0101

0.785

0.747

0.816

0.762

0.697

0.691

    0.870

0.789

0.844

0.791

0.846

0.784


HLA-DRB5*0101

0.760

0.697

0.832

0.776

0.728

0.711

    0.886

0.795

0.848

0.786

0.851

0.798


H-2-IAb

0.800

0.775

0.855

0.830

0.858

0.847

0.853

0.846

    0.866

0.847


Average

0.785

0.711

0.850

0.763

0.726

0.703

0.751

0.691

    0.882

0.782

0.864

0.783

0.871

0.786


Min

0.702

0.637

0.741

0.663

0.600

0.577

0.572

0.553

0.796

0.693

0.772

0.690

0.778

0.692


Max

0.871

0.777

0.932

0.830

0.804

0.779

0.867

0.756

0.956

0.847

0.942

0.850

0.946

0.854


1. SR1stands for similarity reduced.

2. The Consensus-best3 method is based on NN-align, SMM-align and combinatorial peptide library. PROPRED was used for allelic variants when combinatorial peptide library was not available

Best prediction performance for each allelic variant was highlighted. The best performing method for "ALL" dataset was highlighted with underline while the best performing method for "SR" dataset was highlighted in bold.

Wang et al. BMC Bioinformatics 2010 11:568   doi:10.1186/1471-2105-11-568

Open Data