Table 5

LOO benchmark comparison of the pan-specific NetMHCIIpan-2.0 and the NetMHCIIpan-1.0 methods

NetMHCIIpan-1.0

NetMHCIIpan-2.0

TEPITOPE


Allele

#

#bind

PCC

AUC

PCC

AUC

AUC


DRB1*0101

5166

3510

0.571

0.778

0.627

0.794

0.720

DRB1*0301

1020

277

0.465

0.746

0.560

0.792

0.664

DRB1*0401

1024

510

0.591

0.775

0.652

0.802

0.716

DRB1*0404

663

386

0.693

0.852

0.731

0.869

0.770

DRB1*0405

630

425

0.594

0.808

0.626

0.823

0.759

DRB1*0701

853

498

0.655

0.825

0.753

0.886

0.761

DRB1*0802

420

148

0.637

0.841

0.700

0.869

0.766

DRB1*0901

530

254

0.406

0.653

0.474

0.684

DRB1*1101

950

429

0.580

0.799

0.721

0.875

0.721

DRB1*1302

498

199

0.323

0.658

0.337

0.648

0.652

DRB1*1501

934

450

0.533

0.738

0.598

0.769

0.686

DRB3*0101

549

75

0.449

0.716

0.474

0.733

DRB4*0101

446

200

0.448

0.724

0.515

0.762

DRB5*0101

924

478

0.627

0.831

0.722

0.879

0.686


Ave

0.541

0.768

0.606

0.799

Ave*

0.570

0.786

0.639

0.819

0.718


The two methods are compared in a leave-one-out experiment on the peptide binding data described in the original NetMHCIIpan publication [29].

# is the number of peptide binding data for each allele, #bind is the number of peptides with a binding affinity stronger than 500 nM. NetMHCIIpan-1.0 is the method by Nielsen et al. [29], NetMHCIIpan-2.0 is the method described here, and TEPITOPE is the method by Sturniolo et al. [1]. Prediction values for NetMHCIIpan-1.0 were taken from [29]. Ave gives the per allele average, Ave* gives the per allele average of the 11 alleles characterized by the TEPITOPE method. In bold is highlighted the best performing method for each of the 14 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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