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Table 4 Prediction on archived GOA files using BMA (see Eq. (6)) by combining the GO annotations in CC, MF and BP together and then evaluating in each sub-ontology

From: Interspecies gene function prediction using semantic similarity

  

MicroAvgF1

MacroAvgF1

1-RankLoss

Fmax

RAccuracy

CC

H →H

0.8700

0.4416

0.9682

0.8619

0.2057

 

M →H

0.8550

0.4407

0.9310

0.8551

0.1963

 

M+H →H

0.8765

0.4451

0.9791

0.9006

0.2457

 

D →H

0.8543

0.4372

0.9387

0.8610

0.1626

 

D+H →H

0.8666

0.4412

0.9652

0.8773

0.1852

 

A →H

0.8424

0.4388

0.8862

0.8595

0.1428

 

A+H →H

0.8673

0.4358

0.9518

0.8761

0.1895

 

M →M

0.8193

0.4430

0.9487

0.8481

0.1556

 

H →M

0.8155

0.4416

0.9475

0.8514

0.1582

 

H+M →M

0.8256

0.4507

0.9692

0.8795

0.1853

 

D →M

0.8085

0.4433

0.9289

0.8490

0.1446

 

D+M →M

0.8170

0.4474

0.9460

0.8560

0.1452

 

A →M

0.7963

0.4258

0.9121

0.8160

0.1157

 

A+M →M

0.8162

0.4377

0.9241

0.8385

0.1410

MF

H →H

0.8539

0.4287

0.9569

0.8394

0.1983

 

M →H

0.8514

0.4282

0.9468

0.8352

0.1721

 

M+H →H

0.8606

0.4312

0.9721

0.8785

0.2349

 

D →H

0.8513

0.4232

0.9507

0.8290

0.1358

 

D+H →H

0.8532

0.4294

0.9540

0.8451

0.1945

 

A →H

0.8435

0.4217

0.9060

0.8049

0.0921

 

A+H →H

0.8453

0.4239

0.9394

0.8187

0.1508

 

M →M

0.7980

0.4015

0.9426

0.8066

0.1528

 

H →M

0.7963

0.3927

0.9246

0.8001

0.1501

 

H+M →M

0.8078

0.4090

0.9672

0.8629

0.1937

 

D →M

0.7596

0.3936

0.9096

0.7748

0.1108

 

D+M →M

0.7989

0.4053

0.9427

0.8216

0.1563

 

A →M

0.7452

0.3883

0.8856

0.7528

0.0815

 

A+M →M

0.7949

0.3984

0.9274

0.7829

0.1395

BP

H →H

0.8376

0.7977

0.9522

0.8023

0.2058

 

M →H

0.8320

0.7861

0.9267

0.8134

0.1791

 

M+H →H

0.8450

0.8055

0.9694

0.8390

0.2421

 

D →H

0.8374

0.7917

0.9513

0.8041

0.1948

 

D+H →H

0.8370

0.7978

0.9502

0.8098

0.2032

 

A →H

0.8248

0.7840

0.8998

0.8119

0.1433

 

A+H →H

0.8322

0.7830

0.9328

0.7941

0.1796

 

M →M

0.7814

0.6968

0.9372

0.7916

0.1864

 

H →M

0.7892

0.6884

0.9384

0.7901

0.1897

 

H+M →M

0.7949

0.7132

0.9611

0.8276

0.2363

 

D →M

0.7829

0.6999

0.9364

0.7853

0.1818

 

D+M →M

0.7820

0.7033

0.9365

0.7910

0.1883

 

A →M

0.7694

0.6897

0.9023

0.7769

0.1417

 

A+M →M

0.7779

0.6874

0.9199

0.7822

0.1732

  1. H →H directly uses GO annotations of Human to predict annotations of Human genes. M →H only employs annotations of genes from Mouse to predict annotations of Human genes. M+H →H uses GO annotations of genes from Mouse and Human to predict annotations of Human genes. D+H →H uses annotations of genes from Danio rerio and Human to predict annotations of Human genes. A+H →H uses annotations of genes from Arabidopsis thaliana and Human to predict annotations of Human genes. M →M, H+M →M, D+M →M and A+M →M follow the similar protocol, but predict annotations of Mouse genes. The data in boldface is the statistically significant best among these comparing methods for a particular target species, and the significance is checked by paired t-test at 95% confidence intervals