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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