Table 2 Summary of the rule model

Details of classification quality, annotations and classifications are found in Tables 3 and 4

a. Annotations, Rules and Classifications
Annotated genes  within the 23 broad classes of GO biological process	273
Gene probes  associated with the 273 genes within the 23 broad biological process classes	284
Training examples  annotations associated with the genes in the 23 broad biological process classes co-annotations^iassociated with the genes in the 23 broad biological process classes	549 444
Rules generated from the training examples	18064
Estimated quality of classifications of unknown genes (cross-validation estimates)
Sensitivity	84%
Specificity	91%
Fraction of classifications that are correct	49%
Classifications for unknown (uncharacterized) genes	548
classifications were obtained for 211 of the 213 unknown genes
(Re-)Classifications for training examples	728
True positive classifications519
True positive co-classifications^ii356
False positive classifications219
False negative (missing) classifications30
For 272 of the 273 training examples at least one correct (re-)classification was obtained

ⁱpairs of two different biological processes annotated to the genes in the dataset

ⁱⁱclassification of two different biological processes to one gene

b. Number of biological processes annotated or classified per gene
Number of biological processes per gene	Annotations for  training example genes	(Re-)Classifications for training example genes	Classifications for unknown genes
1	105	30	27
2	100	93	84
3	41	96	59
³ 4	27	54	41