Table 4 Classification quality during cross-validation

10-fold cross-validation estimates of the area under the ROC curve (AUC), standard error (SE) for AUC, sensitivity and specificity for each of the 23 biological processes. Sensitivity is TP/(TP+FN) where TP (true positives) is the number of genes classified and annotated to the process and FN (false negatives) is the number of genes annotated but not classified to it. Specificity is TN/(TN+FP) where TN (true negatives) is the number of genes neither annotated nor classified to the process and FP (false positives) is the number of genes classified but not annotated to it. P-values indicate the probability of randomly obtaining an AUC value equal or greater than the AUC value obtained for each biological process. The probabilities were calculating by inducing rule models from examples where annotations were randomly permutated (1000 iterations).

PROCESS	AUC	SE	SENS.	SPEC.	P-VALUES
Ion homeostasis	1.00	0.00	1.00	1.00	0.008
Protein targeting	0.99	0.03	1.00	0.98	0.000
Blood coagulation	0.96	0.08	0.96	0.99	0.000
DNA metabolism	0.94	0.09	0.94	0.93	0.000
Intracellular signaling cascade	0.94	0.06	0.92	0.94	0.000
Energy pathways	0.93	0.12	0.89	0.99	0.000
Cell cycle	0.93	0.04	0.93	0.86	0.004
Oncogenesis	0.92	0.11	0.94	0.93	0.000
Circulation	0.91	0.11	0.87	0.95	0.001
Cell death	0.90	0.10	0.85	0.90	0.000
Developmental processes	0.90	0.07	0.91	0.90	0.000
Transcription	0.88	0.11	0.84	0.82	0.000
Defense (immune) response	0.88	0.05	0.88	0.91	0.002
Cell adhesion	0.87	0.09	0.85	0.91	0.002
Stress response	0.86	0.15	0.87	0.89	0.002
Protein metabolism and modification	0.85	0.10	0.83	0.86	0.000
Cell motility	0.84	0.11	0.83	0.89	0.000
Cell surface rec linked signal transd	0.82	0.15	0.79	0.84	0.005
Lipid metabolism	0.81	0.14	0.77	0.85	0.000
Transport	0.79	0.17	0.72	0.84	0.002
Cell organization and biogenesis	0.79	0.11	0.76	0.91	0.001
Cell proliferation	0.79	0.06	0.76	0.77	0.000
Amino acid and derivative metabolism	0.69	0.06	0.29	0.98	0.288
AVERAGE	0.88	0.09	0.84	0.91