Table 1.

Performance comparison with pathway-based prediction

phenotype	best pathway-based		domain-based
	aucROC	sens × spec	aucROC (avg/std)	sens × spec (avg/std)
Gram stain	0.93	0.90	0.97/0.01	0.96/0.01
Oxygen Requirement	0.93	0.88	0.95/0.02	0.94/0.02

Prediction performance comparison between a pathway-based method [8] and the protein domain profile-based approach. The first column indicates the phenotype category. The second and fourth column represent the phenotype prediction performance in terms of the area under ROC curve (aucROC), the third and fifth column denote the prediction performance in terms of the product of sensitivity (sens) and specificity (spec). For the domain-based method the values denote average (avg) and standard deviation (std) over 100 repetitions of a ten-fold cross-validation with random partitioning. Performance values for the pathway-based methods have been taken from the supplemental material associated with the original work.