Table 2.

Evaluation of predicted interactions by frequency of co-expression and functional similarity of GO terms

	Frequency of co-expression (Mean/Stddev)	Similarity of GO term (BP) Mean/Stddev)	Similarity of GO term(CC)(Mean/Stddev)
Protein – protein interaction datasets
Interolog	3.7/5.9	0.32/0.21	0.40/0.31
interolog + phylogenetic profile	4.18/6.45	0.34/0.22	0.43/0.31
Interologs predicted as false positives by phylogenetic profiles	2.70/4.58	0.29/0.17	0.34/0.30
Ortholog co-occurrence in operons	5.0/8.8	0.41/0.25	0.28/0.35
Ortholog co-occurrence in operons + phylogenetic profile	10.11/15.76	0.51/0.27	0.46/0.37
Negative data
	0.48/1.74	0.23/0.14	0.37/0.24

The interaction datasets were evaluated by co-expression frequency of interacting genes and similarity between gene ontology terms BP (Biological Process) and CC (Cellular component).

See Methods section for the details of co-expression frequency. Similarity between GO terms was calculated by using "getGeneSim" function in GOSim package [36].