. 2009 Dec 14;10:419. doi: 10.1186/1471-2105-10-419

Table 7.

Analysis of prediction results by the gene ontology slims

Results on the yeast data sorted according to AUC
	GO term	# of cases	Best method	AUC	GO term explanation

1	0005198	39513	C¹	0.90	Structural molecular activity

2	0007124	9192	C	0.89	Pseudohyphal growth

3	0006997	10093	C	0.89	Nucleus organization

4	0007047	18668	C	0.89	Cell wall organization

5	0005215	44019	C	0.89	Transporter activity

Results on the yeast data sorted according to P20R

	GO term	# of cases	Best method	P20R	GO term explanation

1	0005618	8689	M2	1.00	Cell wall

2	0006997	10093	C	0.97	Nucleus organization

3	0042254	44304	C	0.95	Ribosome biogenesis

4	0005198	39513	C	0.92	Structural molecule activity

5	0008289	10690	M2	0.92	Lipid binding

Results on the human data sorted according to AUC

	GO term	# of cases	Best method	AUC	GO term explanation

1	0008907	245	C	1.00	Integrase activity

2	0004871	71939	C	0.92	Signal transducer activity

3	0051704	88280	C	0.92	Multi-organism process

4	0008219	98990	C	0.92	Cell death

5	0016740	244001	C	0.91	Transferase activity

Results on the human data sorted according to P20R

	GO term	# of cases	Best method	P20R	GO term explanation

1	0009405	1017	M2	1.00	Pathogenesis

2	0008907	245	M2	1.00	Integrase activity

3	0004871	71939	C	0.91	Signal transducer activity

4	0004872	208752	C	0.88	Receptor activity

5	0016301	110554	C	0.88	Kinase activity

Results on the combined data sorted according to AUC

	GO term	# of cases	Best method	AUC	GO term explanation

1	0008907	245	C	0.99	Integrase activity

2	0004871	77553	C	0.92	Signal transducer activity

3	0015267	7183	C	0.91	Channel activity

4	0004872	208752	C	0.91	Receptor activity

5	0051704	88280	C	0.91	Multi-organism process

Results on the combined data sorted according to P20R

	GO term	# of cases	Best method	P20R	GO term explanation

1	0005618	8689	M2	1.00	Cell wall

2	0009405	1017	M2	1.00	Pathogenesis

3	0008907	245	M2	1.00	Integrase activity

4	0006997	10093	M2	0.97	Nucleus organization

5	0008289	10690	M2	0.92	Lipid binding

¹C: the consensus method that integrates the four methods M1 through M4.

For each combination of a data set (the yeast, the human or the combined data) and an evaluation scheme (AUC or P20R), five GO terms are listed for which best performance was achieved. For each GO term, the number of protein-protein pairs in the data set is shown in the third column for which either protein in the pair is annotated with that GO term. Also shown are the best-performing method (column 4) and its performance (column 5).