Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiaegene function

Table 6 The area under the precision versus recall curve for different classifiers

GO branch	GO specificity	RF	FL1*	FL2*	FL3*	Funckenstein (RF + FL1)	Funckenstein (RF + FL2)	Funckenstein (RF + FL3)
BP	3 to 10	0.215	0.111	0.173	0.245	0.225	0.286	0.286
	11 to 30	0.306	0.197	0.296	0.359	0.331	0.422	0.441
	31 to 100	0.349	0.117	0.329	0.33	0.36	0.454	0.441
	101 to 300	0.394	0.169	0.373	0.394	0.405	0.492	0.491
MF	3 to 10	0.44	0.188	0.134	0.309	0.445	0.489	0.463
	11 to 30	0.557	0.296	0.216	0.383	0.558	0.599	0.565
	31 to 100	0.596	0.29	0.232	0.393	0.597	0.632	0.61
	101 to 300	0.75	0.55	0.24	0.595	0.753	0.77	0.762
CC	3 to 10	0.368	0.242	0.546	0.571	0.413	0.597	0.596
	11 to 30	0.377	0.261	0.441	0.465	0.417	0.523	0.524
	31 to 100	0.489	0.249	0.44	0.496	0.508	0.578	0.586
	101 to 300	0.524	0.271	0.391	0.468	0.537	0.591	0.595

*FL1, FL classifier based on shared gene characteristics in Table 3; FL2, FL classifier based on direct gene-gene relationships in Table 4; FL3, FL classifier based on both relationship types. Entries in bold are the best Funckenstein classifier; entries in italics are the best individual classifier. BP, biological process; CC, cellular component; FL, functional linkage; GO, Gene Ontology; MF, molecular function; RF, random forest.

ISSN: 1474-760X