STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation

BMC Bioinformatics

Table 1 Summary of comparison between STOP and GO annotations

Species	Annotation source/gold standard	Recall	Precision	F-measure
human	Entrez Gene/Entrez Gene	0.993	0.678	0.806
human	Entrez Gene/GOA	0.979	0.674	0.798
	UniProt/GOA	0.998	0.608	0.756
mouse	Entrez Gene/Entrez Gene	0.990	0.791	0.879
mouse	Entrez Gene/MGI	0.990	0.791	0.879
	UniProt/GOA	0.999	0.746	0.854
rat	Entrez Gene/Entrez Gene	0.987	0.724	0.835
rat	Entrez Gene/RGD	0.959	0.713	0.818
	UniProt/GOA	0.999	0.736	0.847
fly	Entrez Gene/Entrez Gene	0.987	0.767	0.863
fly	Entrez Gene/FlyBase	0.978	0.762	0.857
	UniProt/GOA	0.992	0.751	0.855
worm	Entrez Gene/Entrez Gene	0.998	0.783	0.878
worm	Entrez Gene/WormBase	0.998	0.783	0.878
	UniProt/GOA	0.999	0.788	0.881
yeast	Entrez Gene/Entrez Gene	0.994	0.798	0.885
yeast	Entrez Gene/SGD	0.994	0.798	0.885
	UniProt/GOA	0.998	0.630	0.773
E. coli	Entrez Gene/Entrez Gene	1.000	0.611	0.758
E. coli	Entrez Gene/EcoCyc	0.340	0.354	0.347
	UniProt/GOA	0.964	0.826	0.890

Annotations based on Entrez Gene descriptions are compared against the gene2go annotations from Entrez Gene and species-specific databases where the annotations have been downloaded from http://www.geneontology.org, and STOP annotations based on UniProt descriptions are compared against GOA annotations. Recall and Precision are calculated for each gene and subsequently averaged. The F-measure is the harmonic mean of these average Recall and Precision values.

ISSN: 1471-2105