A direct comparison of protein interaction confidence assignment schemes

BMC Bioinformatics

Table 3 Correlation of interaction probabilities with the GO similarity measure, mRNA expression correlation and interaction conservation.*

Prob. Scheme	GO Annotation		Expression Correlation		Interaction Conservation
	SC	WA	SC	WA	SC^#	WA^#
BADER_LOW	0.424	-5.850	0.185	0.494	0.132	0.147
BADER_HIGH	0.501	-5.680	0.223	0.503	0.136	0.158
DEANE	0.385	-5.910	0.016	0.481	0.098	0.139
DENG	0.490	-5.620	0.185	0.511	0.102	0.147
SHARAN	0.471	-5.710	0.050	0.492	0.134	0.158
QI	0.425	-6.040	0.269	0.495	0.080	0.125
EQUAL	--	-6.320	--	0.482	--	0.102

*Bold values indicate the scheme that performs the best. Italicized values indicate potential circularity, i.e., schemes that use GO annotations or mRNA expression profiles for confidence scoring that are similar to those used here for comparative assessment. P-values for all the Spearman correlation measurements are significant. SC: Spearman Correlation; WA: Weighted Average.
^# All measurements were done at an E-value cut-off of 1 × 10^-10.

ISSN: 1471-2105