Table 2. Correlation between gene expression and protein abundances computed by different methods.

For each pair of methods, the partial correlation is computed based on all mitochondrial genes for which comparison could be made. Data for mouse brainstem tissue. Each cell shows partial correlation based on all genes for which quantitative information is available by both methods that are compared, and based on genes quantified by all methods (shown in brackets). Both msInspect and msBID’s results are based on top 3 peptides with largest normalized area intensity. All correlation coefficients are computed using log-transformed gene and protein quantification measures.

	SpectrumMill	msInspect	msBID	NSAF	RPKM	Microarray
SpectrumMill	-	0.91 (0.92)	0.91 (0.91)	0.90 (0.90)	0.49 (0.51)	0.36 (0.40)
msInspect	0.91 (0.92)	-	0.89 (0.91)	0.87 (0.88)	0.51 (0.53)	0.40 (0.44)
msBID	0.91 (0.91)	0.89 (0.91)	-	0.84 (0.89)	0.54 (0.54)	0.41 (0.42)
NSAF	0.90 (0.90)	0.87 (0.88)	0.84 (0.89)	-	0.51 (0.53)	0.42 (0.44)
RPKM	0.49 (0.51)	0.51 (0.53)	0.54 (0.54)	0.51 (0.53)	-	0.62 (0.61)
Microarray	0.36 (0.40)	0.40 (0.44)	0.41 (0.42)	0.42 (0.44)	0.62 (0.61)	-