Table 3.

Comparison of real time RT PCR, array and proteomics results for selected genes

Gene Name	Mmp Number	PCR Ratioa	Array Ratiob	P valuec	Proteomic Ratiod	n1e
16S RNAf	RNA standard	0.999 +/- 0.002
ppsA	Mmp1094	1.0 +/- 0.5	1.00 +/- 0.09	0.73	1.2 +/- 0.5	157
cbiA	Mmp1478	1.0 +/- 0.1g	1.02 +/- 0.07	0.65	1.5 +/- 0.2	10
atpB	Mmp1045	0.8 +/- 0.0	0.7 +/- 0.1	1.0 × 10-3	1.1 +/- 0.4	103
mtrE	Mmp1560	0.9 +/- 0.3g	0.6 +/- 0.2	8.0 × 10-4	1.3 +/- 0.6	8
mtrA	Mmp1564	0.9 +/- 0.2	0.7 +/- 0.2	8.3 × 10-3	1.4 +/- 0.3	17
porEh	Mmp1503	4.4 +/- 2.1g	2.8 +/- 0.6	1.5 × 10-5	2.0 +/- 0.9	29
ehbL	Mmp1623	4.9 +/- 0.2	4.4+/- 0.8	1.0 × 10-6	3.5 +/- 2.1	17

^aExcept as noted, real time RT PCR assays were done in triplicate from a single RNA sample and normalized to 16S rRNA as an unregulated standard.

^bArray ratios were calculated from four biological replicates, each with flipped dye slides containing two copies of the array. See supplementary Table S2 for the complete listing.

^cP values were calculated using a Wilcoxon nonparametric significance test (18) and represent the probability that the null hypothesis (a ratio of 1 indicating no difference between samples) is correct.

^dProteomics ratios were calculated from the average of ¹⁴N:¹⁵N or ¹⁵N:¹⁴N peptide pair ratios of detected peptides. See supplementary Table S2 for the complete listing.

^en₁ = number of peptide pairs used in the proteomic ratio calculation.

^f16S rRNA served to normalize the assays for RNA concentration and was assayed in triplicate for every set of reactions run. This value represents the average of nine measurements.

^gReal time RT-PCR was performed in triplicate on each of two biological samples. Hence, these values represent the average of six measurements.

^hporE encodes one of the subunits of pyruvate oxidoreductase. Pyruvate oxidoreductase activity was measured (3) and had an S40:S2 ratio of 2.6 ⁺/_- 0.9.