Concordance across the transcriptome and proteome data subsets. Concordance across the transcriptome and proteome data subsets. Genes were either upregulated due to germ status (red, GF/C > 1, qmin < 0.1), downregulated (blue, GF/C < 1, qmin < 0.1), unaffected (gray, qmin ≥0.1), or unquantified (n.q.; black). Tallies were used to quantify the overall levels of concordancy (light green) and discordancy (light yellow and red). The overlapping, significantly affected genes were analyzed using HCAs (only rows were clustered; gray = missing value). Each row depicts a gene, and each column depicts a pair of mice (1 GF, one conventional, sex and strain matched, from one microarray; same pairing for the proteome and transcriptome columns). Each standard deviation (σst) was calculated across the columns independently for each data subset and mouse strain using the log2-transformed GF/C ratios. Nathan P. Manes et al. mSystems 2017; doi:10.1128/mSystems.00107-17