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Due to this complication, we used the expression values for Psmc3ip to normalize the data.
Therefore, we used the expression values of 34 type I IFN response genes (Table 2) (described previously [ 13]), which were averaged.
We therefore used the expression values of the probe IDs at 24h (Additional file 1: Table S1) for cluster3 analysis (Additional file 4: Figure S3 b).
To determine the prognostic value of the genes of the clusters identified by network analysis, we used the expression values obtained by microarrays in the two groups of MI patients of the test cohort.
ARTADE1 used the expression values themselves to elucidate the exon structure genome sequence under the assumptions of the Markov model, but did not take correlation into account (Toyoda and Shinozaki, 2005).
Herein we used the expression values of the set of proteins that were unambiguously quantified in the shotgun metaproteomes in the same set of samples used for activity tests (P1, Obese111 and LeanCE01),, to produce metabolic reconstructions of the entire gut metabolic network, where multiple proteins from multiple organisms are co-expressed.
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Following single gene-based significance testing, we used the expression value of DEGs (Pvalue<0.01) with at least 1.5-fold change to cluster the patients.
Following single gene-based significance testing, we used the expression value of DEGs (Pvalue<0.01) to cluster the patients for each comparison.
Clustering Following single miRNA-based significance testing, we used the expression value of miRNAs (P value <0.05 and at least two-fold expression) to cluster the patients for each comparison.
MiRABELLE uses the expression values measured by these probe-sets to calculate a biological activity score for each miRNA seed.
Gpat2 mRNA expression level was estimated by using the expression values of the Affymetrix probe 1456208_AT.
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