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The selected table included fold change values averaged from three data sets per genotype, each having a fold change >2 and p-value <0.01.
We show only the pairs of samples having a fold change supported by statistical significance.
Unchanged genes were defined as genes having a fold change value less than 1.2.
Transcripts were stringently determined as differentially expressed when having a fold change greater than 4 and an adjusted P value less than 0.01.
DE genes were defined as having a fold change in gene expression >1.5 and a Benjamini and Hochberg corrected FDR of <0.05 (Benjamini and Hochberg 1995).
Volcano plots were produced using samples having a fold change of ≥ |1.5| and also having a p-value ≤ 0.05 as compared to the control [ 30].
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"You're absolutely not having a fold-down bed, though".
In xpa-1, we identified 2815 differentially expressed transcripts having a fold-change of ≥1.8 (Supplementary Table 3).
This is particularly evident when the number of differentially expressed genes between two mouse inbred strains (C57 vs. Bl6, 126 genes with 7 genes having a fold-change > 3) is compared to that between diseased and healthy muscle tissue (mdx vs. wild-type, 1298 genes with 221 genes having a fold-change >3).
Of the genes represented the expression of a total of 333 transcripts showed differential regulation by zinc depletion (having a fold-change greater than 1.8 and an adjusted P-value less than 0.1, controlling for a 10% False Discovery Rate).
In total 525 genes were regulated (having a fold-change more than 1.8 fold change and an adjusted P-value less than 0.1 which is controlling a 10% False discovery rate, FDR) by zinc supplementation, but little overlap was observed between genes regulated at successive time-points.
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