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Genes were considered to be differentially expressed if they exhibited a 2-fold perturbation in gene expression magnitude in each of the three biological replicates, in a statistically significant manner (P<0.05).
The different technologies are functionally graded with respect to safety, expression magnitude and expression duration.
We generated simulated case-control expression data that spanned a range of sample sizes, differential expression magnitude (the difference between case and control sample distribution means), and differential expression degree.
The mean counts (white bars) convey information about expression magnitude of each gene by age.
One proviso concerns the interpretation of gene expression magnitude (read counts) in such data.
The process produced 27 clusters of DE genes reflecting temporal expression, magnitude of change, and variance.
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However, the biological importance of expression magnitudes in the systemic inflammatory response is unclear.
The dynamic change and absolute expression magnitudes during fruit ripening were shown in Additional File 9.
By close inspection of the temporal responses the dynamic changes in mRNA abundance revealed a very rapid onset of both pro- and anti-inflammatory mediators and a substantial variation in both expression magnitudes and duration of changes between genes.
This conclusion is based on the larger fold-change expression magnitudes obtained using qPCR relative to the microarray platform in the current study (Tables 2 and 3, Figure 4), as well as two previous studies that compared feeding impacts on gut gene expression using microarrays and quantitative pyrosequencing (showing higher expression by qPCR and pyrosequencing [ 26, 39]).
Viewed in this way, Reuter's initial estimate was not a calculation but an expression of magnitude: an attempt to explain that, as subterranean disasters go, the fire was a really big deal.
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