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As another example, two other groups of genes were expressed periodically during the cell cycle with different phases of peak gene expression.
Temporal trends included: (1) peak gene expression at one of the sewage exposure timepoints with recovery to baseline levels after the depuration phase (e.g. vitelline envelope protein beta), (2) gene expression alterations that did not recover (e.g. glucose transporter 3), and (3) delayed gene expression alterations initiated only at the recovery timepoint (e.g. insulin-like growth factor 2).
Clustering by peak gene expression enabled classification of genes into temporally related groupings.
A large cluster of 510 genes showed peak gene expression 24 h after NTHi inoculation.
In general, the level of peak gene expression does not appear to influence the baySeq likelihood values.
Egr-1 mRNA expression reached a peak (gene expression value of 1.89 ± 0.63) 1 h after the EDRz was transfected.
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Adenoviral vectors have been reported to show peak gene expressions around Day 5 post-infusion and then persist for approximately two weeks [ 29].
Of the genes containing H3K27me3 promoter peaks, gene expression signals were correspondingly measured for 1953 and 1466 Affymetrix probe sets, corresponding to 1430 and 1107 annotated and expressed genes respectively.
Further data analyses were conducted using an in-house R pipeline containing tools for identifying peaks overlapping in two samples, the analysis of genomic distribution of peaks and the integration of peak and gene expression datasets.
Next, a rank score s was defined for every gene as s = F E t 2 + F E p 2, where FE i = 〈 g i(t)〉 T and, FE p denote the time-averaged mean and peak gene fold expression (FE) of the gene's time series, respectively, normalized to the maximal peak and maximal mean fold expression of all measured genes.
There are 1086 genes uniquely DE at 24 hours (Figure 3c), the peak of gene expression for T cell activation.
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