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Data were normalised to the median of relative expression in uninfected, pregnant controls, so the median of expression in the twelve controls = 1.
Figure 2 shows relations between likeliness of circadian oscillation (estimated by a periodicity test p-value) and the overall median of expression signal in time series.
In the initial analyses we used the median of expression ratios as cut off between "low" and "normal" expression, since the low-risk and high-risk separation of patients was equal.
For genes with more than one probe sets, the median of expression values were considered.
For genes with more than one set of probes, the median of expression values were used.
The expression level of PdhR is close to the median of expression levels of all transcription factors.
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Gene median centring was performed on the expression set, where the median of the expression values for a specific gene across all samples was subtracted from that gene.
An ordered list of all genes was generated using the Pearson correlation to the expression pattern of the average expression pattern of OXPHOS genes (the median of the expression patterns of OXPHOS genes that clustered in the hierarchical gene tree).
For this analysis, we selected the median value of expression levels (calculated for the 6 individuals) as the measurement of the level of expression considered for IPA.
Patient survival was determined using the median split of expression scores in a Kaplan Meier analysis.
Using a cutoff at the median value of expression, the authors describe no significant correlation with the outcome.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com