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In this section, we call a gene 'expressed' if its cDNA probes have a median expression probability greater than 95% (see methods).
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Using PROGgene we validated unfavorable overall survival probability for samples with higher than median expression of WNT/CTNNB1 pathway genes (See Additional file 1: Figure S1).
By using as cut-off the median expression level of each kinase to distinguish the low-expressing (expression level lower than the cut-off value) from high-expressing patients (expression level equal or higher than the cut-off value), a trend towards a worse outcome in terms of event-free (AURK-A) and overall survival (AURK-A and AURK-B) probability for high expressors was found.
To evaluate relative centering, we propose modeling the probability that, for a randomly sampled probeset, the control samples will have a median expression value greater than the matched spike-in samples using the logit of a 4 th order polynomial for rankit intensity.
This overexpression translated into reduced survival wherein the 5-year actuarial probability of overall survival was 45% for high EZH2 expressors versus 82% for low expressors, using a median expression value of 10 as the cutoff.
The median expression level and the total expression level are shown as a line and whisker, respectively.
To evaluate if lncRNAs were expressed at high levels in subpopulations of cells, the authors used the lncRNA:mRNA median ratio which compares the median expression of lncRNAs to the median expression of mRNA.
Median expression: we found that the relationships with median expression were not linear (Figure 4).
Briefly, gene expression values are median centered, setting each gene's median expression value to zero.
Median expression values for each tag were calculated.
Median expression values were used for redundant probe sets.
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