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We measured expression level as the geometric mean of expression among different tissues.
A filter procedure eliminated non informative transcripts on the basis of being well measured (expression level > mean + 2 standard deviations of background signal) in 100% of the samples.
Irreversible cell cycle arrest can be indicative of activation of a cell senescence program; we therefore measured expression level of p16INK4a and β-galactosidase activity as hallmarks for senescence.
First, we define the gene expression data matrix G p × n, where n samples are measured for p genes and each cell g ij is the measured expression level of gene i on sample j.
We then identify outlier exons by subtracting the predicted expression level of exons from their measured expression level, with values equaling zero when the measured expression level of an exon was similar to its predicted expression level (formulated in detail under Methods).
This result supports our previous observations about the relationship between measured expression level and tag-position.
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To assess radiation-induced response of protein markers in human lymphocytes irradiated ex vivo, we measured expression levels of our three best candidates, FDXR, DDB2 and ACTN1 protein, 3 days after initial exposure (Fig. 4B).
We also measured expression levels of classical HLA genes in eight HLA homozygous reference cell lines at baseline and after three treatments (heat shock, LPS, and IFN-gamma).
Measured expression levels are all relative to these references.
To test this idea, we measured expression levels of VEGFA in Ire1α−/− MEFs transfected with mouse processed-XBP1 plasmid.
To determine whether PERK signaling is involved in WFS1 upregulation by valproate, we measured expression levels of phosphorylated eIF2α, which reflect PERK activation levels.
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