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This is particularly challenging because these 5000 genes have an expression range of 10 3 102 transcripts per cell, a dynamic range of five orders of magnitude.
Chip sensitivity and signal linearity were estimated by selecting a set of genes which spans an expression range from 60 FU (background level) to 8000 FU.
DAVID heat map analyses identified 26 genes with an expression range of 1.51 to 7.56 that functionally clustered into common GO terms related to oxidation-reduction and oxidoreductase activity.
The linear HMM can be interpreted as a segmentation method, where each state defines an expression range that a time-series follows, e.g. low or high expression, during a particular time interval.
Stem-loop RT-PCR is highly sensitive and can detect an expression range of at least 7 logs [ 26], while microarray platforms can usually detect a 3-4 lof of dynamic range [ 39, 40].
In the scope of this paper, the macroarray setup and assay were optimised for the following crucial parameters: A system designed for the simultaneous analysis of several hundreds of genes must be linear over an expression range that ideally covers the ~ 4.5 orders of magnitude of the mammalian transcriptome.
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Six genes exhibiting a broad expression range from samples harvested 12 hours postinoculation were selected for confirmation by RT-qPCR.
The 6 housekeeping genes studied displayed a wide expression range, with the Ct values from 14 to 33 (Fig. 1).
In contrast, miR-101 was hardly detectable in any of the samples (0.02; 0 0.13), and miR-31 exhibited low expression but a wider expression range (0.04; 0.046).
These genes had a wide expression range, having many genes expression values over 100 and even over 1000, but also lesser than 10.
Our data showed that promoter-methylated genes had a wider expression range and higher median expression than body-methylated genes in most tissues.
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