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Filtering by a minimum expression level obscures the influence of extreme variability of low expressed genes.
This search returned a single hit, which appears to be a fragment of an ICK protein that was expressed exclusively in the venom gland, but did not meet the minimum expression level (>1 eCPM) for inclusion in the venom gland specific set.
For the heat map, the cancer gene list was further filtered by requiring a minimum expression level of at least 1,000 relative fluorescence units in at least 2 different hybridizations.
Figure 2C shows that, at constant Fd/Fa of 2.0/1.5, the Sensitivity of detection of differential expression drops as the restriction for the minimum expression level (Em) decreases.
Conversely, the minimum expression level of either NOR output must be lower than the minimum levels of either switch input.
A time point with the minimum expression level of the regulator gene becomes a splitting point of the time span.
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An additionally significant effect visible from this figure is the fact that the functionality of both signal transduction systems depends on the level of expression of the fluorescently labelled HOG1 protein: If the expression level of this protein is increased more than fivefold over minimum expression levels, neither the light- nor and stress-induced nuclear accumulation are detectable anymore.
In order to test this hypothesis, for each family with k TFs (TF1, TF2, ‥, TFk) and each tissue T, we computed the ratio R = (Emax-Esim)/(Emax-Emin), where Emax and Emin represent the maximum and the minimum expression levels, respectively, among the family members in tissue T. Thus, the R value is normalized for family-specific and tissue-specific gene expression.
For each family of TF (F1, F2, ‥, Fk) and each tissue T, we computed the ratio RI = (Emax-Emax2)/(Emax-Emin), where Emax and Emin represent the maximum and the minimum expression levels and Emax2 represents the second highest expression among the family members in tissue T. The ratio RI captures the increase in expression, i.e., high value of RG represents an expression increase.
The rationale is that these non-zero values represent minimum expression levels of genes and the transcripts are tissue-specific and under dynamic change, even though the expression level is very low.
Then, the normalized value of g x, y) is, where max g(, y) and min g(, y) represent the maximum and the minimum expression levels of gene y in all of the samples, respectively.
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