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Call Γ⊂ R q the set of all possible expression level profiles r(t) indexed by time t1,…, t q.
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For a comparison with Gupta et al. (2006), in which raw data are available and to avoid possible expression level-dependent bias in expression ratios, the correlation between expression ratio and mean expression level was also analyzed without any normalization; the results are virtually identical.
Bimax uses an underlying binary data model which assumes two possible expression levels per gene.
This is not surprising as the focal parameters correspond to the lowest and highest possible expression levels.
These issues should be addressed separately for each host/marker combination; genetic constructs should be optimized to achieve the highest possible expression levels without toxicity or effects on virulence.
Truth table construction: A truth table is a tabulated representation that illustrates the mapping of possible state (expression level) transitions under various input conditions, which obtained from digitized temporal gene expression profiles.
We assumed that for conditional trangenesis it was important to aim at having the lowest possible background expression level, even at the price of having a somewhat lower induced activity.
This could be explained either by differences in sensitivity between the two approaches or by possible miRNA expression level differences across mouse strains.
However, due to the semi-quantitative nature of the RT-PCR used it is possible that expression level differences have been underestimated.
All of the vectors have extensive multiple cloning sites, and versions are available for producing N- or C- terminal GFP fusions at each of the possible relative expression levels.
Although the detection of differential expression was possible, gene expression levels may have been underestimated as tag counts may have been incomplete.
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