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Note that the shape of the expression profile, not its absolute level, dictates its classification.
Variations in this parameter maintain the overall shape of the expression profile, but affect the normalized concentration levels and the timing of the peak.
The shape of the expression curve, as well as amplitude and timing of peak expression, varied between 1-hour and 4-hour sampling.
HMM3 on the other hand is mostly concerned with the overall shape of the expression patterns and therefore ranks the photosynthesis genes highly in all three cases despite their inverted pattern and the presence of noise.
We conclude from the agreement with direct measurements of Fis protein and fis mRNA that reporter genes are a reliable tool for tracking the shape of the expression profile of the host gene.
It implies that when the half-lives of the host-gene products are unknown, we can still obtain a result that preserves the qualitative shape of the expression profile.
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Some genes in FC13 also fall into clusters NP2 and NP24 (Additional file 1), in which the shapes of the expression profiles in the two cultivations are similar, but the expression level is higher during D-xylonate production compared to the control (i.e. less down-regulated in NP2 and more up-regulated in NP24).
The abnormal shape of the wnt4a ectodermal expression domain in tbx1 mutants might reflect a requirement of endodermal contacts for proper expression, as wnt4a expression was lost in sox32 mutants that lack endoderm (supplementary material Fig. S3M).
Because changes in a limited number of genes could not account for a change in the shape of the entire gene expression distribution, changes in variance suggest alterations at global levels of gene expression regulation.
This study shows that the exposure of different tissues in fungi to different types of antagonists shapes the expression pattern of defense loci in a tissue-specific manner.
Hence, both the belonging to a given subset and the activation status contributed strongly and equally to the shaping of the gene expression programs of mature DC subsets.
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