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A supervised, weighted metric such as RF proximity de-emphasizes the diverging time points while emphasizing the common phase of induction, resulting in the grouping of the functionally related genes.
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Samples collected 20 to 100 h after elicitor treatment diverged significantly from earlier time points.
Furthermore, since inferring pattern of divergence between species can be biased when closely related species (e.g. incomplete lineage sorting) or highly divergent species (saturation on synonymous sites) are used, the use of species that diverged at two different time points should reduce these problems.
For ami-13.3, we observed diverging expression profiles at both time points of salt stress as compared with the empty-vector control.
As the figure indicates, while these genes display similar levels at the early time points they diverge at the later time points.
We hypothesised that this could be due to the fact that the survival curves diverged mainly toward the latter time points of the survival assay (Fig. 2).
The pattern of gene set enrichment over time seemed to indicate that the proportion of MCF7 cells in different phases of the cell cycle diverged at early and late time points.
Thus, actin gene sequences within the three types of complex groups plus the orthologous groups in the primates, which had similar phylogenetic structures in dinoflagellates at some extent [ 26], appeared to have diverged from one another at different time points during and after speciation.
In contrast, only the 80 and 100 h control samples diverged from those collected at earlier control time points.
In the case of Ahr we expect co-expression during early time points, whereas expression may diverge later when the influence of Ahr diminishes.
The U0126 and LY294002 signatures when compared to each other were very similar at the 4 h and 8 h time points (average ICC = 0.83), but diverged at 24 h post treatment (average ICC = 0.59).
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