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Between the linear motifs (VIII, IX), Motif IX was more significant than Motif VIII, which indicated that genes tended to be regulated directly by TFs, while miRNAs tended to regulate TFs while they were being formed rather than act as a mediated regulator between TFs and their target genes.
Although HT and HT+SEV tended to regulate individual MMP-2 activity, this tendency could not be confirmed by densitometry employing higher numbers of animals per group (Figure 6C).
That is, common-family TFs tended to regulate the cofunctional subpathways.
In addition, conserved miRNAs tended to regulate rapidly evolving targets, and upstream miRNAs evolved more rapidly than downstream miRNAs.
To explore whether the common-motif TFs tended to regulate cofunctional subpathways, we extracted 1061 human DNA motifs from the Transfac database.
In the left promoter category, the left gene was presented more than the right one (90 vs 71%), which indicates that left promoters regulate left genes; in contrary, the right promoters tended to regulate the right genes.
Similar(54)
According to the results of the top-down and the bottom-up analyses, we came to three conclusions: 1) the single-regulation motifs tend to regulate genes with PPIs.
For example, if the threshold of the synergistic regulation between TFs increases to 40 targets, the significance score would be elevated to 2. This result suggested that regulator pairs with common targets tend to regulate private targets with PPIs.
Correlating co-associations of 119 TFs with miRNAs from ENCODE, Gerstein et al. found that highly-connected TFs tend to regulate more miRNAs and to be more regulated by miRNAs as well [25].
Therefore, the regulators which participate in crosstalk motifs tend to regulate hub proteins, which are usually more essential than non-hub proteins [ 39- 41], and modular proteins, which usually form important protein complexes or modules in human PINs [ 42- 44].
"The basis of business is the belief in the invisible hand" -- Adam Smith's shorthand for the way competitive forces themselves tend to regulate markets -- according to David Colander, the Kelley professor of distinguished teaching at Princeton.
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