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The measure of codon usage bias, CAI, is a significant predictor of expression levels for both species.
Codon usage bias is more likely to reflect the level of expression linked to protein evolution, because it determines the efficiency of translation and therefore will be a good predictor of expression level over the evolutionary history of the gene, rather than at a single time point in the laboratory.
We also found that gene expression variation increases as the number of TFs or the number of cis-elements increases and that the number of TFs regulating a gene is a much better predictor of expression variation than the number of cis-elements.
In this study, we hypothesize that the number of TFs is a significant predictor of expression variation and show that the number of TFs regulating a gene (hereinafter referred to as 'number of TFs') accounts for 8 14% of its expression variation, much higher than that can be explained by the number of cis-elements (0.3 1.7%).
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Transcription factors are highlighted with a † Since the predictive power of multivariate models based on all CpG probes in a CGI + SS is larger than the predictive power of the mean methylation value only, we now investigate which CpG in a CGI + SS are particularly important predictors of expression.
Therefore, PH-GFP expression was not an absolute predictor of CagAEPISA expression in the larval eye epithelium.
For ~18 % of the genes, gene expression in blood was a significant predictor of gene expression in lung.
Even though the CpG O/E of promoter is also a major predictor of the expression level, its effect size is much greater for the expression breadth than for the expression level.
The analysis showed that "group" (UF or F) remained the strongest predictor of differential expression compared to "MNA" (data not shown), which indicate that the altered expression levels of these transcripts are not a secondary effect of MNA.
In most cases this difference is large (Additional file 7), hence, the mean RE-score in a sample may be a much better predictor of the expression level of the targets of any particular miRNA, than is the expression profile of the miRNA itself.
Therefore, the GC content of promoters can be employed as a good predictor of gene expression noise, so that the higher promoter's GC content, the higher the expression variability.
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