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Finally, we evaluated the correlation between expression changes and the presence of intergenic L1s.
We saw no correlation between expression changes and the patient's age, sex, or race.
As soon as the underlying regulatory machinery is impeded (as for the NAP mutants), this coherence between expression changes and the metabolic network is substantially reduced.
A strong correlation between expression changes and nucleosome occupancy, Pol II and H3K4me2 dynamics was not observed (Supplementary Figures S7C S7E).
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To exclude this possibility, we examined the relationship between expression change and either number of TFBSs or SNPs over the same parameter space (see Materials and Methods).
The discrepancies between expression change and the histone modification divergence in these duplicate gene types (TATA-containing, TATA-less, TATA-diverge) are observed.
Because FFRPs can function as activators [ 37] or repressors [ 38] we tested for both positive and negative correlation between expression changes of an FFRP and its target genes.
In rhesus macaques, for example, expression analysis revealed a strong correlation between miRNA expression changes and male sexual maturation [ 6].
These methods are based on a model assuming a linear relationship between gene expression changes and TF-gene binding affinities.
A Spearman rank correlation test was used to assess the correlation between gene expression changes and treatment duration.
A correlation between gene expression changes and growth rates was evaluated on the basis of three gene clusters.
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