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Whether there is interplay between the tissue specificity and the molecular mechanism of mtDNA rearrangement is not clear.

However, it remains largely unknown whether there is a correlation between the tissue specificity of a miRNA and the number of diseases associated with it.

Finally, we observed a negative correlation between the tissue specificity index and the number of diseases in which a miRNA is implicated (Figure 1, R = −0.83, P = 0.058, Spearman's correlation).

Figure 3 shows the results for n = 10, illustrating the correlation between the tissue specificity of gene expression and NXScores.

We made a regression analyses between the tissue specificity and first intron length, average intron length, CDS length, and protein domain numbers.

The striking overlap between the tissue specificity of evolutionarily conserved miRNA and that of their target genes suggests that one of the main functions of primordial miRNAs may have been the regulation of genes implicated in the temporary control of the development of muscle and of the nervous system, in a tissue-specific manner.

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In order to verify this hypothesis, we compared the tissue specificity between the ubiquitously expressed genes (expression breadth ≥ 14) and the intermediately expressed genes (expression breadth = 8 or 9) with similar expression level.

For this reason we examined the relationship between clusters of PWM matches and the tissue specificity of the associated genes using published gene expression data ([ 26, 27]).

In the present study, we observed that the connection between gene expression breadth in chicken and gene compactness to be significantly stronger than the connection between expression level and compactness, and the tissue specificity of genes is positively correlated with first intron length (P < 0.0001, r = 0.07276).

The CGI-related PWMs and CGI-independent PWMs are listed in Tables 2 and 3. To examine the relationship between clusters of predicted TFBS and the tissue specificity of the genes where clusters were found, we generated a list of genes with expression data.

In brackets, number of QTT expected by random chance; backfat (FATB); gonad (GONA); adenohypophysis (AHYP); thyroid (THYG); hypothalamus (HYPO) To assess the tissue specificity of associations between transcripts and metabolites and to which extent QTT and functional gene sets associated with a particular metabolite were shared across tissues, we used two approaches: QTT overlap analysis and GSEA.

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