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This result suggests that the association between gene expression breadth and gene duplication is not as simple as reported previously.
To analyse the involvement of duplicated genes on tissue evolution, we initially focused on the relationship between gene expression breadth and gene duplication.
We observed the connection between gene expression breadth in humans and gene compactness to be significantly weaker than the connection between expression level and compactness, a result that is compatible with the selection hypothesis but not the genome design hypothesis.
They found that the connection between gene expression breadth in humans and gene compactness to be significantly weaker than the connection between expression level and compactness, which is compatible with the selection hypothesis but not the genome design hypothesis [ 13].
However, Lercher et al. reported that there is a strong correlation between gene expression breadth and GC content in human, suggesting that there might be selective pressure favoring the concentration of housekeeping genes in GC-rich isochors.
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).
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One interesting species-specific difference is the relationship between gene expression breadths and synonymous evolutionary rates.
For the comparison of gene expression breadth, expressed miRNA and non-miRNA target genes were first extracted from the dataset.
In contrast, we found a strong negative correlation between codon bias, and gene expression breadth with pathway position in several of the branches (fig. 4), with upstream genes having a higher codon bias and being more widely expressed than genes in downstream positions.
Indeed, the correlation between DNA methylation breadth and gene expression breadth was about twice as stronger as that between promoter CpG contents and gene expression breadths (Supplementary Material, Table S4).
The difference in the gene expression breadth between gbM and unmethylated genes was due to a higher proportion of the gbM genes (82.4 vs. 72% unmethylated genes) having a maximal expression breadth.
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