ArticleBMC research notes2011
Relationship between amino acid composition and gene expression in the mouse genome.
Article in BMC research notes, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- A report on DNA sequence determinants in gene expression.Bioinformation · 2020Article
- Gene expression defines natural changes in mammalian lifespan.Aging cell · 2015Review
- Translational signatures and mRNA levels are highly correlated in human stably expressed genes.BMC genomics · 2013Article
- Three independent determinants of protein evolutionary rate.Journal of molecular evolution · 2013Review
- Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity.Nucleic acids research · 2013Review
- MGC: a metagenomic gene caller.BMC bioinformatics · 2013Article
- A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes.BMC genomics · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCodon bias is a phenomenon that refers to the differences in the frequencies of synonymous codons among different genes. In many organisms, natural selection is considered to be a cause of codon bias because codon usage in highly expressed genes is biased toward optimal codons. Methods have previously been developed to predict the expression level of genes from their nucleotide sequences, which is based on the observation that synonymous codon usage shows an overall bias toward a few codons called major codons. However, the relationship between codon bias and gene expression level, as proposed by the translation-selection model, is less evident in mammals.
findingsWe investigated the correlations between the expression levels of 1,182 mouse genes and amino acid composition, as well as between gene expression and codon preference. We found that a weak but significant correlation exists between gene expression levels and amino acid composition in mouse. In total, less than 10% of variation of expression levels is explained by amino acid components. We found the effect of codon preference on gene expression was weaker than the effect of amino acid composition, because no significant correlations were observed with respect to codon preference.
conclusionThese results suggest that it is difficult to predict expression level from amino acid components or from codon bias in mouse.
Identifiers
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Registered trials
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