Abstract
Multivariate analyses are often used to identify major trends of variation in synonymous codon usage among genes. These analyses need to be performed on properly normalized codon usage data to avoid biases masking this synonymous variation, i.e., gene length, amino acid usage, and codon degeneracy; however, previous studies have failed to do so. In this paper, we demonstrate that the use of alternative normalized data (called 'relative adaptiveness' in the literature) can avoid all these biases and furthermore, can identify more trends of variation among genes, including GC-ending codon usage, GT-ending codon usage, and gene expression level.
| Original language | English |
|---|---|
| Pages (from-to) | 6499-6504 |
| Number of pages | 6 |
| Journal | FEBS Letters |
| Volume | 579 |
| Issue number | 28 |
| DOIs | |
| Publication status | Published - 2005 Nov 21 |
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Keywords
- Amino acid usage
- Codon degeneracy
- GC-ending codon usage
- Gene expression level
- Gene length
- GT-ending codon usage
- Multivariate analysis
- Principal component analysis
- Synonymous codon usage
ASJC Scopus subject areas
- Biochemistry
- Biophysics
- Molecular Biology
Cite this
A problem in multivariate analysis of codon usage data and a possible solution. / Suzuki, Haruo; Saito, Rintaro; Tomita, Masaru.
In: FEBS Letters, Vol. 579, No. 28, 21.11.2005, p. 6499-6504.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A problem in multivariate analysis of codon usage data and a possible solution
AU - Suzuki, Haruo
AU - Saito, Rintaro
AU - Tomita, Masaru
PY - 2005/11/21
Y1 - 2005/11/21
N2 - Multivariate analyses are often used to identify major trends of variation in synonymous codon usage among genes. These analyses need to be performed on properly normalized codon usage data to avoid biases masking this synonymous variation, i.e., gene length, amino acid usage, and codon degeneracy; however, previous studies have failed to do so. In this paper, we demonstrate that the use of alternative normalized data (called 'relative adaptiveness' in the literature) can avoid all these biases and furthermore, can identify more trends of variation among genes, including GC-ending codon usage, GT-ending codon usage, and gene expression level.
AB - Multivariate analyses are often used to identify major trends of variation in synonymous codon usage among genes. These analyses need to be performed on properly normalized codon usage data to avoid biases masking this synonymous variation, i.e., gene length, amino acid usage, and codon degeneracy; however, previous studies have failed to do so. In this paper, we demonstrate that the use of alternative normalized data (called 'relative adaptiveness' in the literature) can avoid all these biases and furthermore, can identify more trends of variation among genes, including GC-ending codon usage, GT-ending codon usage, and gene expression level.
KW - Amino acid usage
KW - Codon degeneracy
KW - GC-ending codon usage
KW - Gene expression level
KW - Gene length
KW - GT-ending codon usage
KW - Multivariate analysis
KW - Principal component analysis
KW - Synonymous codon usage
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UR - http://www.scopus.com/inward/citedby.url?scp=27744507140&partnerID=8YFLogxK
U2 - 10.1016/j.febslet.2005.10.032
DO - 10.1016/j.febslet.2005.10.032
M3 - Article
VL - 579
SP - 6499
EP - 6504
JO - FEBS Letters
JF - FEBS Letters
SN - 0014-5793
IS - 28
ER -