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
N1 - Funding Information:
We thank Akio Kanai, Shigeo Fujimori, Noriyuki Kitagawa, and Kunihiro Baba for useful discussions, and Kazuharu Arakawa, Hayataro Kochi, and Atsuko Kishi for their technical advice on G-language GAE. This work was supported by the Ministry of Education, Culture, Sports, Science, and Technology, Grant-in-Aid for the 21st Century Center of Excellence (COE) Program entitled “Understanding and Control of Life via Systems Biology” (Keio University).
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 - GT-ending codon usage
KW - Gene expression level
KW - Gene length
KW - Multivariate analysis
KW - Principal component analysis
KW - Synonymous codon usage
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U2 - 10.1016/j.febslet.2005.10.032
DO - 10.1016/j.febslet.2005.10.032
M3 - Article
C2 - 16289058
AN - SCOPUS:27744507140
VL - 579
SP - 6499
EP - 6504
JO - FEBS Letters
JF - FEBS Letters
SN - 0014-5793
IS - 28
ER -