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Codon Usage Space
Graphical representation of codon usage space The codon bias for each of the 64 codons in 10 common codon usage tables were compressed into 2 dimensions using principal component analysis where each codon is a vector. Two of the codons, ATG and TGG, are omitted since the bias is 1 for all organisms. Principal component 1 captures 42% of all information and principal component 2 captures 27%, i.e. 69% of all codon distribution information from the 10 organisms x 62 codons can be visually inspected in the graph. ‘Yeast’ denotes the codon distribution for all open reading frames in Saccharomyces cerevisiae, ‘Pichia’ denotes the codon distribution for all sequenced open reading frames in Pichia pastoris, ‘B subtilis’ denotes the codon distribution for all open reading frames in Bacillus subtilis, ‘Coli’ denotes the codon distribution for all open reading frames in Escherichia coli, ‘CHO’ denotes the codon distribution for all sequenced open reading frames in Cricetulus griseus (from where Chinese Hamster ovaries cells are derived), ‘Human’ denotes the codon distribution for all open reading frames in Homo sapiens, ‘Mouse’ denotes the codon distribution for all open reading frames in Mus musculus. ‘Sf9’ denotes the codon distribution for all sequenced open reading frames in Spodoptera frugiperda, ‘Coli 2’ denotes the codon distribution for highly expressed E. coli genes, ‘Sf9/Human’ denotes the codon distribution in a combined Sf9/Human table. The genome codon usage distributions are derived from the codon usage database (http://www.kazusa.or.jp/codon). Adapted from Trends Biotechnol. 2004 22:346-53. Codon Bias and Heterologous Protein Expression. Gustafsson, Govindarajan, Minshull. |
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