Table 1

ICU and CC biasness analysis
E. coli L. lactis P. pastoris S. cerevisiae
Null hypothesis (H0) DH = U DH = DA DH = U DH = DA DH = U DH = DA DH = U DH = DA
Alternative hypothesis (H1) DHU DHDA DHU DHDA DHU DHDA DHU DHDA
No. of biased amino acids (P-value < 0.05) 18 17 19 17 18 19 18 19
No. of unbiased amino acids (P-value ≥ 0.05) 1 2 0 2 1 0 1 0
No. of singular amino acids 2 2 2 2 2 2 2 2
No. of unevaluated amino acids (Expect count < 5) 0 0 0 0 0 0 0 0
Total no. of amino acids 21 21 21 21 21 21 21 21
No. of biased amino acid pairs (P-value < 0.05) 314 99 327 15 354 259 372 282
No. of unbiased amino acid pairs (P-value ≥ 0.05) 26 23 12 65 38 36 19 9
No. of singular amino acid pairs 4 4 4 4 4 4 4 4
No. of unevaluated amino acid pairs (Expect count < 5) 76 294 77 336 24 121 25 125
Total no. of amino acid pairs 420 420 420 420 420 420 420 420

The chi-squared statistic is computed based on the observed occurrence of each codon (pair) and the expected occurrence under the null hypothesis of uniform distribution. Any amino acid (pair) with p-value < 0.05 is considered to exhibit significantly biased codon (pair) usage. Singular amino acids (methionine and tryptophan) and singular amino acid pairs (pairs only consisting of methionine and/or tryptophan) are not amenable to the biasness analysis since they are not encoded by more than one synonymous codon (pair). Chi-squared statistic and p-value are not calculated for amino acid (pair) with expected counts less than 5 (see Materials and Methods for details). Abbreviations: DA, codon (pair) distribution of all genes in the genome; DH, codon (pair) distribution of high-expression genes; U, uniform distribution.

Chung and Lee

Chung and Lee BMC Systems Biology 2012 6:134   doi:10.1186/1752-0509-6-134

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