Table 2.
Partial Spearman Rank Correlation of Codon Bias Statistics and Genomic Variables
| Gene Expression |
Expression Breadth (τ) |
Ks |
Ka/Ks |
Ka |
Gene Length |
Intron Length |
GC_CDS |
GC_ third codon |
GC_ intron |
|||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Microarray |
RNA-seq |
Microarray |
RNA-seq |
Ks ≤2 |
Ks ≤1 |
Ks ≤2 |
Ks ≤1 |
Ks ≤2 |
Ks ≤1 |
|||||||||||||||||||||||
| Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | Rho | P | |||
| Codon usage bias statistic | ||||||||||||||||||||||||||||||||
| ENC | vs. | −0.1208 | 2.5380E- 18 | −0.0836 | 1.4840E- 09 | 0.0233 | 8.6452E- 02 | 0.0764 | 1.8114E- 08 | −0.0991 | 1.0410E- 11 | −0.0401 | 2.5855E- 02 | 0.1700 | 2.7720E- 32 | 0.1674 | 6.7550E- 21 | 0.1216 | 4.8000E- 17 | 0.0723 | 6.6000E- 05 | −0.0569 | 4.9886E- 05 | 0.0421 | 2.6759E- 03 | 0.1029 | 3.0190E- 14 | 0.1698 | 1.0606E- 36 | 0.1400 | 2.9156E- 25 | |
| Fop | vs. | 0.0647 | 3.9400E- 06 | 0.0387 | 5.3886E- 03 | −0.0050 | 7.1610E- 01 | 0.0511 | 1.6971E- 04 | 0.1240 | 8.1000E- 18 | 0.0898 | 8.7120E- 07 | −0.0790 | 8.8760E- 08 | −0.0651 | 3.6670E- 04 | −0.0656 | 7.6971E- 06 | −0.0512 | 5.1389E- 03 | −0.0456 | 1.2025E- 03 | −0.0235 | 9.1829E- 02 | 0.4273 | 8.2376E- 264 | 0.9766 | 0.0000E+ 00 | 0.3879 | 1.1119E- 209 | |
| ENC_prime | vs. | −0.0536 | 1.9512E- 04 | −0.0180 | 2.2357E- 01 | −0.0456 | 1.3748E- 03 | −0.0405 | 2.8932E- 03 | −0.1253 | 1.4040E- 17 | −0.0446 | 1.5730E- 02 | 0.1013 | 5.4600E- 12 | 0.0634 | 6.8209E- 04 | 0.0738 | 7.0500E- 07 | 0.0105 | 6.0351E- 01 | −0.0396 | 5.4170E- 03 | 0.0925 | 3.6760E- 11 | −0.1098 | 4.9028E- 16 | −0.0342 | 1.1883E- 02 | −0.0479 | 4.2922E- 04 | |
Note.—Rank correlations presented are pairwise partial rank correlations in which all the other variables listed in the table were included as covariates. Rho, Spearman’s partial rank correlation statistic; Ks, number of synonymous substitutions per synonymous sites between P. patens and C. purpureus GG1; Ka, number of nonsynonymous substitutions per nonsynonymous sites between P. patens and C. purpureus GG1; Gene length, physical length of genes in nucleotides in the genome; Intron length, physical length of the introns in nucleotides in the genome; GC_CDS, GC content of coding regions; GC_thirdcodon, GC content of third codon positions; GC_intron, GC content of introns; p, Benjamini–Hochberg false discovery rate.