Table 1.
Difference of optimal codons depending on whether they end with -GC or -AT.
| Amino acid | Gene length | Expression | Recombination |
|---|---|---|---|
| FOPAT: FOP for aminoacids with AT-ending optimal codons | |||
|
Ala N = 53719 codons |
+0.0229NS | +0.2546*** | Co:-0.0656** nCo:-0.0217NS spo11:-0.0856*** dmc1:-0.0540* mre110:+0.0147NS mre116:-0.0659** |
|
Arg N = 43139 codons |
+0.0002NS | +0.4301*** | Co:+0.0293NS nCo:+0.0265NS spo11:+0.0297NS dmc1:+0.0488NS mre110:+0.0375NS mre116:-0.0037NS |
|
Cys N = 13614 codons |
+0.0535* | +0.2293*** | Co:-0.0162NS nCo:-0.0239NS spo11:-0.0229NS dmc1:+0.0030NS mre110:+0.0172NS mre116:-0.0158NS |
|
Gln N = 38581 codons |
+0.0603* | +0.2076*** | Co:-0.0777** nCo:-0.0546* spo11:-0.0495NS dmc1:-0.0873*** mre110:-0.0532NS mre116:-0.0565* |
|
Glu N = 65707 codons |
+0.1396*** | +0.1663*** | Co:-0.0658** nCo:-0.0573* spo11:-0.0796** dmc1:-0.1154*** mre110:-0.0252NS mre116:-0.0822** |
|
Gly N = 49861 codons |
+0.0470NS | +0.4385*** | Co:+0.0241S nCo:+0.0230NS spo11:+0.0298NS dmc1:+0.0406NS mre110:+0.0831** mre116:-0.0037NS |
|
Pro N = 43069 codons |
+0.0304NS | +0.3114*** | Co:-0.0509* nCo:-0.0292NS spo11:+0.0105NS dmc1:-0.0481NS mre110:+0.0116NS mre116:-0.0348NS |
|
Grouped N = 307690 codons R2 = 0.300*** P(GL)***,P(Expr)***, P(dmc1)***P(mre110)** |
+0.1271*** | +0.3732*** | Co:-0.0867** mCo:-0.0556* spo11:-0.0086*** dmc1:-0.1643*** mre110:-0.0601* mre116:-0.1074*** |
| FOPGC: FOP for aminoacids with GC-ending optimal codons | |||
| Leu N = 96687 codons |
-0.1031*** | +0.3690*** | Co:+0.1828*** nCo:+0.1451*** spo11:+0.2015*** dmc1:+0.2526*** mre110:+0.1206*** mre116:+0.1344*** |
|
Asn N = 60930 codons |
-0.1588*** | +0.2880*** | Co:+0.2101*** nCo:+0.2000*** spo11:+0.2687*** dmc1:+0.3655*** mre110:+0.1991*** mre116:+0.1866*** |
|
Asp N = 60058 codons |
-0.1995*** | +0.1485*** | Co:+0.1976*** nCo:+0.1500*** spo11:+0.2602*** dmc1:+0.3561*** mre110:+0.1437*** mre116:+0.1997*** |
|
Tyr N = 32887 codons |
-0.1850*** | +0.2240*** | Co:+0.1718*** nCo:+0.1401*** spo11:+0.2499*** dmc1:+0.3186*** mre110:+0.1834*** mre116:+0.1704*** |
|
Phe N = 44129 codons |
-0.1103*** | +0.2729*** | Co:+0.2689*** nCo:+0.1612*** spo11:+0.2628*** dmc1:+0.3413*** mre110:+0.1933*** mre116:+0.1772*** |
|
Lys N = 72564 codons |
-0.2207*** | +0.3210*** | Co:+0.2248*** nCo:+0.1475*** spo11:+0.2843*** dmc1:+0.3632*** mre110:+0.1471*** mre116:+0.2043*** |
|
His N = 21966 codons |
-0.1010*** | +0.1060*** | Co:+0.1193*** nCo:+0.1132*** spo11:+0.1623*** dmc1:+0.2096*** mre110:+0.1086*** mre116:+0.1357*** |
|
Grouped N = 389221 codons R2 = 0.424, P(GL)***,P(Expr)*** P(dmc1, mre110)*** |
-0.2604*** | +0.4005*** | Co:+0.2935*** nCo:+0.2291*** spo11:+0.3667*** dmc1:+0.5090*** mre110:+0.2341*** mre116:+0.2724*** |
Spearman Rank Correlations between optimal codon use, gene length, expression, and various recombination measures for amino acids and groups of amino acids with either AT- or with GC-ending optimal codons. 1554 genes for which all amino acids were present at least four times were used. Presented for grouped variables are also MR results of variables whose log-transformation did not grossly deviate from a normal distribution. *P < 0.05, **P < 0.01,***P < 0.001, NS = not significant.