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Table 5 Substitution patterns.

From: The surprising negative correlation of gene length and optimal codon use - disentangling translational selection from GC-biased gene conversion in yeast

  Gene length Expression Recombination
2761 genes
AT -> GC
n = 47762 conserved, 7014 changes
R2 = 0.038***
P(GL)***,P(Expr)**
P(dmc1)***,P(mre110)NS
+0.1082* -0.1922*** Co:+0.0178NS
nCo:+0.0041NS
spo11:+0.0218NS
dmc1:+0.0290NS
mre110:+0.0252NS
mre116:+0.0287NS
GC -> AT
n = 26739 conserved, 5677 changes
R2 = 0. 068***
P(GL)***,P(exp)**
P(dmc1, mre110)***
+0.2193*** -0.2435*** Co:-0.1277***
nCo:-0.0338**
spo11:-0.1502***
dmc1:-0.1636***
mre0:-0.1193***
mre6:-0.1112***
GC -> GC
n = 26739 conserved, 842 changes
R2 = 0.349***
P(GL)***,P(expr)NS,
P(dmc1)***,P(mre110)**
+0.2048*** -0.1615*** Co:+0.0210NS
nCo: +0.0343NS
spo: +0.0027NS
dmc1:-0.0234NS
mre0:+0.0173NS
mre6:-0.0160NS
AT -> AT
n = 47762 conserved, 281 changes
R2 = 0.746***
P(GL)***,P(expr)***,
P(dmc1, mre110)NS
+0.1559*** -0.0454NS Co:-0.0156NS
nCo:-0.0388*
spo:-0.0804**
dmc1:-0.0735***
mre110:-0.0208NS
mre116:-0.0063NS
AT->GC/(AT->GC+GC->AT) -0.0752*** +0.0441* Co:+0.0983***
nCo:+0.0211 NS
spo11: +0.1103***
dmc1:+0.1213***
mre110:+0.0947***
mre116:+0.0946***
1965 genes; controlling for effects of gene position
AT-> GC
n = 29013 conserved, 4126 changes
R2 = 0.011**
P(GL)NS,P(expr)NS,
P(dmc1, mre110)*
-0.0281NS -0.1210*** Co:+0.0264NS
nCo:-0.0084NS
spo11:+0.0241NS
dmc1:+0.0418NS
mre110:+0.0077NS
mre116:+0.0416NS
GC-> AT
n = 18164 conserved, 3594 changes
R2 = 0.055***
P(GL)NS,P(Expr)* P(dmc1,
mre110)***
+0.0118NS -0.1420*** Co:-0.1025***
nCo:-0.0765***
spo11:-0.0848***
dmc1:-0.1117***
mre110:-0.1004***
mre116:-0.0704***
GC-> GC
n = 18164 conserved, 509 changes
-0.0136NS -0.0748*** Co:+0.0345NS
nCo:+0.0143NS
spo11:+0.0556*
dmc1:+0.0433NS
mre110:+0.0038NS
mre116:+0.0214NS
AT-> AT
n = 29013 conserved, 171 changes
-0.0460* +0.0322NS Co:-0.0151NS
nCo:-0.0644**
spo:-0.0648*
dmc1:-0.0377NS
mre110:+0.0031NS
mre116:+0.0285NS
AT->GC/(AT->GC+GC->AT) -0.0329NS +0.0131NS CO:+0.0824**
nCo:+0.0642**
spo11:+0.0664**
dmc1:+0.0932***
mre110:+0.0609**
mre116:+0.757**
  1. Spearman Rank Correlations of directed substitutions at four-fold degenerated sites (that to not change the non-optimal status) and of the proportion of AT->GC substitutions with gene length, expression, and various recombination measures, with and without controlling for an effect of gene position. Presented 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.