Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation

Ren, Lichen; Gao, Ge; Zhao, Dongxin; Ding, Mingxiao; Luo, Jingchu; Deng, Hongkui

doi:10.1186/gb-2007-8-3-r35

Table 2 The levels of gene expression are correlated with GC3 and GCg

From: Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation

Cell (model)	Rs*	EXP	GC3^†	GCg^†	Ka^#	Ks^#	Ka/Ks^#	Ks_noDS^#
ESC (A)	-0.166^‡	H	0.537^‡	0.442^‡	0.042^‡	0.542^‡	0.069^‡	0.558^‡
		M_L	0.580	0.452	0.057	0.573	0.090	0.604
NSC (A)	-0.098^‡	H	0.551^‡	0.446^‡	0.039^‡	0.537^‡	0.067^‡	0.555^‡
		M_L	0.581	0.453	0.054	0.572	0.089	0.604
HSC (A)	0.010 (0.65)	H	0.579 (0.26)	0.456 (0.20)	0.052^§	0.558 (0.10)	0.084^§	0.581^¶
		M_L	0.582	0.455	0.057	0.572	0.090	0.602
LVB (A)	0.056^§	H	0.583^¶	0.455^§	0.042^‡	0.541^‡	0.070^‡	0.568^‡
		M_L	0.575	0.451	0.054	0.570	0.088	0.601
BM (A)	0.036 (0.09)	H	0.578 (0.38)	0.456^¶	0.054^‡	0.564 (0.19)	0.087^‡	0.577^§
		M_L	0.577	0.453	0.057	0.572	0.093	0.605
ESC (B)	-0.112^‡	H	0.550^‡	0.447^‡	0.042^‡	0.555^¶	0.069^‡	0.573^‡
		M_L	0.583	0.453	0.061	0.568	0.098	0.604
FNSC (B)	0.014 (0.45)	H	0.573 (0.31)	0.452 (0.27)	0.040^‡	0.546^§	0.066^‡	0.565^‡
		M_L	0.574	0.451	0.056	0.568	0.091	0.601
FLHSC (B)	-0.108^‡	H	0.551^‡	0.447^§	0.047^‡	0.554^§	0.077^‡	0.567^‡
		M_L	0.581	0.452	0.062	0.574	0.098	0.607
FLLCP (B)	-0.120^‡	H	0.557^‡	0.450^§	0.047^‡	0.558^¶	0.075^‡	0.572^‡
		M_L	0.585	0.453	0.062	0.573	0.100	0.608
FLMBC (B)	-0.109^‡	H	0.548^‡	0.447^§	0.047^‡	0.547^‡	0.078^‡	0.563^‡
		M_L	0.579	0.451	0.062	0.580	0.098	0.613
LTHSC (B)	0.041 (0.07)	H	0.559 (0.23)	0.446 (0.12)	0.049^‡	0.547^§	0.081^§	0.560^§
		M_L	0.555	0.443	0.055	0.570	0.089	0.593
STHSC (B)	0.015 (0.50)	H	0.552 (0.15)	0.445 (0.48)	0.048^‡	0.550^§	0.078^‡	0.558^‡
		M_L	0.558	0.445	0.056	0.571	0.091	0.597
LCP (B)	-0.092^§	H	0.546^‡	0.444^‡	0.048^‡	0.557^¶	0.077^‡	0.569^‡
		M_L	0.573	0.450	0.058	0.570	0.096	0.602
MBC (B)	-0.056^§	H	0.558^§	0.446^§	0.053^‡	0.555^§	0.084^‡	0.570^‡
		M_L	0.572	0.450	0.059	0.573	0.096	0.606
CD45 (B)	-0.003 (0.87)	H	0.579 (0.35)	0.455^¶	0.050^‡	0.560 (0.09)	0.080^‡	0.577^‡
		M_L	0.580	0.452	0.063	0.572	0.101	0.610

*Rs: Spearman correlation coefficients between EXP (the levels of gene expression) and GC3 (^‡P < 5 × 10^-6, ^§P < 0.005). P values are shown if there was no significance (P > 0.05). ^†Wilcoxon test was used to determine whether GC3 and GCg of highly expressed genes (H) were lower (or higher) than GC3 and GCg of mid to lowly expressed genes (M_L). Highly expressed genes and mid to lowly expressed genes were divided by quantiles of 0.67 (Q_0.67) of the levels of gene expression (^‡P < 0.001, ^§P < 0.01, ^¶P < 0.05). P values are shown if there was no significance (P > 0.05). ^#Wilcoxon test was used to determine whether Ka, Ks, Ka/Ks and Ks_noDS of highly expressed genes (H) were lower than Ka, Ks, Ka/Ks and Ks_noDSof mid to lowly expressed genes (M_L) (^‡P < 0.001, ^§P < 0.01, ^¶P < 0.05). P values are shown if there was no significance (P > 0.05).

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