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 3 Fold changes 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

DP* (model)	Rs ^†	Class		GC3^‡	GCg^‡	Ka^§	Ks^§	Ka/Ks^§	Ks_noDS^§
ESC/NSC (A)	-0.175^¶	DPG	FC > 2	0.522^¶	0.437^¶	0.049 (0.10)	0.555 (0.45)	0.084 (0.14)	0.584 (0.23)
			FC < 0.5	0.584	0.454	0.044 (0.30)	0.545 (0.13)	0.075 (0.27)	0.580 (0.33)
		DSG	ESC	0.607^¥	0.448^¶	0.097^¶	0.627^¶	0.136^¶	0.703^¶
			NSC	0.642	0.469	0.058^#	0.563 (0.29)	0.101^#	0.619^¥
		NDPG		0.557	0.448	0.048	0.561	0.079	0.577
NSC/LVB (A)	-0.378^¶	DPG	FC > 2	0.510^¶	0.433^¶	0.042^#	0.548^¥	0.074^¥	0.570 (0.15)
			FC < 0.5	0.636	0.461	0.042 (0.27)	0.549 (0.25)	0.069 (0.24)	0.589 (0.49)
		DSG	NSC	0.580^¶	0.453 (0.10)	0.050 (0.28)	0.583 (0.16)	0.068 (0.35)	0.632^¥
			LVB	0.635	0.462	0.081^¶	0.592^#	0.123^¶	0.652^¶
		NDPG		0.587	0.457	0.049	0.562	0.081	0.585
ESC/HSC (A)	-0.338^¶	DPG	FC > 2	0.505^¶	0.431^¶	0.042^#	0.542^#	0.072^¥	0.565^¥
			FC < 0.5	0.610	0.469	0.052 (0.17)	0.547 (0.12)	0.082 (0.13)	0.583 (0.45)
		DSG	ESC	0.596^¶	0.447^¶	0.074^¶	0.603^#	0.107^¶	0.663^¶
			HSC	0.646	0.472	0.086^¶	0.593^¥	0.133^¶	0.647^¶
		NDPG		0.579	0.456	0.050	0.566	0.080	0.587
HSC/BM (A)	0.043 (0.08)	DPG	FC > 2	0.592^¥	0.459 (0.08)	0.065^¶	0.590^#	0.099^¶	0.627^#
			FC < 0.5	0.565	0.451	0.067 (0.05)	0.576 (0.20)	0.107 (0.05)	0.609 (0.13)
		DSG	HSC	0.638^#	0.473^#	0.070^¶	0.567 (0.25)	0.104^#	0.639^#
			BM	0.593	0.454	0.096^¶	0.615^#	0.148^¶	0.670^#
		NDPG		0.575	0.454	0.049	0.562	0.080	0.584
ESC/FNSC (B)	-0.238^¶	DPG	FC > 2	0.528^¶	0.442^¶	0.045 (0.50)	0.560 (0.42)	0.081 (0.42)	0.590 (0.31)
			FC < 0.5	0.598	0.454	0.053^¥	0.550 (0.19)	0.088^¥	0.580 (0.36)
		DSG	ESC	0.599^¶	0.455 (0.13)	0.083^¶	0.591^¶	0.125^¶	0.642^¶
			FNSC	0.635	0.460	0.062^¶	0.573 (0.06)	0.100^¶	0.630^¶
		NDPG		0.569	0.452	0.049	0.561	0.079	0.585
ESC/FLHSC (B)	-0.003 (0.90)	DPG	FC > 2	0.566 (0.50)	0.450 (0.09)	0.046 (0.46)	0.576^¥	0.073 (0.36)	0.606^#
			FC < 0.5	0.571	0.447	0.060^#	0.570 (0.08)	0.099^#	0.600^¥
		DSG	ESC	0.608 (0.32)	0.456 (0.44)	0.072^¶	0.571^¥	0.113^¶	0.625^¶
			FLHSC	0.617	0.455	0.097^¶	0.599^¶	0.143^¶	0.640^¶
		NDPG		0.562	0.450	0.051	0.557	0.082	0.579
FLHSC/FLLCP (B)	-0.058^#	DPG	FC > 2	0.572 (0.17)	0.446^¥	0.068 (0.08)	0.563 (0.44)	0.107 (0.06)	0.607 (0.16)
			FC < 0.5	0.587	0.458	0.069^¥	0.594^¥	0.104 (0.07)	0.629^¥
		DSG	FLHSC	0.600^¥	0.447^#	0.082^¶	0.564 (0.49)	0.123^¶	0.590 (0.50)
			FLLCP	0.624	0.460	0.068^¶	0.570 (0.28)	0.110^¶	0.614^¥
		NDPG		0.568	0.450	0.054	0.566	0.087	0.590
FLLCP/FLMBC (B)	0.108^¶	DPG	FC > 2	0.602^#	0.459^#	0.062^#	0.602^¶	0.096^¥	0.631^¶
			FC < 0.5	0.575	0.449	0.068^¶	0.566 (0.27)	0.107^¶	0.616^¥
		DSG	FLLCP	0.631^¶	0.465^¶	0.075^¶	0.581^#	0.116^¶	0.634^¶
			FLMBC	0.594	0.448	0.088^¶	0.600^¶	0.135^¶	0.652^¶
		NDPG		0.559	0.448	0.051	0.559	0.083	0.580
FLHSC/LTHSC (B)	-0.136^¶	DPG	FC > 2	0.537^¶	0.445 (0.82)	0.055 (0.14)	0.578 (0.06)	0.084 (0.41)	0.583 (0.29)
			FC < 0.5	0.587	0.445	0.075^¶	0.567 (0.14)	0.108^¶	0.603^¥
		DSG	FLHSC	0.606 (0.77)	0.463^¶	0.066^¶	0.579^#	0.103^¶	0.622^¶
			LTHSC	0.607	0.439	0.074^¶	0.586 (0.05)	0.112^¶	0.620^¥
		NDPG		0.552	0.444	0.048	0.557	0.081	0.577
LTHSC/STHSC (B)	0.086^#	DPG	FC > 2	0.567 (0.24)	0.437 (0.22)	0.084^¥	0.563 (0.26)	0.128 (0.05)	0.632^¥
			FC < 0.5	0.536	0.448	0.071^¶	0.614^#	0.107^#	0.634^¥
		DSG	LTHSC	0.590 (0.92)	0.446^#	0.063^#	0.564 (0.31)	0.106^¶	0.595 (0.16)
			STHSC	0.585	0.459	0.066^¶	0.575 (0.13)	0.109^¶	0.618^¥
		NDPG		0.553	0.444	0.051	0.560	0.082	0.577
STHSC/LCP (B)	0.141^¶	DPG	FC > 2	0.599^¶	0.449 (0.16)	0.076^¶	0.562 (0.43)	0.123^¶	0.615 (0.05)
			FC < 0.5	0.544	0.441	0.070^#	0.590 (0.06)	0.106^#	0.606 (0.14)
		DSG	STHSC	0.599 (0.99)	0.455 (0.44)	0.083^¶	0.610^#	0.104^#	0.605 (0.13)
			LCP	0.600	0.459	0.063^¶	0.578^¥	0.103^¶	0.617^¶
		NDPG		0.552	0.445	0.050	0.560	0.082	0.580
LCP/MBC (B)	-0.081^#	DPG	FC > 2	0.542^¶	0.443^¥	0.054^¥	0.580^¥	0.086 (0.12)	0.596 (0.16)
			FC < 0.5	0.584	0.450	0.066^#	0.570 (0.19)	0.103^#	0.610^¥
		DSG	LCP	0.606 (0.68)	0.456 (0.64)	0.072^¶	0.589^#	0.120^¶	0.626^#
			MBC	0.610	0.457	0.081^¶	0.590^#	0.124^¶	0.634^¶
		NDPG		0.560	0.448	0.051	0.558	0.084	0.582

*DP, differentiation pairs. ^†Rs: Spearman correlation coefficients (Rs) between FC (the fold change of gene expression) and GC3 (^¶P < 5 × 10^-6, ^#P < 0.005). P values are still shown if there was no significance (P > 0.05). ^‡Wilcoxon test was used to determine whether GC3 and GCg were different in a particular differentiation pair between developmental-pivotal genes (DPGs) enriched in earlier (FC > 2) and later (FC < 0.5) stages, as well as between developmental-specific genes (DSGs) expressed in the earlier and later stages (for example, FNSC refers to developmental specific genes in FNSC of differentiation pair ESC/FNSC (^¶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 DPGs and DSGs were higher (or lower) than Ka, Ks, Ka/Ks and Ks_noDS of non-developmental-pivotal genes (NDPGs) (^¶ P < 0.001, ^#P < 0.01, ^¥P < 0.05). P values are still shown if there was no significance (P > 0.05).

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