Table 3

Fold changes of gene expression are correlated with GC3 and GCg

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).

Ren et al. Genome Biology 2007 8:R35   doi:10.1186/gb-2007-8-3-r35