Table 2

DEGseq analysis of marker genes as well as those highlighted in this study related to digit development

Genes

Tag raw counts

Hand DII-V vs. Hand DI

Hand DII-V vs. Foot

Hand DI vs. Foot


Hand DII-V

Hand DI

Foot

log2(Fold_change) normalized

p-value

log2(Fold_change) normalized

p-value

log2(Fold_change) normalized

p-value


Marker genes

Tbx5

175

134

6*

0.326

0.048

5.6385

1.04E-57

5.3125

1.81E-45

Pitx1

6

9

354*

-0.6441

0.3921

-5.1104

4.08E-67

-4.4663

3.04E-63

Meis2b

73*

12

18

2.5457

1.13E-11

2.7922

5.00E-17

0.2465

0.6365

Hoxd10b

61*

3

10

4.2866

1.09E-14

3.3811

5.17E-17

-0.9056

0.289

Krt17ab

68*

267

455

-2.3284

2.28E-40

-1.9474

4.40E-38

0.381

0.0003

Elongated digits

Tbx3b

118*

21

39

2.4312

4.16E-17

2.3695

2.10E-22

-0.0617

0.8689

Tbx15b

171*

41

89

2.0011

2.79E-19

1.7144

2.10E-21

-0.2868

0.2648

Bmp3b

19*

2

5

3.1888

1.04E-04

2.6983

2.64E-05

-0.4905

0.6626

Rgmbb

727*

133

289

2.3914

5.76E-95

2.1031

8.28E-112

-0.2882

0.0435

Smad1

264*

122

250

1.0545

4.34E-12

0.8509

1.01E-11

-0.2036

0.1782

Smad4

412*

244

351

0.6966

1.19E-09

1.0034

1.60E-22

0.3068

0.0086

Noga

5**

17

44

-2.1207

1.53E-03

-2.3427

6.61E-06

-0.2219

0.5543

Hoxd8

19*

1

4

4.1888

1.81E-05

3.0202

8.64E-06

-1.1686

0.4084

Hoxd9

45*

10

13

2.1108

1.88E-06

2.5637

3.17E-10

0.4529

0.4442

Satb1

397*

117

286

1.7035

1.48E-34

1.2454

3.85E-30

-0.4581

0.0019

Hoxa1b

61*

14

12

2.0642

4.50E-08

3.118

5.91E-16

1.0538

0.0577

Twist1b

2521*

809

1767

1.5806

7.26E-189

1.285

4.31E-191

-0.2957

3.08E-07

Tmeff2b

95*

22

50

2.0513

1.06E-11

1.6983

2.01E-12

-0.353

0.3091

Enpp2b

27*

0

6

5.6957

8.71E-08

2.9422

1.64E-07

-2.7535

0.0698

Thumb &Foot

Tbx4ab

20*

102

390

-2.7057

3.65E-19

-3.4906

2.48E-60

-0.7849

1.61E-08

Pitx2

21*

66

127

-1.7112

3.08E-07

-1.8241

6.16E-11

-0.1129

0.589

Acta1ab

412*

1463

4918

-2.1834

1.81E-197

-2.7825

0

-0.5991

9.29E-57

Tnnc2b

115*

534

1544

-2.2744

5.62E-69

-2.9747

6.36E-204

-0.7003

4.41E-26

Atp2a1

17*

103

223

-2.6582

3.49E-17

-2.9412

1.12E-30

-0.283

0.0813

Hrc

9*

40

67

-2.2112

2.34E-06

-2.1239

1.52E-07

0.0873

0.7535

Myoz1

8*

34

58

-2.1466

1.93E-05

-2.0857

1.37E-06

0.0609

0.8391


a, homologs of mouse genes, all others are the homologs of human genes; b, genes expression patterns validated by RT-qPCR; * indicates gene expression in the library is significantly higher or lower than in other two libraries (*, p < 0.001; **, p < 0.01).

Wang et al. BMC Genomics 2010 11:619   doi:10.1186/1471-2164-11-619

Open Data