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Table 1 Down-regulated genes in Smad4 null ES cells and/or day 4 embryoid bodies

From: Smad4-dependent pathways control basement membrane deposition and endodermal cell migration at early stages of mouse development

Down-regulated

Embryonic Stem Cell Array

Day 4 Embryoid Body Array

Gene ID

Gene Description

RefSeq

Chr

ES Array Fold Change

Q-PCR data Fold Change

P-value

EB Array Fold Change

Q-PCR data Fold Change

P-value

Tgf-beta pathway

Id1

Inhibitor of DNA binding 1

NM_010495

2

9.2

8.43 ± 2.09

0.013

7.4

23.3 ± 4.14

0.0017

Id2

Inhibitor of DNA binding 2

NM_010496

12

3.8

7.23 ± 2.32

0.1193

1.7

n.d.

n.d.

Id3

Inhibitor of DNA binding 3

NM_008321

4

2.8

3.13 ± 0.72

0.0279

1.8

n.d.

n.d.

Gdf1

Growth differentiation factor 1

NM_008107

8

4.0

3.73 ± 0.18

<0.0001

1.75

4.01 ± 0.56

0.0018

Lefty2 (Ebaf)

Left-right determination factor 2

NM_177099

1

3.7

5.47 ± 1.18

0.0096

1.47

n.d.

n.d.

Lefty1

Left-right determination factor 1

NM_010094

1

1.6

1.77 ± 0.1

0.0004

-

n.d.

n.d.

Tgfb2

Transforming growth factor, beta 2

NM_009367

1

3.0

n.d.

n.d.

-

n.d.

n.d.

Msx1

Homeobox, msh-like 1

NM_010835

5

1.7

n.d.

n.d.

2.5

n.d.

n.d.

Extracellular matrix related

Mmp14

Matrix metalloproteinase 14 (membrane-inserted)

NM_008608

14

4.5

5.44 ± 0.57

0.0002

3.2

5.16 ± 0.85

0.0028

Mmp9

Matrix metalloproteinase 9

NM_013599

2

1.6

2.97 ± 0.33

0.001

1.54

1.79 ± 0.28

0.092*

Cd44

CD44 antigen

NM_009851

2

2.7

7.25 ± 2.73

0.0625*

1.9

5.28 ± 1.62

0.0409

Tgfb1i1 (Hic5)

Transforming growth factor beta 1 induced transcript 1

NM_009365

7

2.8

7.39 ± 2.54

0.046

2.1

6.26 ± 1.95

0.0357

Gastrulation markers

Gsc

Goosecoid homeobox

NM_010351

12

-

n.d.

n.d.

15

7.11 ± 0.79

< 0.0001

Fgf8

Fibroblast growth factor 8

NM_010205

19

2.0

n.d.

n.d.

14.1

13.85 ± 2.58

0.0006

Sp5

Trans-acting transcription factor 5

NM_022435

2

2.4

n.d.

n.d.

12

n.d.

n.d.

T

Brachyury

NM_009309

17

2.3

n.d.

n.d.

10.6

60.7 ± 8.43

0.0004

Lhx1

LIM homeobox protein 1

NM_008498

11

-

n.d.

n.d.

10.6

n.d.

n.d.

MixL1

Mix1 homeobox-like 1

NM_013729

1

-

n.d.

n.d.

6

13.98 ± 2.93

0.0046

En1

Engrailed 1

NM_010133

1

1.6

n.d.

n.d.

4.95

n.d.

n.d.

Wnt8a

Wingless-related MMTV integration site 8A

NM_009290

18

-

n.d.

n.d.

4.4

n.d.

n.d.

Sox9

SRY-box containing gene 9

NM_011448

11

-

n.d.

n.d.

3.5

n.d.

n.d.

Fgf17

Fibroblast growth factor 17

NM_008004

14

2.5

n.d.

n.d.

2.4

n.d.

n.d.

Wnt9a

Wingless-type MMTV integration site 9A

NM_139298

11

2.4

n.d.

n.d.

-

n.d.

n.d.

Eomes

Eomesodermin

NM_010136

9

-

n.d.

n.d.

2.1

8.03 ± 0.67

< 0.0001

Chrd

Chordin

NM_009893

16

-

n.d.

n.d.

1.97

n.d.

n.d.

Cer1

Cerberus 1 homolog

NM_009887

4

-

n.d.

n.d.

1.91

n.d.

n.d.

Foxa2

Forkhead box A2

NM_010446

2

-

n.d.

n.d.

1.8

8.98 ± 2.55

0.0216

Fgf5

Fibroblast growth factor 5

NM_010203

5

-

n.d.

n.d.

2.16

3.16 ± 0.14

< 0.0001

Igf2

Insulin-like growth factor 2

NM_010514

7

3.3

3.9 ± 0.72

0.0078

1.7

n.d.

n.d.

  1. Micro-array and Q-PCR results are presented as fold change ratios relative to normalised wild-type values. The ES array results denote the average fold change of the two independent null cell lines. Genes with a 1.5 fold decrease were considered as differentially expressed. Q-PCR data is displayed as the mean ± standard error of the mean (SEM) of mRNA expression levels relative to Hprt. Genes validated by Q-PCR are significantly differentially expressed (p < 0.05), except for those indicated by an asterisk. n.d. validation not determined. A subset of differentially expressed transcripts is shown. * indicates higher than 0.05 P value for Q-PCR validation.