Skip to main content

Advertisement

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.