Table 2 |
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Differential expression data based on array experiments and Q-PCR of ectoderm marker genes |
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|
Ectoderm markers |
Expression |
Regulation |
P value |
Q-PCR ratio ± error |
|
|
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|
Bmp2/4 SpSMBLIT_68K21 |
Oral |
Li 1.32 Zn 1.54 |
3.13 × e-01 7.33 × e-01 |
1.27 ± 0.29 0.97 ± 0.25 |
|
Chordin 537REA_13L23 |
Oral |
Li nd Zn 0.40 |
nd 4.55 × e-05 |
1.19 ± 0,19 0.41 ± 0,12 |
|
Goosecoid RUDIREA_9C8 |
Oral |
Li 1.05 Zn 0.27 |
8.43 × e-01 4.13 × e-03 |
0.75 ± 0.08a 0.16 ± 0.06 |
|
Lefty 536REAsu4_7H9 |
Oral |
Li 1.80 Zn nd |
1.91 × e-07 nd |
0.98 ± 0.22a 2.17 ± 0,14 |
|
Nodal 536REA_98I13 |
Oral |
Li na Zn na |
na na |
1.34 ± 0,11 4.12 ± 0,23 |
|
IrxA SpSMBLAS_51E6 |
Aboral |
Li 0.38 Zn |
2.51 × e-09 |
0.08 ± 0.05 1.60 ± 0.02 |
|
Nkx2.2 536REAsu4_10G11 |
Aboral |
Li 0.37 Zn nd |
7.69 × e-08 nd |
0.15 ± 0.13 5.87 ± 0.15 |
|
Spec2A |
Aboral |
Li nd Zn nd |
nd nd |
na 10.64 ± 1.67 |
|
Tbx2 RUDIREA_26D12 |
Aboral |
Li 0.20 Zn |
3.50 × e-12 |
0.12 ± 0.01 1.42 ± 0.24 |
|
Dp-Hbn SpSMBLAS_141N1 |
Apical |
Li 0.14 Zn nd |
1.41 × e-07 nd |
0.05 ± 0.02 1.03 ± 0.21 |
|
FoxJ RUDIREA_13I13 |
Apical |
Li 1.40 Zn 2.29 |
2.86 × e-02 3.26 × e-07 |
0.93 ± 0.20a 1.84 ± 0.04 |
|
FoxQ 537REA_3F18 |
Apical |
Li 0.24 Zn 4.51 |
3.55 × e-14 5.01 × e-07 |
0.15 ± 0.03 4.66 ± 0.78 |
|
Glass 536REAsu2_5I1 |
Apical |
Li 0.52 Zn na |
2.99 × e-01 na |
ne 0.03± 0.01 |
|
ZFhpf4 537REA_15C23 |
Apical |
Li 0.24 Zn na |
7.78 × e-07 na |
1.20 ± 0.00 2.05 ± 0.15 |
|
Hypothetical RUDIREA_15C22 |
Apical + SMC late |
Li 0.59 Zn 4.27 |
4.79 × e-01 3.24 × e-02 |
0.20 ± 0.06 1.11 ± 0.10 |
|
Mox SpSMBLAS_131A20 |
Apical, serotonergic |
Li 0.49 Zn nd |
8.23 × e-02 nd |
1.76 ± 0.22a 1.39 ± 0.21 |
|
Radical spoke protein RUDIREA_39F2 |
Apical |
Li 1.56 Zn na |
5.75 × e-04 na |
1.14 ± 0.10 2.11 ± 0.45 |
|
sFRP1/5 536REAsu4_11O4 |
Apical |
Li 0.42 Zn 1.99 |
7.10 × e-04 3.67 × e-04 |
0.11 ± 0.04 2.14 ± 0.08 |
|
Hairy1 537REA_10P14 |
Cilliary band +?E |
Li 0.77 Zn |
5.78 × e-06 |
0.62 ± 0.04 1.54 ± 0.25 |
|
onecut 538REA_9E3 |
Cilliary band |
Li 0.40 Zn 0.74 |
3.20 × e-04 5.88 × e-03 |
0.68 ± 0.06 1.84 ± 0.24a |
|
Pax2 RUDIREA_22J20 |
Cilliary band |
Li 1.14 Zn na |
7.71 × e-01 na |
3.72 ± 0.50 0.11 ± 0.02 |
|
AEX3 RUDIREA_5J10 |
Entire ectoderm, off vegetal |
Li 0.64 Zn 5.34 |
1.37 × e-08 3.83 × e-12 |
0.78 ± 0.26 9.11 ± 0.90 |
|
Hatching enzyme 538REA_2G05 |
Entire ectoderm |
Li 3,39 Zn 4.35 |
4.42 × e-07 1.25 × e-03 |
7.55 ± 0.55 11.42 ± 0.87 |
|
Otx 537REA_12D12 |
Entire ectoderm |
Li 0.65 Zn na |
1.01 × e-04 na |
0.96 ± 0.09 2.43 ± 0.14 |
|
Soxb1 RUDIREA_25A17 |
Entire ectoderm |
Li 1.28 Zn nd |
9.93 × e-02 nd |
0.87 ± 0.05a 1.43 ± 0.27 |
|
Soxb2 536REAsu4_4A13 |
Entire ectoderm |
Li 1.44 Zn |
6.71 × e-05 |
0.79 ± 0.12a 1.12 ± 0.27 |
|
SpAN RUDIREA_29D20 |
Entire ectoderm |
Li 2.19 Zn nd |
7.72 × e-07 nd |
1.88 ± 0.13 1.73 ± 0.14 |
|
|
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The first column gives the gene name and the clone ID, both of which can be used to query the described database [22] for additional data. In the second column the localization of expression in the embryo is given, where E is endoderm and SMC is secondary mesenchyme cell. The third column (Regulation) gives the differential expression ratios (expression in treatment/expression control) based on the array experiment for lithium (Li) and zinc (Zn) treated embryos (values above 1 indicate upregulation and values below 1 indicate downregulation). The column 'P value' indicates the statistical probability that the regulation could happen by chance (see Materials and methods for detail). The column Q-PCR (quantitative real-time polymerase chain reaction) gives the differential expression ratios (expression in treatment/expression control) and the error, as determined by Q-PCR. (Values expressed in copies of mRNA molecules/embryo are provided via the expressed sequence tag database [75]; see Materials and methods for details on Q-PCR). aDifferential expression based on array and Q-PCR data do not correlate. na, not analyzed; nd, no statistically relevant differential expression; ne, not expressed; ?, expression pattern unknown. |
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Poustka et al. Genome Biology 2007 8:R85 doi:10.1186/gb-2007-8-5-r85 |
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