A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks

Poustka, Albert J; Kühn, Alexander; Groth, Detlef; Weise, Vesna; Yaguchi, Shunsuke; Burke, Robert D; Herwig, Ralf; Lehrach, Hans; Panopoulou, Georgia

doi:10.1186/gb-2007-8-5-r85

Table 2 Differential expression data based on array experiments and Q-PCR of ectoderm marker genes

From: A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks

Ectoderm markers	Expression	Regulation	P value	Q-PCR ratio ± error
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 ± 0.08^a 0.16 ± 0.06
Lefty 536REAsu4_7H9	Oral	Li 1.80 Zn nd	1.91 × e^-07 nd	0.98 ± 0.22^a 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 ± 0.20^a 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 ± 0.22^a 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 ± 0.24^a
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 ± 0.05^a 1.43 ± 0.27
Soxb2 536REAsu4_4A13	Entire ectoderm	Li 1.44 Zn	6.71 × e^-05	0.79 ± 0.12^a 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

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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