Table 2

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

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 ± 0.08a

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


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.

Poustka et al. Genome Biology 2007 8:R85   doi:10.1186/gb-2007-8-5-r85

Open Data