Skip to main content

Table 1 Differential expression data based on array experiments and Q-PCR of endomesoderm marker genes

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

EM markers Expression Regulation P value Q-PCR ratio ± error
Brachyury
537REA_5B8
EM Li 1.69
Zn 0.42
1.08 × e-06
3.89 × e-03
1.64 ± 0.21
0.33 ± 0.10
Blimp1
537REA_16B13
E Li 1.33
Zn 0.42
3.98 × e-02
2.58 × e-03
1.78 ± 0.09
0.53 ± 0.04
CoA-reductase
536REAsu2_4L15
EM Li 0.40
Zn 1.31
5.68 × e-08
1.20 × e-03
0.44 ± 0.03
1.71 ± 0.50
Delta
536REAsu4_17C2
SMC Li 1.79
Zn NA
1.64 × e-01
NA
4.86 ± 1.05
0.95 ± 0.14
Dlx
537REA_9O11
EM-Oect Li 0.09
Zn NA
2.60 × e-05
NA
0.03 ± 0.00
0.58 ± 0.26
Endo16
536REAsu2_5N1
E Li 1.20
Zn 0.46
3.00 × e-01
2.05 × e-04
1.76 ± 0.34
1.70 ± 0.12a
Eve
537REA_2G8
E Li 1.33
Zn nd
4.89 × e-03
nd
0.93 ± 0.01a
1.73 ± 0.10
FoxA
537REA_10P13
EM+Oect Li 1.37
Zn na
1.37 × e-06
na
3.18 ± 0.12
1.69 ± 0.43
GataE
537REA_3C9
E Li 1.55
Zn 0.48
2.77 × e-03
1.71 × e-03
3.06 ± 0.92
0.23 ± 0.04
Hex
SpSMBLAS_124N22
M Li 1.54
Zn nd
3.99 × e-01
nd
3.22 ± 0.53
0.33 ± 0.03
Hox11/13b
537REA_12K1
E Li 1.69
Zn na
3.44 × e-09
na
na
na
KRL
PMC_BG781437
EM Li
Zn
  1.90 ± 0.03
5.95 ± 0.66
Lox
536REAsu4_13M18
E Li ne
Zn 0.36
ne
5.17 × e-03
ne
0.04 ± 0.01
Notch
RUDIREA_30E15
E Li 1.27
Zn na
4.84 × e-01
na
1.81 ± 0.18
13.5 ± 3.41
P19
537REA_15K13
PMC Li 1.07
Zn 1.58
7.82 × e-01
3.43 × e-03
1.66 ± 0.33
2.14 ± 0.22
PMAR1 PMC Li na
Zn na
na
na
1.77 ± 0.29
0.50 ± 0.02
Prox
RUDIREA_15N17
M Li 0.57
Zn na
2.40 × e-04
na
0.81 ± 0.16
1.46 ± 0.27
Six3
RUDIREA_40B23
Apical, later +EM Li 0.72
Zn 0.10
7.83 × e-02
6.46 × e-03
0.39 ± 0.04
1.15 ± 0.15a
SM50
RUDIREA_5L2
PMC Li 0.57
Zn 1.55
1.09 × e-05
1.20 × e-04
1.07 ± 0.19a
18.12 ± 2.93
SMAD2
RUDIREA_24O7
PMC Li 0.50
Zn NA
2.49 × e-01
NA
0.52 ± 0.09
1.20 ± 0.32
Snail
RUDIREA_13L18
EM Li 0.99
Zn 0.26
9.72 × e-01
9.05 × e-05
0.24 ± 0.01
0.09 ± 0.01
Sox4
RUDIREA_2H10
EM, later +apical Li 1.15
Zn nd
4.23 × e-01
nd
1.67 ± 0.21
1.05 ± 0.08
SuH
621REA_14C17
EM Li 0.24
Zn NA
3.75 × e-02
NA
4.24 ± 0.95a
4.61 ± 1.50
T-Brain
621Rea_6N24
M Li 0.82
Zn na
6.93 × e-01
na
1.40 ± 0.31a
2.18 ± 0.12
Tbx6
RUDIREA_29D1
M Li 0.64
Zn 0.74
6.71 × e-05
1.78 × e-05
0.33 ± 0.15
0.16 ± 0.04
Unknown
536REAsu4_13G12
EM Li 2.23
Zn 4.05
2.69 × e-07
5.52 × e-10
4,68 ± 0.72
11,01 ± 0,27
Wnt3
RUDIREA_28M14
EM Li 0.89
Zn NA
7.86 × e-01
NA
2.29 ± 0.97a
0.09 ± 0.03
Wnt5
RUDIREA_16P23
EM Li 1.25
Zn NA
1.97 × e-01
NA
6.31 ± 2.31
1.08 ± 0.08
Wnt8
537REA_10K11
EM Li 1.35
Zn NA
4.19 × e-03
NA
2.49 ± 0.07
11.36 ± 1.13
  1. 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 EM is endomesoderm, E is endoderm, M is mesoderm, PMC is primary mesenchyme cell, and SMC is secondary mesenchyme cell, Oect is oral ectoderm. 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.