Table 3 |
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|
Analysis of X-Gal staining in zebrafish embryos co-injected with the HSP promoter and SCEs or control fragments |
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|
Gene |
Trans dev |
Name |
SCE bp |
SCE Class |
ENH |
Embryo |
Cell |
ce/emb |
P value |
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|
|
|||||||||||||||
|
Muscle |
Notochord |
CNS |
Eye |
Ear |
Vessels |
Other |
|||||||||
|
|
|||||||||||||||
|
No |
NA |
lacZ |
Neg control |
161 |
40 |
0.25 |
|||||||||
|
Shh |
Y |
ArC |
Pos control |
96 |
242 |
2.52 |
8.48E-07 |
||||||||
|
Shh |
Y |
12058 |
45 |
Rev |
Y |
139 |
69 |
0.5 |
6.86E-09 |
||||||
|
Otx2 |
Y |
13988 |
51 |
Mov |
Y |
111 |
93 |
0.84 |
0.6444 |
0.006269 |
0.5536 |
0.3155 |
|||
|
Gata3 |
Y |
15402 |
40 |
Mre |
Y |
107 |
103 |
0.96 |
0.398 |
0.5764 |
0.1906 |
1 |
|||
|
Ets |
Y |
8744 |
40 |
Mov |
Y |
105 |
180 |
1.57 |
0.002593 |
4.78E-09 |
|||||
|
Ets |
Y |
8745 |
46 |
Mov |
Y |
133 |
210 |
1.58 |
0.1558 |
0.6015 |
0.3619 |
2.15E-06 |
|||
|
Ets |
Y |
8726 |
41 |
Mre |
Y |
159 |
345 |
2.17 |
0.05534 |
0.6136 |
0.1485 |
2.08E-06 |
|||
|
Ets |
Y |
8728 |
48 |
Mre |
Y |
149 |
176 |
1.18 |
0.0444 |
0.129 |
0.07924 |
1.31E-05 |
|||
|
Pax2b |
Y |
31027 |
39 |
Col |
Y |
149 |
105 |
0.7 |
0.002374 |
0.06327 |
0.1902 |
||||
|
Pax6a |
Y |
15696 |
33 |
Mov |
Y |
133 |
122 |
0.92 |
8.21E-06 |
0.3343 |
0.01268 |
||||
|
Pax3 |
Y |
24781 |
42 |
Mov |
N |
124 |
67 |
0.54 |
0.02982 |
0.5287 |
1 |
||||
|
Zfpm2 |
Y |
23818 |
48 |
Col |
Y |
140 |
119 |
0.85 |
1.49E-06 |
0.01296 |
1 |
||||
|
Zfpm2 |
Y |
23838 |
48 |
Mre |
Y |
131 |
148 |
0.98 |
0.0003576 |
0.04369 |
0.1231 |
||||
|
Tmeff2 |
N |
26014 |
48 |
Mov |
N |
164 |
125 |
0.76 |
0.7654 |
0.02301 |
0.3371 |
0.2801 |
|||
|
Tmeff2 |
N |
26015 |
38 |
Mov |
Y |
120 |
159 |
1.33 |
0.001035 |
0.303 |
0.2088 |
||||
|
Tmeff2 |
N |
26016 |
51 |
Mre |
Y |
109 |
148 |
1.36 |
0.0006309 |
0.0149 |
0.5862 |
||||
|
Jag1b |
Y |
16407 |
37 |
Col |
N |
136 |
98 |
0.72 |
1 |
0.1849 |
1 |
1 |
|||
|
Jag1b |
Y |
16408 |
55 |
Col |
Y |
142 |
109 |
0.86 |
5.45E-08 |
0.006524 |
0.3245 |
||||
|
Jag1b |
Y |
16409 |
44 |
Rev |
N |
106 |
54 |
0.51 |
1 |
0.5088 |
1 |
0.5058 |
|||
|
Mapkap1 |
N |
17058 |
37 |
Mov |
Y |
143 |
295 |
2.06 |
0.6825 |
0.05292 |
0.3788 |
0.6065 |
1 |
||
|
Mapkap1 |
N |
17059 |
39 |
Mov |
Y |
136 |
171 |
1.26 |
0.6686 |
0.004037 |
0.5973 |
0.077 |
0.5197 |
||
|
Mab21l2 |
Y |
23001 |
42 |
Col |
Y |
142 |
317 |
2.23 |
1.24E-07 |
0.004985 |
0.2339 |
||||
|
Mab21l2 |
Y |
23002 |
37 |
Mre |
Y |
155 |
122 |
0.79 |
7.85E-08 |
0.004138 |
|||||
|
Hmx3 |
Y |
11669 |
150 |
Col |
Y |
165 |
136 |
0.82 |
0.001029 |
0.07062 |
0.01423 |
||||
|
Lmx1b |
Y |
17027 |
300 |
Col |
Y |
116 |
105 |
0.91 |
0.00762 |
0.1876 |
1 |
||||
|
3110004L20Rik |
N |
5803 |
45 |
Mre |
N |
65 |
16 |
0.25 |
0.2929 |
1 |
|||||
|
3110004L20Rik |
N |
5802 |
39 |
Mov |
Y |
122 |
320 |
2.62 |
0.1874 |
0.01209 |
|||||
|
Elmo1 |
N |
6026 |
45 |
Rev |
Y |
103 |
76 |
0.74 |
0.007132 |
0.6848 |
|||||
|
Ets |
Y |
11216 |
NA |
Ctrl |
N |
104 |
74 |
0.71 |
1 |
0.6954 |
|||||
|
Gata3 |
Y |
3255 |
NA |
Ctrl |
N |
174 |
110 |
0.63 |
0.04481 |
0.281 |
0.5739 |
0.02163 |
|||
|
1300007F04Rik |
N |
2797 |
NA |
Ctrl |
N |
157 |
115 |
0.73 |
|||||||
|
Tmeff2 |
N |
198 |
NA |
Ctrl |
N |
145 |
23 |
0.16 |
0.7448 |
0.6597 |
0.3651 |
||||
|
Mab21l2 |
Y |
909 |
NA |
Ctrl |
N |
165 |
92 |
0.56 |
0.06359 |
1 |
1 |
1 |
|||
|
3110004L20Rik |
N |
410 |
NA |
Ctrl |
N |
107 |
23 |
0.21 |
0.01984 |
||||||
|
Elmo1 |
N |
10157 |
NA |
Ctrl |
N |
146 |
38 |
0.26 |
0.287 |
0.8126 |
|||||
|
Shh |
Y |
11271 |
NA |
Ctrl |
Y |
165 |
83 |
0.5 |
3.34E-07 |
1 |
1 |
1 |
|||
|
Impact |
Y |
5990 |
NA |
Ctrl |
N |
150 |
101 |
0.67 |
0.6496 |
0.2754 |
0.0622 |
||||
|
Ubl7 |
N |
268 |
NA |
Ctrl |
Y |
117 |
644 |
5.5 |
0.0003325 |
7.15E-11 |
0.02555 |
0.6197 |
|||
|
Lmx1b |
Y |
11767 |
NA |
Ctrl |
N |
116 |
15 |
0.13 |
0.2743 |
0.0707 |
1 |
||||
|
Irx3 |
Y |
5945 |
NA |
Ctrl |
N |
93 |
15 |
0.16 |
0.03938 |
||||||
|
|
|||||||||||||||
|
For each DNA fragment tested the following information is given, from left to right: the gene locus in which the DNA fragment is found; indication about the GO classification of the gene in the 'trans-dev' class (Y = yes, N = no); the identifier given to the SCE or control fragment; the size of the SCE; the class (rev = reversed, mov = moved, mre = moved and reversed, col = collinear, Ctrl = control); summary about the potentially enhancer function of the element (Y = yes, N = no); the number of embryos injected; the total number of cells X-gal-stained; the ratio of stained cells divided by the number of embryos observed (with bold highlighting those with significant generalized enhancer activity); the P values for the significance of the number of cells observed in the fragment tested versus the lacZ:HSP control for each tissue (bold for P values < 0.01; see Materials and methods). See Additional data file 3 for further info on the fragments tested. CNS, central nervous system; SCE, shuffled conserved element. |
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|
Sanges et al. Genome Biology 2006 7:R56 doi:10.1186/gb-2006-7-7-r56 |
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