Table 3 |
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|
Summary of SAGE tag K-means cluster data |
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|
Cluster |
Number of tags in the cluster |
Number of genes in the cluster |
Number of genome maps in the cluster |
Number assessed by GenePaint* |
Number assessed by QPCR |
Median S† |
Previously characterized genes in the cluster |
Selected GO categories and KEGG pathways enriched in the cluster‡ |
|
|
||||||||
|
1 |
154 |
85 |
61 |
37 |
3 |
0.0079 |
Nkx6-2 |
Transcriptional activator activity p = 0.02; development p = 0.049 |
|
2 |
49 |
29 |
19 |
15 |
2 |
0.0037 |
Metabolism p = 0.01; cell organization and biogenesis p = 0.035 |
|
|
3 |
58 |
40 |
15 |
14 |
2 |
0.0044 |
Receptor activity p = 0.028; development p = 0.030 |
|
|
4 |
292 |
115 |
175 |
45 |
4 |
0.00895 |
Hes6, Pdx1, Sox9 |
Regulation of transcription p = 0.027; maturity onset diabetes of the young p = 0.002 |
|
5 |
1,008 |
427 |
542 |
175 |
13 |
0.03555 |
Arx, Gcg, Ghrl, Iapp, Isl1, Nkx2-2, Myt1, Neurog3, Neurod1, Pax4, Pax6, Pou3f4, Pyy |
Secretory pathway p < 0.001; hormone activity p = 0.049; maturity onset diabetes of the young p < 0.001 |
|
6 |
60 |
41 |
17 |
16 |
1 |
0.00465 |
||
|
7 |
21 |
11 |
10 |
7 |
1 |
0.008 |
||
|
8 |
78 |
46 |
28 |
29 |
5 |
0.012 |
Pax6 |
Eye morphogenesis p = 0.020; type II diabetes mellitus p = 0.001 |
|
9 |
23 |
16 |
6 |
10 |
2 |
0.0041 |
Cell proliferation p = 0.028 |
|
|
10 |
401 |
281 |
107 |
122 |
4 |
0.0158 |
Id2 |
Response to endogenous stimulus p = 0.021 |
|
11 |
76 |
57 |
10 |
23 |
1 |
0.00555 |
Amy1, Cel, Clps, Ela1, Pnliprp2, Reg1 |
Protein catabolism p = 0.002 |
|
12 |
154 |
122 |
13 |
56 |
3 |
0.0074 |
Ela1, Pnlip, Reg3d |
Growth factor binding p = 0.005; carboxypeptidase activity p = 0.013; regulation of cell growth p = 0.027 |
|
13 |
136 |
84 |
42 |
30 |
3 |
0.01835 |
Iapp, Ins1, Ins2 |
Secretion p = 0.03; maturity onset diabetes of the young p < 0.001; type II diabetes mellitus p < 0.001; type I diabetes mellitus p = 0.003 |
|
14 |
56 |
47 |
4 |
22 |
0 |
0.00335 |
Protein metabolism p = 0.020 |
|
|
|
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|
*Refers to the number of genes analyzed by in situ hybridization using GenePaint [62] on TS22 whole embryo cryo-sections that gave informative staining. †S is the specificity of the tag. Specificity is calculated as described in the Materials and methods. ‡GO term enrichments and p-values were calculated using EASE while KEGG pathway enrichments and p-values using Webgestalt as described in the Materials and methods. |
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|
Hoffman et al. Genome Biology 2008 9:R99 doi:10.1186/gb-2008-9-6-r99 |
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