Table 1 |
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|
Summary of module analysis |
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|
Regulators |
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|
|
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|
No. |
Module* |
No. of target genes |
Coherence (%)† |
Significant gene annotations |
R1 |
R2 |
R3 |
E‡ |
G§ |
L¶ |
|
|
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|
1 |
Calcium-dependent cell-cell adhesion |
12 |
8 |
Hey2 |
Npas4 |
√ |
√ |
|||
|
2 |
Sialyltransferase activity |
6 |
17 |
Neurod6 |
Neurod1 |
√ |
√ |
|||
|
3 |
Transition metal ion binding |
4 |
50 |
Neurod6 |
Max |
√ |
√ |
|||
|
4 |
Monocyte differentiation |
2 |
50 |
Tcf4 |
√ |
√ |
||||
|
5 |
Endoplasmic reticulum |
7 |
29 |
Npas4 |
Neurod6 |
√ |
√ |
|||
|
6 |
Protein heterodimerization activity |
2 |
50 |
Npas4 |
||||||
|
7 |
Eye development (sensu) vertebrata) |
6 |
33 |
Npas4 |
Heatr1 |
√ |
√ |
|||
|
8 |
Neurotransmitter metabolism |
7 |
14 |
Hes5 |
Npas4 |
√ |
√ |
|||
|
9 |
Anion channel activity |
1 |
100 |
Npas4 |
Neurod6 |
√ |
√ |
|||
|
10 |
Protein kinase activator activity |
3 |
33 |
Hey2 |
Neurod6 |
√ |
√ |
|||
|
11 |
Cation antiporter activity |
5 |
20 |
Olig1 |
√ |
√ |
||||
|
12 |
Cell surface receptor linked signal transduction |
5 |
60 |
Neurod6 |
Max |
√ |
√ |
|||
|
13 |
Regulation of cell proliferation |
6 |
33 |
Hes3 |
Ascl1 |
√ |
√ |
|||
|
14 |
Stem cell division and DNA repair |
2 |
50 |
Tcf4 |
√ |
√ |
||||
|
15 |
Cellular morphogenesis |
5 |
60 |
P < 0.05 |
Neurod6 |
Hey2 |
√ |
√ |
||
|
16 |
Sequence-specific DNA binding |
8 |
25 |
Olig1 |
√ |
√ |
||||
|
17 |
Lipid biosynthesis |
12 |
25 |
P < 0.05 |
Neurod6 |
√ |
√ |
|||
|
18 |
Cytoskeletal regulatory protein binding |
6 |
17 |
Ascl1 |
Bhlhb5 |
√ |
√ |
|||
|
19 |
Negative regulation of metabolism |
18 |
17 |
Olig1 |
Neurod6 |
Mitf |
√ |
√ |
√ |
|
|
20 |
Monovalent inorganic cation transporter activity |
4 |
25 |
Nhlh2 |
√ |
√ |
||||
|
21 |
Intracellular non-membrane-bound organelle |
6 |
50 |
Mitf |
Npas4 |
√ |
√ |
√ |
||
|
22 |
Ribosome |
8 |
13 |
Olig1 |
Max |
√ |
√ |
√ |
||
|
23 |
Calcium ion binding |
9 |
33 |
Hey2 |
√ |
√ |
√ |
|||
|
24 |
Menstrual cycle |
7 |
14 |
Max |
Nhlh2 |
√ |
√ |
|||
|
25 |
Cytokine activity |
7 |
14 |
Bhlhb5 |
Myf6 |
√ |
√ |
√ |
||
|
26 |
Endosome |
12 |
8 |
Olig1 |
Neurod6 |
Idb2 |
√ |
√ |
||
|
27 |
Morphogenesis of embryonic epithelium |
5 |
20 |
Hey2 |
Neurod6 |
√ |
√ |
|||
|
28 |
Carboxylic ester hydrolase activity |
2 |
50 |
Npas4 |
√ |
|||||
|
|
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|
*Each module was assigned a name based on the smallest P value for enrichment of GO categories of genes in the module. †GO coherence of each module, measured as the percentage of genes in the module covered by the category with the smallest P value. ‡E, experimental evidence showing at least one of the genes in the module is regulated by, or interacts with, the respective TF or the relationship between the TF and its target was proved by the match with an experimentally confirmed DBM. §G, TF-target pair was supported by the match with grouping-DBM in the promoter sequence of genes in the module. ¶L, literature data mining provided support for the relationship between a TF and its target gene. |
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|
Li et al. Genome Biology 2007 8:R244 doi:10.1186/gb-2007-8-11-r244 |
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