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Table 1 Summary of module analysis

From: Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain

      Regulators    
No. Module* No. of target genes Coherence (%) Significant gene annotations R1 R2 R3 E G§ L
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     
  1. *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.