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

Table 1 Summary of module analysis

					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				√

*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.