Table 1.

Predominant physiological function of the 40 largest regulons as determined by analysis of overrepresentation of GO terms.

Regulon	# of genes in regulon	Postulated physiological function	Best adjusted p-value*
1	332	Plasma membrane part	8.7 × 10−7
2	203	Immune response, signal transducer activity	2.2 × 10−35
3	193	Structural constitute of ribosome, translation elongation	1.5 × 10−140
4	120	Regulation of actin cytoskeleton organization, protein binding	2.9 × 10−11
5	95	DNA replication, cell cycle process, cell division, protein binding	3.4 × 10−51
6	84	Cell adhesion, extracellular matrix, cytoskeleton organization and biogenesis	2.0 × 10−9
7	69	Proteasome complex, anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process, threonine-type endopeptidase activity	2.2 × 10−9
8	48	Not clear, protein amino acid phosphorylation	1,5 × 10−2
9	46	Cell communication, signal transduction, immune response, T-cell receptor complex	2.2 × 10−16
10	39	Immunoglobulin, antigen binding, immune response	1.4 × 10−10
11	36	Mitochondrial inner membrane transporter, oxidation reduction, respiratory electron transport chain, nucleotide metabolic process	6.6 × 10−29
12	35	Organ development, development process, lymphocyte mediated immunity, ion transport, cell adhesion, extracellular organization and biogenesis	1.0 × 10−19
13	27	Nuclear part, macromolecular complex assembly, mRNA transport, protein import into nucleus, biopolymer biosynthetic process	2.8 × 10−8
14	25	GTPase activity	1.6 × 10−4
15	24	Muscle cell development, muscle contraction, regulation of muscle contraction	1.2 × 10−24
16	22	Immune response, defense response	2.8 × 10−5
17	19	Sphingolipid catabolic process, lysosome, vacuole	1.6 × 10−5
18	18	NADH dehydrogenase activity, oxidation reduction, phosphorus metabolic process, purine nucleotide metabolic process, mitochondrial envelope	2.4 × 10−24
19	16	NADPH metabolic process, polyamine metabolic process, V-type ATPase	2.7 × 10−5
20	16	Oncosis, nuclear part	2.4 × 10−3
21	15	Regulation of transcription	4.2 × 10−3
22	15	Not clear, nitrogen fixation	3.7 × 10−3
23	14	RNA splicing, splicesomal complex, nuclear speck	4.2 × 10−7
24	14	Response to cAMP, negative regulation of myeloid cell differentiation, regulation of gene expression, methylation, transcription, protein kinase cascade	4.7 × 10−7
25	14	Not clear, pentose-phosphate shunt, non-oxidative branch	5.5 × 10−3
26	14	Cysteine-type endopetidase activity, protein kinase cascade, PML body	2.1 × 10−4
27	14	MHC class II protein complex, antigen processing and presentation	1.3 × 10−24
28	12	Vesicle coating_mRNA splicing, transportation	3.8 × 10−4
29	12	RNA splicing, spliceosomal complex, nuclear speck	1.8 × 10−11
30	12	Nuclear speck	1.4 × 10−4
31	12	Not Clear, polytene chromosome	4.7 × 10−3
32	12	Calcium-independent cell-cell adhesion, cell-cell junction	8.2 × 10−7
33	11	Cell cycle, negative regulation of ligase activity	2.0 × 10−7
34	11	Protein export from nucleus, splicesomal snRNP biogenesis, ribonucleoprotein complex	2.3 × 10−5
35	11	Translation	1.6 × 10−5
36	11	UDP catabolic process, MLL5-L complex	1.0 × 10−3
37	11	Response to hormone stimulus	8.9 × 10−4
38	11	Axon target recognition, neuron projection	4.7 × 10−6
39	10	mRNA processing, RNA splicing, nuclear body	3.0 × 10−8
40	10	Gene expression, U2 SnRNP	2.0 × 10−3

^*Best adjusted p-value is the term for the lowest adjusted p-value associated with the most overrepresented GO term among all GO terms. The p-value adjustment is implemented using the Bonfferoni method, in R package “GOHyperGAll” [12].