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Table 1
Predominant functions of the regulons
Regulon	# of genes	Postulated physiological function	FC^a

1	1629	mixed (tricellular and mature pollen-specific) ^b	ND
2	1136	Photosynthesis	29
3	869	protein synthesis	65
4	583	Mitosis	49
5	507	membrane transporters -metal, toxins removal (root-preferential)	77
6	417	embryo maturation (fruit and seed-preferential)	25
7	330	developmental regulation (leaf apex- preferential)	38
8	281	information (uninucleate microspore and bicellular pollen-specific)	64
9	234	response to environmental stimuli	26
10	223	protein modification, defense response	66
11	215	nuclear, others with very low expression	ND
12	182	mixed (fruit-preferential)	ND
13	154	upregulated in 'response to CO₂levels' experiment	ND
14	140	regulation of organ development	61
15	138	plastid stress and circadian rhythm	56
16	121	Information	58
17	115	Information	51
18	100	cell wall, respiration/catabolism (pollen-specific; highest in tricellular pollen)	46
19	96	mixed (flower-preferential)	ND
20	94	Information	80
21	92	secondary products, secondary wall (flower-specific, mostly tapetum)	54
22	81	cell wall biosynthesis, carbohydrate metabolism	47
23	77	membrane proteins	69
24	71	defense response	70
25	70	defense response	77
26	68	Information	79
27	68	regulation, root (root- and hypocotyl-preferential)	73
28	66	nucleic acid binding, regulation	60
29	63	aerobic respiration in mitochondria	92
30	56	Signalling	89
31	52	defense response	25
32	48	nuclear genes, RNA processing, DNA replication	70
33	48	chloroplast organization and biogenesis	62
34	47	mitochondrial genes	96
35	45	kinases, signaling, disease resistance	69
36	43	lipid modification and cuticular wax synthesis (flowers and shoot apex-specific)	54
37	42	heat shock response	60
38	40	RNA processing, translation, transcription regulation	82
39	40	catabolic processes deriving energy	51
40	40	transcription, translation, protein folding and transport	86
41	36	regulation, information	83
42	34	Regulation	78
43	33	flower/fruit, cell wall depositions (flower/fruit-preferential)	48
44	31	metabolic processes in flowers/fruit (flower/fruit-specific)	22
45	30	proteasome complex	87
46	29	defense response	50
47	29	nuclear, replication, chromosome organization, cell cycle	67
48	28	cell culture and tumor specific	ND
49	27	chloroplast-encoded	100
50	27	Signalling	90
51	26	organ specification in shoot (leaf apex- and hypocotyl-preferential)	35
52	26	endoplasmic reticulum: protein folding and secretion/redox function	73
53	25	fatty acid biosynthesis	83
54	23	protein degradation and lipid modification	59
55	23	epidermal/cuticular deposits	43
56	22	nectaries/carpel specific function (carpel-specific)	29
57	22	phloem specific (vasculature tissues-specific)	26
58	22	transposases, mostly CACTA-type	100
59	21	metabolism and transport of triterpenoids (root hairs-preferential)	71
60	21	ubiquitin ligase	53
61	20	metabolism of glutathione and glutamate, redox	56
62	20	information, nuclear	78
63	20	stress-induced catabolism, mediated by jasmonic acid	72
64	20	information, nuclear	87
65	20	secondary metabolism/pathogen infection	61
66	20	exocytosis	29
67	20	Ca ²⁺– triggered exocytosis (pathogen response?)	60
68	20	shoot meristem development and nucleic acid binding (leaf apex and hypocotyl – preferential)	69
69	20	leucine/glucosinolates metabolism	65

Regulons with 20 or more genes are shown. Annotations are postulated based on GO terms supplemented with information from the published literature. ^aFunctional Coherence, calculated as percentage of annotated genes whose TAIR annotation is consistent with the cluster functional classification. (Genes designated "hypothetical" or "unknown" are not included in this calculation.) ^bprevalent locations of expression are indicated in parenthesis. "specific" refers to virtually all expression in the given location; "preferential" refers to most expression being in the given location
Mentzen and Wurtele BMC Plant Biology 2008 8:99 doi:10.1186/1471-2229-8-99

Table 1