Table 2.

Functional enrichment of expression clusters.

Significantly over-represented functional groups in each SOM cluster were identified with Genomica software and TAIR gene ontologies. Numbers in the table indicate fold-enrichment in each cluster relative to the percentage of hits in the ATH1 GeneChip set. Enrichment of 2–3.99 fold is highlighted in yellow and of 4-fold or greater in red

2–2.99

3–3.99

4–4.99

>=5

category/cluster	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
genes	214	184	193	408	92	261	308	845	16	517	120	433	317	226	511	644
Process
electron transport or energy pathways								1.65			3.88		1.76	2.27
protein metabolism			1.73	1.78		1.88
response to abiotic or biotic stimulus	3.26	3.29		1.94	2.78	1.96	2.27	1.73		1.71	2.33
response to stress		3.28						2.27
signal transduction				2.19	3.02	2.13	2.01			2.03		2.14
transcription										1.77
transport								1.41
Function
DNA or RNA binding										1.45
hydrolase activity																1.68
kinase activity	2.43	1.92	3.56	3.37	3.03	3.13	2.17	1.49				1.67
nucleotide binding							2.32
other enzyme activity								1.73					1.54	1.57
protein binding			2.55	1.81			1.87
receptor binding or activity	3.73		4.72				7.75
structural molecule activity											6.91
transcription factor activity										2.25		1.73
transferase activity			1.79	1.57			2.00	1.59					1.56
transporter activity	2.00							1.55
Component
chloroplast											3.54		2.73	2.98	1.65	2.67
cytosol								2.23
ER								4.12
nucleus										1.74
other cytoplasmic components											5.81		3.54	2.82		1.51
other intracellular components											4.09		2.57	2.22
plasma membrane				3.83
plastid											14.56		8.43	6.87		3.17
ribosome											7.86