Table II.

Overrepresented functions in transcript clusters relative to ATH1 probe sets

GO categorization data were determined on July 18, 2007. P-values were obtained using Fisher's exact test.

Cluster No.	By GO Cellular Component	P-Value	By GO Molecular Function	P-Value
Up-regulated
1	Nucleus	0.015	Transcription factor activity	0.00002
	Cell wall	0.0009	Nucleotide binding	0.0003
	Other membranes	0.029	Transferase activity	0.02
			DNA or RNA binding	0.03
2	Cell wall	0.0007	Hydrolase activity	0.002
	Extracellular	0.017	Other enzyme Activity	0.0004
	Endoplasmic reticulum	0.007
3	Nucleus	0.03	Transcription factor activity	0.00001
	Cell wall	0.003	Other enzyme activity	0.008
	Other membranes	0.0019
Up-regulated early; down-regulated late
4	Other membranes	0.003	Transporter activity	0.037
	Mitochondria	0.042
Down-regulated
5	Extracellular	0.019	Transferase activity	0.008
	Other membranes	0.00003	Hydrolase activity	0.0004
6	Nucleus	0.0004	Transcription factor activity	1.5 e-7
	Cell wall	0.03	DNA or RNA binding	0.001
	Extracellular	0.016
	Plasma membrane	0.04
7	Mitochondria	0.03	Transferase activity	0.03
	Other membranes	0.016	Hydrolase activity	0.04
Down-regulated early; up-regulated late
8	–		Transporter activity	0.025
			Other enzyme activity	0.027