Table 1.

Groups of Genes That Overlapped Significantly with Those Genes Whose Expression Was Suppressed in nst1-1 nst3-1 Plants

Groups of Genes	Number of Genes	Overlapping Genes	P Value	Odds Ratio	Reference or Resource
Upregulated genes in 35S:NST1 plants	636	75	2.20E-16	11.25747	Mitsuda et al. (2005)
Xylem-biased genes	254	33	2.20E-16	10.58139	Zhao et al. (2005)
Secondary cell wall biosynthesis genes (GO: 0009834)	6	5	5.26E-09	317.756	http://www.arabidopsis.org/
Genes involved in the cinnamate- monolignol pathway	60	10	2.73E-08	13.06842	Tokimatsu et al. (2005)
Genes involved in lignin biosynthesis	32	7	4.99E-07	18.10865	http://www.arabidopsis.org/
Genes involved in xyloglucan biosynthesis and modification	98	9	2.23E-05	6.568023	Tokimatsu et al. (2005)
Lignin biosynthesis genes (GO: 0009809)	21	4	0.00028	15.0599	http://www.arabidopsis.org/
Cellulose biosynthesis genes (GO: 0030244)	34	4	0.001853	8.527619	http://www.arabidopsis.org/

Selected groups of genes that significantly overlapped with genes whose expression was suppressed (0.5-fold or below, with a Q-value < 0.1) in nst1-1 nst3-1 plants are listed. The number of genes in each group examined by microarray analysis is given in the second column, and, of these, the number of genes that is the same as those suppressed in the nst1-1 nst3-1 plants is listed in the third column. P values and odds ratios (= number of genes that actually overlapped/number of genes expected by chance) from Fisher's exact test are listed in the fourth and fifth columns, respectively. The data resource or reference is listed in sixth column. GO and 2.2E-016 represent gene ontology, as defined by the consortium and values below 2.2E-016, respectively.