A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive

Table 2 NO₃^-/Hormone Response Interaction.

Description of Comparison	Coefficient Estimate	P-value
N/H-bicluster 1 vs. Exclusive +N/H-bicluster 6	1721.4	4.08E-05
N/H-Bicluster 16, 19, 20 vs. Exclusive + N/H-bicluster 6	761.8	0.0099
Treated vs. Control	1290.1	5.82E-07
N/H-bicluster: Treated	2190.2	0.00022
N/H-Bicluster 16, 19, 20: Treated	1011.9	0.01539

Analysis of variance that examines the response to nitrate treatment of N-bicluster 9 genes that fell into various hormone biclusters or failed to appear in a hormone bicluster. Coefficients and p-values in the simplest model that retained explanatory power. The gene-expression response variable is determined by main effects of Treatment (with 2 levels: control and treated), N/H bicluster (with 3 compound levels), and an interaction term between N/H bicluster and Treatment. In this model, N-bicluster 9 exclusive genes and N/H bicluster 6 genes form an aggregate "control" group with no significant difference between them. A second, significantly different, aggregate group is comprised of genes in N/H-biclusters 16,19 and 20. A third group includes genes from N/H-bicluster 1 only. The control level for the Treatment factor is KCl. In this table each main-effect coefficient represents a difference in expression from the group comprised of N-bicluster 9 exclusive and N/H bicluster 6 genes under KCl treatment. The interaction term is over and above the main effects. For example, the difference between the mean expression of N/H-bicluster 1 genes under nitrate treatment and the mean expression of the control-group genes under control treatment (KCl) is obtained by summing: the main effect of N/H-bicluster 1 (1721.4); the main effect of (nitrate) Treated (761.8); and the term representing the interaction between N/H-bicluster 1 and Treated (2190.2).

ISSN: 1752-0509