Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome

BMC Genomics

Table 3 Summary for associations between the presence of AuxRE_P&_S and auxin response detected by statistical analysis of 16 microarray experiments (Table 2).

Up- or down-regulation		up	down	up	down
Number, orientation and location of AuxRE_P&S		[-300;5'UTR]		[-1500;5'UTR]
Single	AuxRE_P&S	7*	3	5*	1
	AuxRE_P&S+	4*		4*
	AuxRE_P&S−	3		3
Multiple	AuxRE_P&S		2	7*	1
	AuxRE_P&S+		2	1	3
	AuxRE_P&S−		2	6*	1

For each microarray experiment, we estimated, if the difference in portions of auxin regulated genes (>1.5-fold change, p < 0.05) between the subsets of gene having specifically localized and/or oriented AuxRE_P&_S and whole set of genes tested was significant in the microarray. In the cells, we present the number of microarrays in which the significant difference was found, empty cells mean no difference. The threshold at which the association between the presence of AuxRE_P&_S and auxin responsive expression was considered as significant was set as three microarrays (see Methods). (+) means direct orientation; (−) - reverse orientation of the AuxRE_P&S elements.
*Significant associations

ISSN: 1471-2164