Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response

BMC Genomics

Table 2 GO Slim Terms Over Represented in Candidate Genes from Comparison Between Clark Plants Grown in Iron Sufficient and Iron Deficient Hydroponics Solutions

GO Slim ID	GO Term Description	Number of Genes with GO ID	Bonferroni Corrected P-Value
GO:0000004 BP	Unknown Function	128	0
GO:0006270 BP	DNA Replication Initiation	10	0
GO:0009611 BP	Response to Wounding	36	0
GO:0009695 BP	Jasmonic Acid Biosynthesis	24	0
GO:0006826 BP	Iron Ion Transport	9	1.2E-07
GO:0006879 BP	Iron Ion Homeostasis	10	3.6E-07
GO:0010039 BP	Response to Iron Ion	9	5.28E-06
GO:0009617 BP	Response to Bacterium	8	0.000018
GO:0006275 BP	Regulation of DNA Replication	4	0.00303
GO:0006972 BP	Hyperosmotic Response	4	0.00303
GO:0030397 BP	Membrane Disassembly	8	0.004381
GO:0008299 BP	Isoprenoid Biosynthesis	10	0.006706
GO:0009408 BP	Response to Heat	20	0.014334
GO:0019373 BP	Epoxygenase P450	5	0.045066
GO:0008199 MF	Ferric Iron Binding	9	0
GO:0008094 MF	DNA-dependent ATPase Activity	10	1.29E-06
GO:0016165 MF	Lipoxygenase Activity	12	0.000128
GO:0047763 MF	Cafeate O-Methyltransferase	8	0.001014
GO:0030337 MF	DNA Polymerase Processivity Factor	4	0.001426
GO:0005544 MF	Calcium Dependent Lipid Binding	8	0.001965
GO:0009978 MF	Allene Oxide Synthase	5	0.017949
GO:0046423 MF	Allene Oxide Cyclase	4	0.020157
GO:0008815 MF	Citrate (Pro-3S) Lyase	5	0.029946
GO:0009346 CC	Citrate Lyase	5	0.002807

GO Slim ID's statistically over or under represented in the list of differentially expressed genes comparing Clark plants grown in iron sufficient and iron limiting hydroponics conditions in comparison to their presence on the Affymetrix^® GeneChip^®. The GO Slim Column provides the GO Slim ID number and corresponding category. GO Slim categories are Biological Process (BP), Molecular Function (MF), and Cellular Component (CC). The GO Term Description column contains the best description for the GO Slim ID. The number of genes with GO ID column is the number of genes differentially expressed between Clark plants grown in iron sufficient and iron deficient hydroponics solutions with the corresponding GO Slim ID. The Bonferroni Corrected P-value is the statistical significance of the GO Slim ID. Only GO Slim IDs with P-values equal to or less than 0.5 were considered statistically over or under represented in the list of differentially expressed genes in comparison to the presence of the GO Slim ID on the GeneChip^®.

ISSN: 1471-2164