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MADIBA: Rice Results

Fujiwara S, Tanaka N, Kaneda T, Takayama S, Isogai A, Che FS: Rice cDNA microarray-based gene expression profiling of the response to flagellin perception in cultured rice cells. Mol Plant Microbe Interact 2004, 17:986-998.

Annotation results

In red: known gene functions of a cluster found by Fujiwara et al.
In green: known gene functions of a cluster found by MADIBA.

A "known" gene function is a gene that has been annotated as something other than "unknown", "no homology", "expressed protein", "hypothetical protein" and the like.

Cluster	Genes	Regulation	% known	% same annotation
1	20	Up *	40 / 70	25
2	28	Up *	64.3 / 82.1	42.9
3	20	Up *	70 / 65	0
4	16	Up *	62.5 / 62.5	37.5
5	7	Up *	57.1 / 85.7	57.1
6	3	Up *	100 / 100	66.7
7	3	Up §	66.7 / 66.7	100
8	2	Up §	100 / 100	100
9	32	Down *	65.6 / 84.4	50

*: Incompatible reaction
§: Compatible reaction

Gene Ontology results

Cluster	Highly Significant GO terms (p-val < 10-5	Significant GO terms (10-5 < p-val < 0.05)
1	Organic anion transporter activity
2	3,4-dihydroxy-2-butanone-4-phosphate synthase activity GDP-l-fucose synthase activity GDP-mannose 3,5-epimerase activity MAP-kinase activity Phosphoserine transaminase activity Riboflavin biosynthesis
3	Amine oxidase activity Brassinosteroid metabolism Eceptor signaling protein serine/threonine kinase activity Gluconeogenesis Isocitrate dehydrogenase (NAD+) activity Phosphoenolpyruvate carboxykinase (ATP) activity Receptor signaling protein serine/threonine kinase activity Root epidermal cell differentiation Steroid hydroxylase activity Systemic acquired resistance, salicylic acid mediated signaling pathway UDP-glucose 4-epimerase activity
4	Brassinosteroid metabolism Calcium- and calmodulin-dependent protein kinase activity Cold acclimation Hyperosmotic salinity response Response to chitin Response to jasmonic acid stimulus Response to wounding	Response to light stimulus Response to salt stress
5	asmonic acid mediated signaling pathway Response to jasmonic acid stimulus	Response to wounding Response to salicylic acid stimulus
6	Aging Copper ion binding Electron transporter activity
7	Gibberellic acid mediated signaling Hydrolase activity, hydrolyzing O-glycosyl compounds Response to gibberellic acid stimulus
8	Cysteine-type peptidase activity Pyruvate decarboxylase activity
9	Phosphogluconate dehydrogenase (decarboxylating) activity Protein biosynthesis Translation elongation factor activity

Metabolic Pathways results

Cluster	Metabolic Pathways
1
2	Phenylalanine metabolism (3 enzymes)
3
4
5
6
7
8
9