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MADIBA: Arabidopsis Results

Ramonell KM, Zhang B, Ewing RM, Chen Y, Xu D, Stacey G, Somerville S: Microarray analysis of chitin elicitation in Arabidopsis thaliana. Molecular Plant Pathology 2002, 3:301-311.

Annotation results

In red: known gene functions of a cluster found by Ramonell 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	5	Up	100 / 100	100
2	22	Down	54.5 / 77.3	54.5
3	19	Initially up, then down	68.4 / 63.2	57.9
4	16	Initially down, then up	62.5 / 62.5	37.5

Gene Ontology results

Cluster	Highly Significant GO terms (p-val < 10-5	Significant GO terms (10-5 < p-val < 0.05)
1	Malate dehydrogenase (oxaloacetate-decarboxylating) (nadp+) activity Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD or NADH as one donor, and incorporation of one atom of oxygen Peroxidase activity Indole glucosinolate biosynthesis Indoleacetic acid biosynthesis Malate metabolism Response to pathogenic bacteria Tryptophan biosynthesis
2	1,4-alpha-glucan branching enzyme activity Aminoacylase activity MAP kinase activity Methionine synthase activity O-methyltransferase activity Activation of MAPK activity during osmolarity sensing Cold acclimation Ethylene biosynthesis Ethylene biosynthesis Proteolysis Regulation of transcription, DNA-dependent Response to chitin Response to salt stress	Response to cold Response to heat Response to osmotic stress Response to oxidative stress Response to wounding
3	1-deoxy-d-xylulose-5-phosphate synthase activity Catalase activity Glyoxylate cycle Glyoxylate cycle Hydrogen peroxide catabolism Isocitrate lyase activity Isopentenyl diphosphate biosynthesis, mevalonate-independent pathway Nutrient reservoir activity Sigma factor activity	Chlorophyll biosynthesis Gibberellic acid mediated signaling Lipid transport Regulation of transcription Response to pathogen
4	Calcium-dependent phospholipid binding Lipid binding Magnesium chelatase activity Methionyl aminopeptidase activity Naringenin-chalcone synthase activity Nucleotide binding Protein binding Chalcone biosynthesis Lipid transport Photosynthesis, light harvesting Polysaccharide transport Protein processing Response to chemical stimulus Response to drug Response to gravity Response to UV	Response to wounding

Metabolic Pathways results

Cluster	Metabolic pathway
1	Lignin Production CO2 Production
2
3
4