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MADIBA: Arabidopsis Results

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
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