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MADIBA: Plasmodium Results

Le Roch et al. KG, Zhou Y, Blair PL, Grainger M, Moch JK, Haynes JD, De la Vega P, Holder AA, Batalov S, Carucci DJ et al.: Discovery of Gene Function by Expression Profiling of the Malaria Parasite Life Cycle. Science 2003, 301:1503-1508.

Gene Ontology Results

In red: known gene functions found in a cluster by Le Roch et al.
In green: known gene functions found in a cluster by the Gene Ontology module of MADIBA.
In blue: similar annotations found by the two methods.

Cluster	Genes	Stage	Known genes	Gene Ontology (Le Roch et al)	MADIBA Gene Ontology Biological Process (e-value < 10-5)
1	107	Sporozoite	41% / 52%	rifin antigenic variation	physiological processes iron-sulphur cluster assembly metal ion homeostasis positive refulation of cell proliferation immune evasion
2	152	Sporozoite Gametocyte	21% / 24%		reproduction double-strand break repair gemetogenesis chitin catabolism lactate metabolism protein kinase cascade
3	219	Gametocyte	12% / 16%		fructose metabolism meiotic recombination
4	96	Ring Schizont Merozoite	33% / 41%	lipid metabolism fatty acid metabolism	fatty acid metabolism fatty acid elongation
5	109	Ring Early Trophozoite	38% / 39%		pyridoxine metabolism
6	167	Ring Trophozoite	65% / 68%	macromolecule biosynthesis hexose metabolism	adenosine deaminase reaction carbohydrate metabolism and catabolism RNA localization macromolecule biosynthesis nucleoside catabolism protein metabolism
7	93	Ring Trophozoite	52% / 55%	cytosolic ribosome	binding to mRNA cap macromolecule biosynthesis indole and derivative metabolism protein biosynthesis tryptophan metabolism indolalkylamine metabolism histidine family amino acid metabolism glutamine familty amino acid metabolism aromatic amino acid family biosynthesis
8	125	Trophozoite Gametocyte	43% / 46%		mitochondrial translocation nitrogen metabolism urea cycle intermediate metabolism
9	120	Trophozoite Gametocyte	28% / 31%		amino sugar metabolism nucleotide catabolism
10	226	Trophozoite Gametocyte	41% / 44%	DNA replication mitotic cell cycle	peroxidase reaction heavy metal ion transport terpene metabolism DNA replication mitotic cell cycle
11	110	Sporozoite Trophozoite Schizont Gametocyte	52% / 58%	proteasome endopeptidase 26S proteasome 20S proteasome	macromolecule catabolism proteolysis and peptidolysis aspartate metabolism phosophlipid biosynthesis putrescine metabolism
12	240	Trophozoite Gametocyte	39% / 43%	mitotic cell cycle mitochondrion	oxidied glutathione reduction electron transport 2-oxo-gluterate metabolism glycerphosphate shuttle mitotic cell cycle tricarbozylic acid cycle oxidative phosphorylation
13	180	Schizont Gametocyte	33% / 37%		ethanolamine metabolism glycolipid metabolism nucleoside diphosphate metabolism cyclic nucleotide biosynthesis
14	163	Sporozoite Schizont Gametocyte	25% / 29%	actin filament-based process	chromatin silencing cutrate metabolism Rho protein signal transduction
15	130	Schizont	29% / 34%	cell invasion apical complex rhoptry	cell motility cell invasion

Metabolic Pathways, Chromosomal Localisation, Transcription regulation and Plasmodium Characteristics results

Cluster	Metabolic Pathways	Chromosomal Localisation	Putative cis-elements (RSATools)	Genes without human homologues
1		subtelomeric	gcatgc (in 26 genes of the cluster, 4.3% of the genome)	79%
2		central		71%
3	fructose and mannose (3 enzymes)	central		84%
4		subtelomeric		70%
5	purine (3 enzymes)	central		35%
6	glycolysis (9 enzymes) purine metabolism (7 enzymes)	central		29%
7	purine (6 enzymes)	central		46%
8	purine (4 enzymes)	central		60%
9	aminosugar (3 enzymes) purine (3 enzymes)	central		68%
10	sterol biosynthesis (3 enzymes) nucleotide metabolism (purine and pyrimidine)	central		60%
11	purine (3 enzymes)	central		32%
12	citrate cycle (8 enzymes) glycerolipid metabolism (4 enzymes)	central		58%
13	glycolysis (9 enzymes) purine metabolism (7 enzymes)	central		67%
14		central		69%
15		central		81%