MaGnET: Malaria Genome Exploration Tool

Free software tool for visualisation and exploration of integrated Plasmodium falciparum 3D7 functional genomics datasets

Datasets and sources

Gene and protein sequences and sequencing centre annotations


P. falciparum 3D7
Nuclear chromosomes:
PlasmoDB download
Version 9.0 May 2012
Mitochondrial and plastid chromosomes:
PlasmoDB download
Version 9.0 May 2012

Original genome sequence publication: Gardner et al. Genome sequence of the human malaria parasite Plasmodium falciparum. (2002) Nature, 419: 498-511.

Gene Ontology annotations


P. falciparum 3D7
PlasmoDB download
Version 9.0 May 2012

InterPro predicted sequence features (domains etc)


P. falciparum 3D7
PlasmoDB download
Version 9.0 May 2012

Ortholog/paralog groups


P. falciparum 3D7, P. falciparum IT, P. vivax, P. knowlesi, P. berghei, P. c. chabaudi, P. y. yoelii
PlasmoDB download
Version 9.0 May 2012
Data generated by OrthoMCL

Protein-protein interactions


P. falciparum 3D7
LaCount et al. A protein interaction network of the malaria parasite Plasmodium falciparum. (2005) Nature, 438(7064):103-7.

Protein experimentally-solved 3D structures


P. falciparum 3D7
RCSB Protein Data Bank
Various dates

Protein comparatively-modelled 3D structures


P. falciparum 3D7
ModBase
Various dates

RNASeq data


P. falciparum 3D7
Otto et al. New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. (2010) Mol Microbiol., 76(1): 12-24.

P. falciparum 3D7
Bártfai et al. H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3. (2010) PLoS Pathog., 6(12): e1001223.

mRNA expression data


P. falciparum 3D7, Dd2 and HB3
Llinas et al. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. (2006) Nucleic Acids Research, 34(4): 1166-73. [website]
HB3 data originally from Bozdech et al. The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum. (2003) PLoS Biology, 1(1): e5.

P. falciparum 3D7 and NF54
Young et al. The Plasmodium falciparum sexual development transcriptome: A microarray analysis using ontology-based pattern identification. (2005) Molecular and Biochemical Parasitology, 143(1): 67-79. [website]
P. falciparum 3D7

Le Roch et al. Discovery of Gene Function by Expression Profiling of the Malaria Parasite Life Cycle. (2003) Science, 301(5639): 1503-8. [website]

mRNA decay data

P. falciparum 3D7
Shock et al. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during intra-erythrocytic development cycle. (2007) Genome Biology, 8(7): R134.

Protein expression data


P. falciparum 3D7
Dataset was downloaded as a supplementary table from Le Roch et al. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. (2004) Genome Research, 14: 2308-18.
Original data from Florens et al. A proteomic view of the Plasmodium falciparum life cycle. (2002) Nature, 419: 520-26.

P. falciparum NF54
Lasonder et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. (2002) Nature, 419: 537-42.