Free software tool for visualisation and exploration of integrated Plasmodium falciparum 3D7 functional genomics datasets
MaGnET is a software tool for visualisation and exploration of large-scale datasets relating to the malaria parasite. At present the program is focused on Plasmodium falciparum, as this was the first Plasmodium species to have its genome sequenced and is the focus of several genomic-scale gene characterisation studies.
The program allows users to examine features of groups of genes across different datasets. It offers alternative views of the data, for example, while in the whole genome view, you may select a gene expression dataset to display against the genomic location of the genes. If you click on a chromosome it will open in a chromosome viewing window allowing you to examine the genes more closely. The protein-protein interaction viewer allows you to navigate the interaction network for genes of interest. Overlaying messenger RNA and protein expression data onto the interactome is a useful feature. Another section allows you to query the database and retrieve results in the form of a table. The expression data viewer currently offers the capability to view the gene expression profile of individual genes and to compare the profiles of small groups of genes. In addition, a whole-genome expression viewer is planned and will hopefully be available soon. In all cases, it is possible to open a fact sheet listing detailed genomic and functional information about a particular gene. The fact sheet also provides the protein and and nucleotide sequences, ortholog and paralog data, list of known interactions, Gene Ontology and InterPro annotation, links to protein structures (solved and modelled) and linkouts to other online resources.
View screenshots of MaGnET in action!
We recommend taking the MaGnET tutorial available from this website, which takes you through the basics of using MaGnET (should take around 10-20 minutes to complete). There are also help pages available within the program offering guidance about how to use each section.
The datasets included within MaGnET are all publicly available, including gene annotations downloaded from the Plasmodium annotation project at the Sanger Institute, public databases, such as the PDB, and supplementary information from various published functional genomic studies.
MaGnET is currently available to use either as a Java Web Start application (downloads the application to your computer and accesses the database on the FfAME server) or as a downloadable application and database (recommended, because it offers significant advantages of speed - large datasets can be slow to load over a network using the Web Start version). MaGnET requires Java to be installed on your computer (for more information see the MaGnET online page). There is currently no MaGnET app but we are thinking about that, too, of course... don't hesitate to encourage us by sending us email!
MaGnET has been based on a concept and prototype tool developed by Richard Orton for the budding yeast Saccharomyces cerevisiae - the Yeast Exploration Tool Integrator (YETI).
MaGnET also makes use of several open-source tools and libraries. For visualisation of protein structures the Jmol molecular viewer is utilised. For the time-series graphs in the expression data viewer the JFreeChart library was employed. The compute server at FfAME where the MaGnET database is currently stored, runs the MySQL database management system.