metaSHARK: a WWW platform for interactive exploration of metabolic networks

Abstract

The metaSHARK (metabolic search and reconstruction kit) web server offers users an intuitive, fully interactive way to explore the KEGG metabolic network via a WWW browser. Metabolic reconstruction information for specific organisms, produced by our automated SHARKhunt tool or from other programs or genome annotations, may be uploaded to the website and overlaid on the generic network. Additional data from gene expression experiments can also be incorporated, allowing the visualization of differential gene expression in the context of the predicted metabolic network. metaSHARK is available at http://bioinformatics.leeds.ac.uk/shark/.

Figure 1

(a) A section of the glycolysis pathway from an automated metabolic reconstruction of the human malaria parasite P.falciparum, visualized using SHARKview. Metabolites are represented as circles, reactions as squares and enzymes as round-edged rectangles. Directed arcs between nodes show the effect of a reaction as the consumption and production of different metabolites. Nodes in green show reactions catalysed by enzymes for which good evidence has been found in the P.falciparum genome. Nodes in red show reactions catalysed by enzymes for which only tentative evidence has been found. Grey nodes show that no evidence for a catalysing enzyme was found. (b) The same pathway section for P.falciparum, with the enzyme nodes coloured according to their level of co-expression with lactate dehydrogenase (EC 1.1.1.27). Blue nodes show a high positive co-expression, whereas a colour towards pink shows a high negative co-expression.