Abstract
METscout (http://metscout.mpg.de) brings together metabolism and gene expression landscapes. It is a MySQL relational database linking biochemical pathway information with 3D patterns of gene expression determined by robotic in situ hybridization in the E14.5 mouse embryo. The sites of expression of ∼1500 metabolic enzymes and of ∼350 solute carriers (SLCs) were included and are accessible as single cell resolution images and in the form of semi-quantitative image abstractions. METscout provides several graphical web-interfaces allowing navigation through complex anatomical and metabolic information. Specifically, the database shows where in the organism each of the many metabolic reactions take place and where SLCs transport metabolites. To link enzymatic reactions and transport, the KEGG metabolic reaction network was extended to include metabolite transport. This network in conjunction with spatial expression pattern of the network genes allows for a tracing of metabolic reactions and transport processes across the entire body of the embryo.
Highlights
Digital atlases of spatiotemporal gene expression patterns have been generated for vertebrates [1] and invertebrates [2]
We have developed the ‘METscout’ (Metabolites Enzymes and Transporters) database in which we bring together metabolic pathway maps with the expression patterns of 1500 metabolic enzyme genes and 350 metabolite transporter genes
METscout is currently based on expression data for the E14.5 mouse embryo but tissue anatomy and histology and metabolic needs at E14.5 resemble those of postnatal stages
Summary
Digital atlases of spatiotemporal gene expression patterns have been generated for vertebrates [1] and invertebrates [2]. Efforts have been undertaken to exploit such atlases for addressing biological questions on an -omic scale [6,7,8], these resources are thought to be underutilized [9] and have much additional potential that is barely used In part, this is because an expression atlas per se contains only one type of data and it would be useful to generate databases in which data of different modalities can be used in combinatorial queries. As an alternative entry point the home page of the METscout database offers a Quick Start panel with randomly changing content This is meant to allow the user to instantly explore different aspects of database functionality within the context of a particular metabolic pathway such as the TCA cycle (Figure 1). Each query will bring up the Result Page though choosing a module will open the ModuleView window
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