Displaying modules of metabolism in a hierarchical format

Following sample networks are examples used in the perspective paper titled "Towards zoomable multidimensional maps of the cell"

A zoomable map of metabolic modules. Edges between modules indicate that one or more components are shared. 

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Module hierarchy is based on KEGG database. A plugin is developed to load and parse the hierarchy. A tutorial regarding this plugin will be available soon

Note: double-click on metanode to expand/contract

Note: Click the left image for full-size screen-shot that is taken after the network is saved as SVG file.

Note: To save this file, you need to turn on database online under File menu, then login and save the file

Using a metagraph to integrate two annotation methods.

A) Hierarchy of GO terms under which 34 genes are annotated according to Saccharomyces Genome Database (SGD). B) Functional association network of 34 genes according to the VisANT-Predictome system with edges representing associations based on different assays. C) A metagraph with expanded nodes com-bines the information from both A and B. D) The metagraph with collapsed nodes and edges

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Note: double-click on metanode to expand/contract

Note: Click the left image for full-size screen-shot that is taken after the network is saved as SVG file.

Note: To save this file, you need to turn on database online under File menu, then login and save the file

The complexes were determined by tandem affinity mass spectrometry and were colored to indicate subsequent functional assignments. The gray edges connect complexes that share protein components. The components of each complex are included in the model and are visible when the metanode representing the complex is expanded. As an example, the complex labeled as 175 is expanded so that its components, as well as the one being shared (shadowed) with complex 36, are visible.

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Note: double-click on metanode to expand/contract

Note: Click the left image for full-size screen-shot that is taken after the network is saved as SVG file.

This network can be rearranged based annotated functions as appeared in the paper:

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A network using the same set of complexes as Fig. 2, only with edges representing interactions derived by large-scale two-hybrid assays. The integration of interaction data enables the internal connectivity of the complexes to be revealed when a node is expanded. An expansion of node 175 would reveal an interaction between Exo84 and Sec5, and between Sec8 and Sec10.

Load this network in VisANT 

Download this network (VisML)

Note: double-click on metanode to expand/contract

Note: Click the left image for full-size screen-shot that is taken after the network is saved as SVG file.

This network can also be rearranged based annotated functions as appeared in the paper:

Load rearranged network in VisANT

Download this network (VisML)