Small Example Graph

This example contains a very small graph, showing a small interaction network in yeast.

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PCA Layout
This graphs show a clustering of ca. 1300 variant genes in yeast, laid out according to their first two principal components.

Nodes coloured according to their cluster membership:

Nodes coloured according to the first experiment:

Cluster comparison
MGV can use data from several datasets, for example to compare clusterings. In this example two partitioning clusterings in yeast are prepared.

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Pathway Intersections
In this example, all MetaCyc pathways of yeast are represented as nodes. The edges represent metabolites shared between two pathways. The nodes are coloured according to their degree: green: low, red: large

BioPax Pathway
The chorismalte biosythesis pathway in yeast, shown as a SBGN process description diagram.
Hint: In MGV, you can change the display style to see the expression levels of the enzymes by pressing <Space>.

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To view the graphs in MGV, run Mayday, open the dataset (see below) and run the MGV from any probe list. To do so, select a probe list, and from the main menu, choose “Visualization” -> “Graph Viewer”.

Data used: All examples are created with MGV using this dataset (GEO accession number GSE1723)
The citation for this dataset is:

Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P et al. Exploiting combinatorial cultivation conditions to infer transcriptional regulation. BMC Genomics 2007 Jan 22;8:25. PMID: 17241460

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