Small Example Graph
This graphs show a clustering of ca. 1300 variant genes in yeast, laid out according to their first two principal components.
MGV can use data from several datasets, for example to compare clusterings. In this example two partitioning clusterings in yeast are prepared.
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
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>.
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