cMonkey and MAGGIE Gaggle Demo/Tutorial

A demonstration showing how biclusters of coregulated genes in Halobacterium can be projected onto Pyrococcus using Gaggle.


In this demo, we show how to view the regulatory network for Halobacterium produced by the cMonkey and Inferelator algorithms. A helper application shows expression profiles, regulatory motifs, and protein-protein interactions for each bicluster. In order to investigate conservation of these features, we choose a bicluster in Halobacterium and look up orthologous genes in Pyrococcus. Finally, we display interactions among the selected Pyrococcus orthologs.

Here are the links to start each of the relevant Gaggle tools (numbered by the corresponding step in the tutorial).
To load some others, please refer to the MAGGIE Gaggle page.
  1. Gaggle Boss
  2. cMonkey bicluster network Viewer in Cytoscape
  3. Gaggled bicluster viewer
  4. Pyrococcus - Halobacterium ortholog translator
  5. Pyrococcus Prolinks network
Additional (optional) web starts:

For more information on cMonkey, please refer to the cMonkey web page and the BMC Bioinformatics article.