Resources for exploring EGRIN for oxidative stress

Oxidative stress (OS) is a condition reached when certain environmental stresses or genetic defects cause the production of ROS to exceed the management capacity. EGRIN_os is a multi-tiered systems scale program for OS management that was constructed using network inference algorithms cMonkey and Inferelator.  You can find details of how this was done in the following manuscript:

Coordination of frontline defense mechanisms under severe oxidative stress. Amardeep Kaur, Phu T. Van, Courtney R. Busch, Courtney K. Robinson, Min Pan, Wyming Lee Pang, David Reiss, Jocelyne DiRuggiero, and Nitin S. Baliga. Molecular Systems Biology. in press.

EGRIN_os can be accessed in 5 formats:

1. Web interface
2. Cytoscape 1 webstart
   • Requires Java to be installed on your machine
   • You can use this network visualization in Cytoscape in conjunction with other tools in the Gaggle
     • MeV
     • R
     • Data Matrix Viewer (DMV) (with ratio and lambda data)
     • Prolinks network
     • Firegoose
       1. once the firegoose is installed you can also explore EGRIN_os interactively with
          • the Halobacterium NRC-1 annotations database
          • the Cytoscape webstart ( for example, to get more information on regulators, biclusters and constituent genes)
3. CYS file for Cytoscape 2.7 and above. Save this file and open it with the Cytoscape network viewer.
4. Sif (simple interaction format used by Cytoscape).
5. BioTapestry
   • Requires Java to be installed on your machine

You may view some additional instructions here, or email us if you have any questions.