EGRIN (Environment And Gene Regulatory Influence Network)

EGRIN is a product of an integrated systems analysis of transcriptional response of Halobacterium salinarum NRC-1 to diverse enviromental & genetic insults. The network represents a predictive model for transcriptional control of physiology encoded by 1,929 of the total 2,400 genes in this organism. Details on the construction of analyses of this network are described in the paper published in Cell.

EGRIN can be accessed in 5 formats:

1. Web interface
2. Cytoscape 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 (please be sure to use the new Gaggle API)
     
     • MeV
     • R
     • DMV (with Halobacterium NRC-1 microarray data)
     • Prolinks network
     • Firegoose
       
       1. once the firegoose is installed you can also explore EGRIN interactively with
          
          • the Halobacterium NRC-1 annotations database
          • the Cytoscape webstart ( for example, to get more information on regulators, biclusters and constituent genes)
3. Cytoscape CYS file for Cytoscape 2.7.0 and higher
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.