Dear Bharath

Sorry, I did not understand... You need a general work-flow of the analysis or You will upload the specific graph to get suggestions/impression/thoughts?

Dear Sir,

                    I need a general work-flow

Ok, for this I would start from this article

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000108

 Dear Sir,

                             I have gone through the paper and understood the basic principles, Can you provide me a details on parameter settings in Cyoog.

Dear Bharath

I am sorry, I never used CyOog. I guess there is a manual of the software. It looks that here is a simple tutorial http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Power_Graph_Analysis_with_CyOog

Dear Sir,

                Then which tool you are using to derive powergraphs?

It was another plugin for old Cytoscape. I worked with power graphs only ones, because I mostly deal with metabolic and gene co-expresson networks and not with protein-protein interactions were it can be really useful. So, I think if You need to work with protein networks, it will be good to study this CyOog. I see a lot of manuals in the Internet. http://opentutorials.cgl.ucsf.edu/images/2/27/PowerGraph_Presentation.pdf