I have microarray data and i want to measure gene regulatory network for that i have to compute gene gene interaction. So can one guide me how to compute that and how to put weights on gene graph. What should be the threshold value to be activator or inhibator?

Waiting Positive

You can use ARACNE or WGCNA to compute a adjacency matrix, which is the numerical basis for a graph. This can be loaded into cytoscape for visualisation etc.