I'd suggest you take a look at the people behind the RECOMB satellite meeting on Regulatory Genomics and see what they are doing in their research. I attended that conference in 2009 and 2010. I recall a nice tool presented by Grace Huang from U of Pittsburgh (Panayiotis Benos group). They incorporate evidence from gene expression to build disease-specific modules that also use transcription factors and microRNAs.

Added on 2 June 2011:

Two new papers that might be relevant to this are:

More than half of your DNA is devoted to regulating how genes carry out their tasks. A new paper by Bert O'Malley and Jun Qin appears in the current issue of the journal Cell.

An integrated approach to characterize genetic interaction networks in yeast metabolism, by Balazs Szappanos, Karoly Kovacs, et al. in Nature Genetics.

Have a look at the DREAM Project here. They provide yearly challenges to participants that focus on regulatory networks (not just on genes but also proteins). I am pretty sure a wide range of methods are used in the challenges and so it should provide a good overview.

There is a "seminal" review of Hidde de Jong (where you can find a "seminal" paper for each reviewed method) :

de Jong. Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol (2002) vol. 9 (1) pp. 67-103

Wikipedia gives a book named "Computational Modeling of Genetic and Biochemical Networks" by James M. Bower and Hamid Bolouri. However, it is 10 years old.