Construction, modeling and analysis of genetic regulatory networks (GRNs) is one of the objective of Systems Biology. Once the GRN is constructed, we can infer many kind of information that can lead to discovery of various therapies. We have various popularly known methods like Boolean, ODEs, Bayesian, Dynamic Bayesian, Machine learning based techniques, etc. Is there any matured software tool that can be used for the construction of GRN?
Cytoscape is a powerfull tool to build GRN, and has also plugins like ClueGO to sort specific GO of interacting genes, but you may need a formation to use it accurately
http://www.cytoscape.org/
http://www.ici.upmc.fr/cluego/ClueGODocumentation.pdf
Hope it can help
A very popular one is ARACNE from Califano Lab.
It is well documented and maintained.
Here the original publication:
http://www.ncbi.nlm.nih.gov/pubmed/16723010
Here the software page: http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/ARACNE
HEFALMP (http://hefalmp.princeton.edu/) is tool to detect virtual interactions between genes based on gene expression and physical interaction data. I find it very useful.
If you just want to do network visualization (nodes, edges and annotations) Osprey is a useful java-based tool. It connects to BioGrid which has >50000 interactions (genetic, physical and enzymatic) in yeast (budding and fission), Drosophila, C. elegans, mouse, zebrafish, rat and human. Editing of the "graphs" is pretty straightforward. You can also load your own datasets to make custom networks. It is similar to Cytoscape, but I personally prefer Osprey (Osprey is less complicated/more intuitive but is consequently also a little less powerful because it doesn't have all the application-specific plugins).
http://biodata.mshri.on.ca/osprey/servlet/Index
Also, in terms of synthetic biology, my colleagues have developed a web-based genetic design tool GenoCAD (http://www.genocad.org) to assemble genetic parts (each associated with a DNA sequence) into expression vectors and outputs the entire sequence design. It uses defined "grammars" to ensure proper design to simplify the design and production of genetic networks. It has recently been upgraded to include "attribute grammars" so that you can assign behavioural values to the parts (e.g. kinetic rates, rate laws, and types of interactions) and it performs simulations of the genetic networks (e.g. toggle switch, repressilator) so that you can test your designs before production.
If you have microarray data, then you need to go with ARACNE tool. It's very powerful and has huge number of citations. You can find a user friendly and very easy implementation in GenePattern Website. All you have to do is just to upload your data and run the analysis on their website. You can click on email reminder to notify you when the analysis is done. Let me know if you need any help in file formats to run your analysis.
Noteworthy, ARACNE has the assumption that the more data you have, the more accurate results you will obtain. I have extracted and normalized microarray data for more than 2500 highly diversed expression profiles. They are all normalized with the same algorithm (RMA). So I can also help you with the data if you are interested.
My colleagues have some usable packages here: http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/
I would recommend the CSI package at the bottom of the page, and the wrapper for VBSSM.
Other than ARACNE from Califano lab, another option can be BANJO from Hartemink Lab for the inference of GRN. The link for ARACNE has been provided above in one of the responses. Here is the link for BANJO:
https://www.cs.duke.edu/~amink/software/banjo/
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