Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

What are commonly used tools to reconstruct the transcriptional regulatory circuits that govern diverse cellular responses and what input data sets do they accept?

share|improve this question

2 Answers 2

I'd like to add regulonDB which is not as integrated, but has a tremendous map of the e coli regulome which would be useful for any bacterial model.

I agree with @DanielStandage that this is not a well understood and there don't even appear to be standard representations for this sort of data.

share|improve this answer
2  
The Systems Biology Markup Language (SBML) is the closest thing to a standard representation out there, but it's been adopted about as widely as every other XML-based bioinformatics format I've encountered. –  Daniel Standage May 30 '12 at 20:04

Inferring transcriptional / regulatory networks from empirical data is an active area of research, and to my knowledge there aren't many mature tools for this type of analysis. I see mostly mathematicians, statisticians, and engineers working on this problem, probably because of the intense quantitative theory involved. Even if mature tools do exist, I doubt they're tailored for the typical biologist--more likely, they are geared toward scientists with a more quantitative background.

That being said, I am aware of 2 or 3 pieces of software that may provide a starting point for the curious or the adventurous: AIRnet (described here), iBioSim (described by Barker's PhD thesis, currently the second hit on this Google search), and maybe Ingenuity Pathways Analysis (which requires a paid license). The only one of these tools I've even tried to use is iBioSim, and at the time (2 or so years ago) it was a very kludgy process.

share|improve this answer

Your Answer

 
discard

By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.