Inferring Gene Regulatory Networks Using Bayesian Inference

Question

[Diana]

Hello everyone,

Does anyone know of any R packages that can be used to infer gene regulatory networks from expression data using Bayesian inference?

Thanks!

Answer 1

[Nathan Harmston]

if you have a time series, how about GRENITS?

http://www.bioconductor.org/packages/devel/bioc/html/GRENITS.html

or BIRTA?

http://www.bioconductor.org/packages/2.10/bioc/html/birta.html

[Dave Bridges]

do you have any experience with these, and how well they work?

[Diana]

Thanks for your answer Nathan. Have you used these packages before? because I have a question regarding the input data. My data has a time series at 3,5 and 7 hrs and each time point has a control and treatment condition and we have 3 replicates of control and treatment experiments at each time point. All data is normalized. Should I use the values of all replicates or mean of the triplicates for building the network? Thanks!