I am writing to ask if you could kindly share with me the yeast cell cycle binarized expression data that you used in Loregic’s paper.
In our group we would like to find a method to identify the logic rules that govern cooperativity of multiple regulators, in GRNs built from differentially expressed genes.
The amount of samples we will have is limited, so we will be mainly relying on literature information, and as a first step we would like to test our method on your binarized expression data.
We used BoolNet to binarize data,
http://cran.r-project.org/web/packages/BoolNet/index.html . We also
http://cran.r-project.org/web/packages/ArrayBin/index.html, which gave
very similar Loregic results with BoolNet (see Supplemental Figure).
The yeast cell cycle data we used was the classical microarray data
published in 1998 (Spellman & Cho):