Current release is 0.11.
Release 0.11 is the second release associated with the paper, containing scripts for recreating the results given.
The toolboxes required to run the code are listed below.
The CHIPDYNO software can be downloaded here.
Current release is 0.121.
As well as downloading the CHIPDYNO software you need to obtain the toolboxes specified below. These can be downloaded using the same password you get from registering for the CHIPDYNO software.
Finally you will also need the NETLAB toolbox in your path.
demSpellmanwhich run the code on the metabolic and cell cycle data sets. The function
chipdynoTransFactcomputes the posterior, gene specific, transcription factor activities for a given transcription factor. The function
chipdynoTransFactNoisedoes the same thing for expression levels with associated noise (such as computed by mmgMOS). The function
chipdynoGeneActsorts the transcription factor activities for a particular gene. The function
chipdynoTransFactCorrelnormalises the correlations and presents the most correlated TFs. Some scripts have been added to recreate the further validatory experiments detailed in the Supplementary material. Specifically,
demSpellmanp5run the code on the cell cycle data set with connectivity matrix obtained using different cut-offs at p=0.001, p=0.0002 and p=0.005 respectively.
demSpellmanp5p2do the same thing but only use the genes and transcription factors active at p=0.0002, so that the systems have the same dimensions. The script
chipDynoCompareXcan then be used to compare the matrices of effective regulations in the different cases.