This directory contains the code that implements the method described in:

Zhang, Speed and Wildermuth, (2007) Transcription Factor Binding Site Prediction with Multivariate Gene
Expression Data.

You should start by looking at the file:

cellcycle_testcontrol_len567_pc123_interact.m

which performs the analysis described in the paper on the yeast data set.  The code in this file assumes that you have a filtered data file stored in "cellcycle_testcontrol_2.mat", and that you have precomputed the matrices that stores the motif counts.  These "starter" files are available in the directory "yeastdata/". 

If you want to see how to filter the data, pre-process the promoter sequences, and pre-compute the matrices, you can look at the file:

cellcycle_startupscript.m

However, these data pre-processing steps would differ based on the organism and experiments you are analyzing.