Input the following command:
BASEsurv1.0.exe CelCycle1.txt 6178 5 ChRatioYPD203.txt 6229 203 1000 CCres1.xls

Note:
[1]BASEsurv1.0.exe -- the program name
[2]CelCycle1.txt -- the expression data file (in log ratio scale), the first row is the experiment name; the first column is gene names
[3]6178 -- the name of genes in the expression data
[4]5 -- the number of profiles in the expression data
[5]ChRatioYPD203.txt -- ChIP-chip data (contains the binding scores of 203 TF for 6229 genes 
[6]6229 -- the number of genes in ChIP-chip data
[7]203 -- the number of TFs in ChIP-chip data; binding in YPD medium condition
[8]1000  -- permutation times
[9]CCres1.xls  -- the output files

Run the program:
Click the file "run.bat"; you can change the bat file by yourself