The applications of pathway analysis and of cis-regulary sequence verification are available online. They are described in detail in the paper, together with application examples.
Pathway AnalysisApplication Instructions (PDF) Instructions (HTML)
Cis-regulatory Sequence AnalysisApplication Instructions (PDF) Instructions (HTML)

Note: There are sometimes problems with the Java applet on Macs. If possible, the analysis should be run from a PC. The online-program is mostly for illustration purposes. The execution time of the stand-alone program is significantly shorter, and we recommend to use it for more comprehensive analyses.