S 6 Comparison studies on simulated data

In this document we illustrate the module preservation statistics on simulated data. We describe the simulation method and seven simulation studies in more detail than in the main text. The design and main results of the simulations are summarized in Figure 8 of the main article which we reproduce here for convenience in Figure 1. A complete table of results can be found in the accompanying Supplementary Table S5. This is a flat comma separated value (CSV) text file that can be viewed in most standard spreadsheet software such as MS Excel or OpenOffice Calc. The columns indicate the simulation, module label, module size, observed preservation statistics, and their Z scores, for each module in each of the simulated comparisons. R software tutorials describing the results of additional simulation studies can be found on our web page.