The Ingredients
Though there are a variety of datasets we could have drawn from, we chose to restrict the physical network to DIP (the database of interacting proteins), as of the March 2, 2003 release. At that time, DIP contained 15,114 physical interactions among 4,716 proteins.

Xenarios, I. et al. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Research 30, 303-305. (2002)

We did consider other physical interaction networks, such as BIND (protein-protein interactions) and the transcriptional data (protein-DNA interactions) published by Lee, et al. in 2002. For the publication, we considered only DIP; but for reference, We show the results of using different physical networks here.

Finally:

• Download the 15,114-interaction DIP physical network here.
(note: this file has become corrupted -owo 2007.02)