There seems to be some claims that biologists are interested in finding network motifs (i.e. subgraphs) that occur more often than expected in large networks -- thus suggesting a demand for software packages such as FANMOD, which finds (or estimates) the number of times each non-isomorphic subgraph on n vertices appears in a given network.
Question: What are some examples of where large networks arise in biological systems and where motifs play a role (or are suspected to play a role)?
If possible, I would also like to be able to access these networks directly (i.e. download them) and test them myself.