Table 5.

Results of Applying LocalCut to Different Datasets

	Modules		BPMs
Dataset	Accepted	Enriched	Accepted	Enriched for same function	Enriched for same or related function	Enriched for different functions	One mod enriched	No mods enriched
Collins et al.	112	103	58	39 (67%)	43 (74%)	6 (10%)	9 (16%)	0 (0%)
Fiedler et al.	10	8	5	0 (0%)	4 (80%)	0 (0%)	0 (0%)	1 (20%)
Boone (Full)	285	104	149	8 (5%)	17 (11%)	9 (6%)	56 (38%)	67 (45%)
S. pombe	31	18	16	1 (6%)	1 (6%)	4 (25%)	9 (56%)	2 (13%)

Notice that the BPM network motif is very rare among the Fiedler et al. cell signaling genes, as compared to the others, implying perhaps that this network is organized at a different level of complexity or with different mechanisms of fault-tolerance. On the other hand, the fact that fewer modules and BPMs are enriched in the full Boone dataset across nearly all S. cerevisiae genes and the S. pombe network is more likely caused by the fact that our knowledge and therefore annotation of basic S. cervisiae cell cycle genes far exceeds our knowledge of the other networks, rather than intrinsic differences in network organization.