Figure 1

Properties of the yeast protein interaction networks under random sampling. (A) The degree distribution for the full network and the average for the subnets (averaged over the ensemble) generated by sampling 80%, 60%, 40% and 20% of the nodes in the Saccharomyces cerevisiae protein interaction network. Nodes with degree k = 0 have been dropped from the analysis, reflecting the content of interaction databases. (B) The horizontal line shows the clustering coefficient of the full network. From the boxplots it is apparent that with decreasing subnet size the clustering coefficient will tend to decrease, reflecting the increasingly sparse network with a correlated structure. (C) Z-scores for the six 4-motifs in the true network and 20 random subnets for sampling fractions p = 80%, 60%, 40% and 20%. (D) Median Z-scores for each motif in each of the subnet ensembles and the Z-score of the motif in the full network. In (C) and (D) a positive Z-score indicates that the motif is overrepresented in the true network compared with randomly rewired versions of the true network; a negative Z-score indicates under-representation.