Recent evidence indicates that the abundance of recurring elementary interaction patterns in complex networks, often called subgraphs or motifs, carry significant information about their function and overall organization. Yet, the underlying reasons for the variable quantity of different subgraph types, their propensity to form clusters, and their relationship with the networks' global organization remain poorly understood. Here we show that a network's large-scale topological organization and its local subgraph structure mutually define and predict each other, as confirmed by direct measurements in five well studied cellular networks. We also demonstrate the inherent existence of two distinct classes of subgraphs, and show that, in contrast to the low-density type II subgraphs, the highly abundant type I subgraphs cannot exist in isolation but must naturally aggregate into subgraph clusters. The identified topological framework may have important implications for our understanding of the origin and function of subgraphs in all complex networks.aggregation ͉ subgraphs A number of complex biological and nonbiological networks were recently found to contain network motifs, representing elementary interaction patterns between small groups of nodes (subgraphs) that occur substantially more often than would be expected in a random network of similar size and connectivity (1, 2). Theoretical and experimental evidence indicates that at least some of these recurring elementary interaction patterns carry significant information about the given network's function and overall organization (1-4). For example, transcriptional regulatory networks of cells (1, 2, 5, 6), neural networks of C. elegans (2), and some electronic circuits (2) are all information processing networks that contain a significant number of feed-forward loop (FFL) motifs. However, in transcriptional regulatory networks these motifs do not exist in isolation but meld into motif clusters (7), while other networks are devoid of FFLs altogether (2).In general, all subgraphs have two important properties: their topology and the directionality of their links. In cellular networks, these two properties can be clearly separated from each other. In protein-protein interaction (PPI) networks all links are by definition nondirectional. In contrast, in transcriptional regulatory networks information flow between a transcription factor and the operon (gene) regulated by it is almost always unidirectional (1, 2). Metabolic networks occupy an intermediate position between these two extremes, because most, but not all, metabolic reactions are reversible under various growth conditions. Despite the difference in the relative role of link directionality, the large-scale organization of the three different network types is quite similar, most being characterized by a scale-free connectivity distribution and hierarchical modularity (8-12). The only exception is the incoming degree distribution (i.e., the number of transcription factors regulating a target gene) of regulatory...