1. Clustering of protein networks: Graph theory and terminology Scale-free architecture Modularity Robustness Reading: Barabasi and Oltvai 2004, Milo et al. 2002 Lecturer: Trey Ideker

2. Yeast protein-protein interaction network What are its network properties?

3. Graphs Graph G=(V,E) is a set of vertices V and edges E A subgraph G’ of G is induced by some V’  V and E’  E Graph properties: –Node degree –Directed vs. undirected –Loops –Paths –Cyclic vs. acyclic –Simple vs. multigraph –Complete –Connected –Bipartite

4. Paths A path is a sequence {x 1, x 2,…, x n } such that (x 1,x 2 ), (x 2,x 3 ), …, (x n-1,x n ) are edges of the graph.sequence edgesgraph A closed path x n =x 1 on a graph is called a graph cycle or circuit. graph cycle

5. Network measures Degree k i The number of edges involving node i Degree distribution P(k) The probability (frequency) of nodes of degree k Mean path length The avg. shortest path between all node pairs Network Diameter “The longest shortest path” How do the above definitions differ between undirected and directed networks?

6. Clustering coefficient The combination “k choose 2” # edges between node I’s neighbors # of neighbors of I The density of the network surrounding node I, characterized as the number of triangles through I. Related to network modularity C(k) = avg. clustering coefficient for nodes of degree k

7. Directionality and Degree What is the clustering coefficient of A in either case?

8. WHAT DOES SCALE FREE REALLY MEAN, ANYWAY? P(k) is probability of each degree k For scale free: P(k) ~ k  What happens for small vs. large  ?

9. Generating random networks Erdos-Renyi Start with N nodes and connect each pair with equal probability p Scale-free Add nodes incrementally. New nodes connect to each existing node I with probability proportional to its degree: Scale-free networks have small avg. path lengths ~ log (log N)– this is called the ‘small world’ effect

10. How do scale-free networks arise in evolution? Both are well-explained by gene duplication. When a protein duplicates, it initially retains all of its previous interactions. This process drives network hubs to get even bigger. Due to 2 basic mechanisms: (1)Network Growth (2)Preferential attachment

11. Neither network produces modular structure C(k) is avg. cluster coefficient of each degree k

12. Hierarchical networks This class of random networks are generated based on replicating a four node “module”.

14. The amazing result from that paper % Essential P(k) kk

15. Robustness Complex systems, from the cell to the Internet, can be amazingly resilient to component failure Network topology plays an important role in this robustness Even if ~80% of nodes fail, the remaining ~20% still maintain network connectivity This also leads to attack vulnerability if hubs are selectively targeted In yeast, only ~20% of proteins are lethal when deleted, and are 5 times more likely to have degree k>15 than k<5.

16. Network Motifs (Milo et al.) Motifs are “patterns of interconnections occurring in complex networks.” That is, connected subgraphs of a particular isomorphic topology The approach queries the network for small motifs (e.g., of < 5 nodes) that occur much more frequently than would be expected in random networks Significant motifs have been found in a variety of biological networks and, for instance, correspond to feed-forward and feed-back loops that are well known in circuit design and other engineering fields. Pioneered by Uri Alon and colleagues

17. Motif searches in 3 different contexts

18. All 3-node directed subgraphs What is the frequency of each in the network?

19. Outline of the Approach Search network to identify all possible n-node connected subgraphs (here n=3 or 4) Get # occurrences of each subgraph type The significance for each type is determined using permutation testing, in which the above process is repeated for many randomized networks (preserving node degrees– why?) Use random distributions to compute a p-value for each subgraph type. The “network motifs” are subgraphs with p < 0.001

20. Schematic view of network motif detection Networks are randomized preserving node degree

21. Concentration of feedforward motif: Mean+/-SD of 400 subnetworks (Num. appearances of motif divided by all 3 node connected subgraphs)

22. Transcriptional network results

23. Neural networks

24. Food webs

25. World Wide Web

26. Electronic circuits

27. Interesting questions Which networks have motifs in common? Which networks have completely distinct motifs versus the others? Does this tell us anything about the design constraints on each network? E.g., the feedforward loop may function to activate output only if the input signal is persistent (i.e., reject noisy or transient signals) and to allow rapid deactivation when the input turns off E.g., food webs evolve to allow flow of energy from top to bottom (?!**!???), whereas transcriptional networks evolve to process information