1. VL Netzwerke, WS 2007/08 Edda Klipp 1 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Networks in Metabolism and Signaling Edda Klipp Humboldt University Berlin Lecture 10 / WS 2007/08 Final Considerations

2. VL Netzwerke, WS 2007/08 Edda Klipp 2 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Network Motifs R. Milo, …, U. Alon, Network Motifs: Simple Building Blocks of Complex Networks, Science, 2002

3. VL Netzwerke, WS 2007/08 Edda Klipp 3 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Network Motifs R. Milo, …, U. Alon, Network Motifs: Simple Building Blocks of Complex Networks, Science, 2002

4. VL Netzwerke, WS 2007/08 Edda Klipp 4 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Network Motifs R. Milo, …, U. Alon, Network Motifs: Simple Building Blocks of Complex Networks, Science, 2002 Schematic view of network motif detection. Network motifs are patterns that recur much more frequently (A) in the real network than (B) in an ensemble of randomized networks. Each node in the randomized networks has the same number of incoming and outgoing edges as does the corresponding node in the real network. Red dashed lines indicate edges that participate in the feedforward loop motif, which occurs five times in the real network.

5. VL Netzwerke, WS 2007/08 Edda Klipp 5 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Network Motifs X Y X Y Z X Z 1 Z 2 Z 3 Z n X 1 X 2 X 3 X m Z 1 Z 2 Z 3 Z n Single input High Density Feedforward loop Feedback loop Activation Inhibition R. Milo, …, U. Alon, Network Motifs: Simple Building Blocks of Complex Networks, Science, 2002

6. VL Netzwerke, WS 2007/08 Edda Klipp 6 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Network Motifs U. Alon, An Introduction to Systems Biology. 2007 OscillatorRepressilator

7. VL Netzwerke, WS 2007/08 Edda Klipp 7 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Network Motifs U. Alon, An Introduction to Systems Biology. 2007 X Y Z Delay in transcription cascades x y z x y z

8. VL Netzwerke, WS 2007/08 Edda Klipp 8 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Modularity Wikipedia: the concept that organisms or metabolic pathways are composed of modules Modules: parts of network with few interfaces to other parts of the network

9. VL Netzwerke, WS 2007/08 Edda Klipp 9 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Robustness Robustness is the quality of being able to withstand stresses, pressures, or changes in procedure or circumstance. A system, organism or design may be said to be "robust" if it is capable of coping well with variations (sometimes unpredictable variations) in its operating environment with minimal damage, alteration or loss of functionality.

10. VL Netzwerke, WS 2007/08 Edda Klipp 10 Max Planck Institute Molecular Genetics Humboldt University Berlin Theoretical Biophysics Robustness Function robust against parameter variation. -Fluxes against perturbation of enzyme concentration -Developmental pattern against perturbations