Humboldt University Berlin Theoretical Biophysics Max Planck Institute

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

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

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

Humboldt University Berlin Theoretical Biophysics Max Planck Institute Molecular Genetics Network Motifs 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. R. Milo, …, U. Alon, Network Motifs: Simple Building Blocks of Complex Networks, Science, 2002 VL Netzwerke, WS 2007/08 Edda Klipp 4

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

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

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

Humboldt University Berlin Theoretical Biophysics Max Planck Institute Molecular Genetics 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 VL Netzwerke, WS 2007/08 Edda Klipp 8

Humboldt University Berlin Theoretical Biophysics Max Planck Institute Molecular Genetics 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. VL Netzwerke, WS 2007/08 Edda Klipp 9

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