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Design principle of biological networks—network motif

Design principle of biological networks—network motif. Definition of motifs. Motifs are those subgraphs that occur significantly more often in the real network than in randomized networks. Network motifs. Random version of original network. Original network. Criteria for network motif.

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Design principle of biological networks—network motif

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  1. Design principle of biological networks—network motif

  2. Definition of motifs • Motifs are those subgraphs that occur significantly more often in the real network than in randomized networks.

  3. Network motifs Random version of original network Original network

  4. Criteria for network motif

  5. Motifs in genetic network of yeast

  6. Motifs in genetic network of E. coli

  7. Enumeration methods to identify motifs • Generating an ensemble of random networks • Counting subgraphs in real network and random network

  8. Subgraph concentration

  9. Random sampling of n node subgraphs • Pick a random edge from the network and expand the subgraph iteratively by picking random neighboring edges until the subgraph reaches n nodes.

  10. Sampling algorithm

  11. P: probability of sampling a specific subgraph • Define a score Si for each subgraph of type i, and set to Si zero initially. • Si= Si+1/P until ST samplings are finished. • Assume L types of subgraphs were sampled.

  12. Compare between sampling and enumeration

  13. Runtime complexity analysis

  14. Conservation of network motif constituents Drosophila melanogaster Homo Sapiens Mus musculus Orthologs Four nodes motif Saccharomyces cerevisiae C. elegans Arabidopsis thaliana

  15. Inparanoid: Eukaryotic Ortholog Groups

  16. Evolution conservation of motif

  17. Evolution conservation of motif

  18. Network motif software

  19. Homework • Download the mfinder motif detection software from Uri Alon’s web page, http://www.weizmann.ac.il/mcb/UriAlon Read the manual and make yourself being familiar with this software. Use this software to find the motifs for the E. coli gene regulatory network. The interaction file can be downloaded from Uri Alon’s homepage.

  20. References • Uri Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits

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