Design principle of biological networksnetwork motif

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Design principle of biological networksnetwork
motif
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Definition of motifs

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

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Network motifs
Random version of original network
Original network
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Criteria for network motif
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Motifs in genetic network of yeast
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Motifs in genetic network of E. coli
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Enumeration methods to identify motifs

• Generating an ensemble of random networks
• Counting subgraphs in real network and random
  network

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Subgraph concentration
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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.

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Sampling algorithm
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• P probability of sampling a specific subgraph
• Define a score Si for each subgraph of type i,
  and set to Si zero initially.
• Si Si1/P until ST samplings are finished.
• Assume L types of subgraphs were sampled.

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Compare between sampling and enumeration
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Runtime complexity analysis
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Conservation of network motif constituents
Drosophila melanogaster
Homo Sapiens
Mus musculus
Orthologs
Four nodes motif
Saccharomyces cerevisiae
C. elegans
Arabidopsis thaliana
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Inparanoid Eukaryotic Ortholog Groups
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Evolution conservation of motif
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Evolution conservation of motif
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Network motif software
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Homework

• Download the mfinder motif detection software
  from Uri Alons web page, http//www.weizmann.ac.i
  l/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 Alons homepage.

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References

• Uri Alon, An Introduction to Systems Biology
  Design Principles of Biological Circuits