Hierarchical modularity of nested bow-ties in metabolic networks

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Hierarchical modularity of nested bow-ties in
metabolic networks Jing Zhao Jzhao_at_scbit.org Sha
nghai Jiao Tong University Shanghai Center for
Bioinformation and Technology 5 August,2007
Zhao J, Yu H, Luo J, Cao Z, Li Y Hierarchical
modularity of nested bow-ties in metabolic
networks. BMC Bioinformatics 20067386.
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Outline

• Background
• Bow-tie pattern
• Hierarchical organization
• Results
• Topological features
• Relationship between topology and
  functionality
• 3. Discussion

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Outline

• Background
• Bow-tie pattern
• Hierarchical organization
• Results
• Topological features
• Relationship between topology and
  functionality
• 3. Discussion

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Biological viewpoint of metabolic system bow-tie
Csete M, Doyle J Bow ties, metabolism and
disease. Trends in Biotechnology 2004,
22446-450.
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Topological viewpoint of metabolic networks bow
tie
E.coli metabolic network
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Topological viewpoint of metabolic networks bow
tie
Ma H-W, Zeng A-P The connectivity structure,
giant strong component and centrality of
metabolic networks. Bioinformatics 2003,
191423-1430.
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Topological viewpoint of metabolic networks bow
tie Robust yet frangile
Bow-tie structure in the coarse-grained graph of
the E.coli metabolic network
Zhao J, Yu H, Luo J, Cao Z, Li Y Complex
networks theory for analyzing metabolic networks.
Chinese Science Bulletin 2006, 51(13)1529-1537.
Zhao J, Tao L, Yu H, Luo J-H, Cao ZW, Li Y
Bow-tie topological features of metabolic
networks and the functional significance.
arXivq-bioMN/0611013, to appear in Chinese
Science Bulletin 2007.
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Outline

• Background
• Bow-tie pattern
• Hierarchical organization
• Results
• Topological features
• Relationship between topology and
  functionality
• 3. Discussion

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Biological viewpoint of biological systems
hierarchical organization
Lifes complex Pyramid
Oltvai, Z.N., Barabási, A.-L., Lifes Complexity
Pyramid, SCIENCE, 2002, 298763-764.
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Topological viewpoint of metabolic networks
hierarchical modularity
Ravasz E, Somera A L, Mongru D A, Oltvai Z N,
Barabasi A L, Hierarchical organization of
modularity in metabolic networks,
Science,2002,297 1551-1556
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Different viewpoint of modules
Functional modules protein complexes,
signalling/metabolic pathways and transcriptional
clusters
Network topological modules
Protocols the rules by which modules interact.
Har Hartwell LH, Hopfield JJ, Leibler S, Murray
AW From molecular to modular cell biology.
Nature 1999, 402C47-C52. Newman MEJ, Girvan M
Finding and evaluating community structure in
networks. Physical Review E 2004, 69026113.
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Outline

• Background
• Bow-tie pattern
• Hierarchical organization
• Results
• Topological features
• Relationship between topology and
  functionality
• 3. Discussion

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Topological feature bow-tie modules
Decomposition of the E.coli metabolic network
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Topological feature hierarchically nested
bow-tie organization
The connections among the GSC parts of the twelve
bow-tie like modules.
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Topological feature Compared with randomized
counterparts
Comparison of the Core of E.coli network with
that of a randomized network.
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Outline

• Background
• Bow-tie pattern
• Hierarchical organization
• Results
• Topological features
• Relationship between topology and
  functionality
• 3. Discussion

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Topology vs. functionality functional clustering
of bow-tie modules
Cartographic representation of the metabolic
network for E.coli..
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Topology vs. functionality
Are
bow-tie modules also functional modules?
Case 1 most modules are dominated by one major
category of metabolisms
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Topology vs. functionality
Are
bow-tie modules also functional modules?
Case 2 Some modules are mixtures of pieces of
several conventional biochemical pathways.
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Topology vs. functionality
Are
bow-tie modules also functional modules?
Case 3 A standard textbook pathway can break
into several modules.
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Topology vs. functionality
e
Bow-tie topology of functional modules

• Chemical modules 75 organisms
• carbohydrate metabolism bow-tie
• lipid metabolism not bow-tie
• amino acid metabolism not bow-tie

2. Spatial modules yeast cytosol
bow-tie mitochondrion bow-tie
peroxisome not bow-tie
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Outline

• Background
• Bow-tie pattern
• Hierarchical organization
• Results
• Topological features
• Relationship between topology and
  functionality
• 3. Discussion

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Significance of nested bow-tie organization

• Bow-tie modules may act as another kind of
  building block of metabolic networks
• Nested bow-tie organization contributes to
  system robustness
• Thick bow-tie vs Thin bow-tie

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Thanks!