Three faces of metabolites: pathways, localizations and network positions

Jing Zhao( 赵静） 1, Petter Holme2,3

1 Department of Mathematics, Logistical Engineering University, China2 Department of Physics, Umeå University, Sweden3 Department of Energy Science, Sungkyunkwan University, Korea

The Fourth International Conference on Computational Systems Biology (ISB 2010) , September 9-11, 2010 Suzhou, China

Outline Background Relation between the categories of

metabolites Quantitative difference between

categories Network structures of the categories Conclusion

Metabolism

metabolic network

Cytoplasm, [c]Extracellular Space, [e]Mitochondrion, [m]Golgi Apparatus, [g]Endoplasmic Reticulum, [r]Lysosome, [l]Peroxisome, [x]Nucleus, [n]

Subcellular compartments

Carbohydrate Metabolism, CEnergy Metabolism, ELipid Metabolism, LNucleotide Metabolism, NAmino Acid Metabolism, AGlycan Biosynthesis and Metabolism, GMetabolism of Cofactors and Vitamins, VXenobiotics Biodegradation and Metabolism, XBiosynthesis of Secondary Metabolites, STransport, T

Pathways

Modular topology of metabolic network

])([maxmax 2

1

jij

r

iii eeM

Simulated annealing method

M: the modularity metric for a given decomposition of the network

eij: the fraction of edges that leads between vertices of cluster i and j

the sum is over the partition into clusters

This study…

BiGG database

Duarte, N. C.; Becker, S. A.; Jamshidi, N.; Thiele, I.; Mo, M. L.; Vo, T. D.; Srivas, R.; Palsson, B. O., Global reconstruction of the human metabolic network based on genomic and bibliomic data. PNAS 2007, 104, (6), 1777-1782.

Data used

Relation between the categorizations

M=0.676

Quantitative difference between categories: overlap score

XY (x,y) X (x)Y (y)yY

xX

),max( YYXX

XYXY

Prototypical overlap score

Normalized overlap score

X ,Y : two categorizations

X(x) ,Y(y) : the fraction of metabolites in category x  X, y Y, respectively

XY(x,y): the joint frequency of x and y, i.e. the fraction of vertices that are categorized both as x  X and y  Y.

Quantative difference between a feature of the real metabolic network and its randomized counterparts: Z-score

r

r

f

ffZ

f : the metric of the feature in the real network

rf

rf: the standard deviation of the corresponding metric in the randomized ensemble

: the mean of the corresponding metric in the randomized ensemble

Localization vs. network clusters : = 0.72, z =108.46;

Network clusters vs. pathways: = 0.37, z = 45.94;

Pathways vs. localization : = 0.42, z = 54.69

Overlap scores between categories

Network structure of the categories of the three categorizations

Conclusions

• We have investigated three ways of grouping metabolites according to pathways, localization, and network clusters respectively.

• The compartmentalization is clearly organized into a core of extracellular media and cytoplasm, and a periphery of organelles; while the core and periphery modules of the pathway interactions correspond to housekeeping and advanced specific functions respectively.

• Qualitative and quantitative analysis shows that the three categories are significantly correlated with each other, suggesting the interrelationship between biochemical specific functions, spatial isolations in cells, and topological compact regions in metabolic networks.

National Natural Science Foundation of China (10971227)

Swedish Foundation for Strategic Research

Swedish Research Council

the WCU program through NRF Korea funded by MEST R31–2008–000–10029–0

Acknowledges

Thanks!