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First published online April 20, 2007
Journal of Experimental Biology 210, 1548-1558 (2007)
Published by The Company of Biologists 2007
doi: 10.1242/jeb.003731

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Biological impacts and context of network theory

Eivind Almaas

Microbial Systems Biology, Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, PO Box 808, L-452, Livermore, CA 94550, USA

View larger version (59K): [in this window] [in a new window]   Fig. 1. (A) Protein interaction network of the nematode Caenorhabditis elegans using data from The BioGRID (version 2.0.20; http://www.thebiogrid.org/). Nodes (proteins) in blue have a connectivity of one. Nodes in green have a connectivity between two and nine, while the red nodes have a connectivity of 10. Comparison of a linear (B) and logarithmic plot (C) of a Poisson connectivity distribution (broken line) with mean =10 and a power-law connectivity distribution (solid line) with exponent =2.5.

View larger version (12K): [in this window] [in a new window]   Fig. 2. Connectivity distribution P(k) for the protein interaction networks of (A) the yeast S. cerevisiae, (B) the nematode C. elegans and (C) the fly D. melanogaster from The BioGRID (version 2.0.20; http://www.thebiogrid.org/). The colors in B correspond to the node-colors in Fig. 1; nodes with a connectivity of one are blue, a connectivity between two and nine is green, and highly connected nodes (10) are red.

View larger version (11K): [in this window] [in a new window]   Fig. 3. Average nearest neighbor connectivity knn(k) for the protein interaction networks of (A) S. cerevisiae, (B) C. elegans and (C) D. melanogaster from The BioGRID (version 2.0.20; http://www.thebiogrid.org/).

View larger version (10K): [in this window] [in a new window]   Fig. 4. Cellular metabolism can be represented as a network. (A) Toy metabolic reaction set. Network description of the reaction set: (B) connecting all metabolites in a single reaction with undirected links; (C) substrates are only connected to products with undirected links; and (D) same as in C with directed links. (E) Bipartite network representation of the reaction set. (F) Network with reactions as nodes, and reactions that share a metabolite as educt–product are connected.

View larger version (10K): [in this window] [in a new window]   Fig. 5. Connectivity distributions P(k) of E. coli metabolism using the three metabolic network representations in Fig. 4. Panel A corresponds to Fig. 4B; B corresponds to Fig. 4C; C corresponds to Fig. 4D.

View larger version (8K): [in this window] [in a new window]   Fig. 6. Distribution of metabolic reaction flux values (link weights) from FBA analysis for the metabolic network of the budding yeast S. cerevisiae in (A) aerobic, glucose-limited and (B) aerobic, acetate-limited conditions.

View larger version (8K): [in this window] [in a new window]   Fig. 7. Distribution of node strength values for S. cerevisiae metabolism in (A) aerobic, glucose-limited and (B) aerobic, acetate-limited conditions.

View larger version (11K): [in this window] [in a new window]   Fig. 8. Correlation between (normalized) link weights and local connectivity for (A) metabolic fluxes in S. cerevisiae in glucose-limited and (B) acetate-limited conditions, as well as (C) betweenness-centrality for the Barabási–Albert model. The broken lines serve as visual guides only.