spacer gif spacer gif spacer gif spacer gif spacer gif
QUICK SEARCH:   [advanced]


spacer gif
     Home     Help     Feedback     Subscriptions     Archive     Search     Table of Contents    

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
This Article
Right arrow Summary Freely available
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Glossary
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Related articles in JEB
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Almaas, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Almaas, E.
Social Bookmarking
Add to CiteULike   Add to Complore   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati   Add to Twitter  
What's this?

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


Figure 1
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 {lambda}=10 and a power-law connectivity distribution (solid line) with exponent {gamma}=2.5.

 

Figure 2
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.

 

Figure 3
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/).

 

Figure 4
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.

 

Figure 5
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.

 

Figure 6
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.

 

Figure 7
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.

 

Figure 8
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.

 

Add to CiteULike CiteULike   Add to Complore Complore   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati   Add to Twitter Twitter    What's this?



© The Company of Biologists Ltd 2007