Metabolic networks include these chemical reactions and the compounds participating in them.
These metabolic networks include KEGG, Recon1, and Edinburgh human metabolic network.
Current limitations of any statistical approach to analyze constrained evolution of metabolic networks include the limited number of available genomes.
Available reconstructed metabolic networks include Recon 1 [ 161], Recon 2 [ 150], SEED [ 163], IOMA [ 165], and MADE [ 172].
However, we cannot directly use the metabolic networks, which are analyzed in Reference [ 18] because the metabolic networks include cycles, which are drawn by the network representation.
For instance, gene regulatory networks include directionality, while protein protein interaction networks are undirected; signal transduction and metabolic networks are directed hypergraphs (representable as bipartite graphs) (Klamt et al., 2009), whereas metabolic networks include stoichiometry and biologically meaningful node labels (representing chemical structure).
In the unicellular eukaryote Saccharomyces cerevisiae, which offers the advantage of cell populations that are homogenous and a relatively simple genome with only 6,608 genes (SGD project "Saccharomyces Genome Database", January 13 , 2008[ 1]), the operation of metabolic networks, including glycolysis and purine metabolism, has been revealed from transcriptome datasets alone [ 2- 4].
There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses.
Recently, several amino acid producers have been successfully developed by systems metabolic engineering, where the metabolic engineering procedures were performed within a systems biology framework, and entire metabolic networks, including complex regulatory circuits, were engineered in an integrated manner.
However, there are also multiple pathways representing metabolic networks including pyrimidine, purine, protein ubiquitination, glycolysis/gluconeogenesis, aryl hydrocarbon receptor signaling and aminoacyl-tRNA biosynthesis.
For instance, the Arabidopsis metabolic networks includes genes involved in major energetic and carbon flux pathways that are essential for each cells survival, such as photosynthesis, the calvin cycle, and the TCA cycle (AraCyc; www.arabidopsis.org/biocyc/index.jsp).jsp
