Pathway databases networks

Table 1 describes all the microbe-specific databases, and Table 2 lists databases for the microbial community. These databases provide genomic sequence data, gene and protein information, gene expression data, metabolic reactions and pathways, interaction network,... 

The analysis of network structure from the viewpoint of computer theory requires an introduction to some background information, which will be provided here. We will introduce the data involved for modeling metabolic pathways and the KEGG pathway database in particular. Furthermore, a basic introduction to graphs as used in computer science will be provided. 

Chapter 7—Pathways and Networks Minch and Vatcheva discuss the different types of pathway data, and they detail the various techniques of pathway analysis. They also include a useful summary of common public and commercial pathway tools and databases. 

A discussion of the mathematical and computational tools already available for the analysis of GRN models is given in the next section. Most of the models extracted from pathways databases are expected to be qualitative and incomplete in nature hence, the discussion focuses on qualitative network structures and how these structures influence the capacity of the system to exhibit certain dynamical behavior. 

Figure 1.3 Simplified pathways and network of the common sphingolipid classes and other related lipids. The network and the pathways are derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases. The pathways indicate the origins of sphingoid base core structures and their derivatives. Other sphingoid bases can be biosynthesized from other fatty acyl CoA by the replacement of palmitoyl CoA or some other amino acids replacing serine. The structures of individual lipid classes and their abbreviations used in the book are indicated in Figure 1.6.

The experimental exploration and confirmation of protein functions are relatively slow processes and always require dedicated experiments. The analysis of protein-protein associations as such improved remarkably in quality and speed. This is accompanied by the creation of new databases that will reflect the network of interacting proteins (the Protein Function and Metabolic Pathway project, http //bioinformer.ebi. ac.uk 80/newsletter/archives/4/pfmp.html, and the Biomolecular Interaction Network Database project http //bioinfo.mshri.on.ca/ BIND/). These activities contribute to the idea that cellular mechanisms can be better understood when they are seen as a multicomponent networked process. 

While it is important and informative to create individual databases, the complexity of modeling pathways requires that individual databases be integrated or networked. Bader and Enright (2005) asked the question What would we want to know from an ideal cell biological experiment and then provided their answer ... 

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