Metabolic pathways interaction network

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 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. 

Fig. 1. The generalized protein-protein interaction network that includes (A) direct protein-protein interactions such as in the signal transduction pathway, (B) enzyme-enzyme relations in the metabolic pathway, and (C) transcription factor-expressed gene product relations in the gene regulatory pathway. The interactions in (B) and (C) are termed indirect protein-protein interactions.

Table V shows a classification of binary relations gene-gene relations, protein-protein relations, and other molecule-molecule relations. Different sets of binary relations can then be related to different types of graphs. For example, the generalized protein-protein interaction network is equivalent to a set of protein-protein binary relations. The KEGG metabolic pathway is a generalized protein-protein network, but it is also a network of chemical compounds that can be converted to a set of com-...

Nearly every area of modem research in biology and biomedical science is targeted in one way or another on gaining quantitative understanding of the behavior of biochemical systems. Cellular metabolic pathways, genetic regulatory systems, and protein interaction networks represent different examples of biochemical systems that obey a common set of physicochemical laws, and may be analyzed and simulated based on a common set of principles derived from such laws. It is the purpose of this book to introduce and make use of the methods for the analysis and simulation of biochemical systems that lie at the foundation of current and future research in biological and biomedical science. 

BioCyc Knowledge Library Biomolecular Interaction Network (BIND) SRI International Consists of EcoCyc and MetaCyc collection of metabolic pathways for individual organisms and a reference source on metabolic pathways from many organisms, respectively Interaction, molecular complex, and pathway records... 

Metabolomics is the technology behind the measurement of metabolite concentrations, fluxes, and secretions in cells and tissues (metabolome). Metabolomics is at the cross-roads of genotype/phenotype interactions, where the interrelationship of metabolic pathways is considered to be the fundamental component of an organism s phenotype. Metabolomics is distinguished by the fact that metabolites are not directly linked to the genetic code but actually are products of a concerted action of many enzyme networks and other regulatory proteins (243). Metabolites also are more complex than nucleic acids, which are composed of four nucleotides, or proteins, which in turn are composed of 20 different amino acids. As a result, metabolites cannot be... 

Figure 1 A schematic representation of a gene regulatory network involving modules of molecular classes (shown in boxes) the modules shown are the transcriptional units in the genome (G), primary transcripts (Ro), mature transcripts (R), primary proteins (Po), modified proteins (P), and metabolites (M). The labeled steps shown in black lines are transcription (x), RNA processing (p), translation (a), protein modification (p), metabolic pathways (ti), and genome replication (a). The feedback interactions shown in gray lines are discussed in the text. Filled circles represent either inhibition or activation.

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