Metabolic signaling database

Metabolic signaling databases contain detailed information on metabolic pathways. These DBs have well-established data structures but have nonuniform ontologies. BioCyc is a collection of pathway/genome databases for many bacteria and up to 14 species of other organisms. Enzyme catalyzed... 

Metacore (table 7.1) is a suite of software oriented toward understanding the function of gene sets discovered by expression analysis. It includes a database of annotated metabolic, signaling, and regulatory pathways and a graphical pathway display/editor. 

MetaBase is a curated database of human protein-protein and protein-DNA interactions, transcriptional factors, signaling, metabolism and bioactive molecules. MetaCore provides intuitive tools for data visualization, mapping and exchange, multiple networking algorithms and data mining. 

Target Information database - The Database contains information such as Protein-Protein interactions, Metabolic and Signaling Pathways, Transcription factors, post-Translational modifications, Disease information, various Drugs and Clinical compounds and the Companies of interest. 

To use metabolic footprinting as a technique for high-throughput applications, benchmark spectra databases with identified peaks are required so that peak patterns obtained from MS or NMR analysis can be rapidly translated into relevant biological information. Common experimental procedures should, ideally, also be established for metabolite analysis [80] such as those existing in proteomics or transcriptomics. Nevertheless, the scientific community has only recently attempted to achieve these tasks. Several databases for identification of metabolomics signals by MS are now available, for instance, BIGG [81], BioCyc [82], MSlib [83], NIST [84], Metlin [85], and HMDB [86] databases. For a more comprehensive list of resources we refer to the review of Werner and coworkers [68]. 

The Case Western Reserve University s Pathways Database System [Ozsoyoglu, Nadeau, and Ozsoyoglu 2003] comes with a sample set of metabolic and signaling pathways, most drawn from Michal s Biochemical Pathways [Michal 1999], It consists of a suite of tools, including query interfaces, viewers, and a pathway editor. 

Pathway Articulator or PathArt (table 7.1) is built around a database of signaling and metabolic pathways derived from manual curation of the literature. Database elements are annotated with links to several vocabularies (GO, Locuslink, CAS, etc.), and displayed in an editable pathway visualizer. 

BioPAX14 is a consortium of pathway databases that aims to develop an exchange language for biological pathways (BioPAX). Pathways include the metabolic, regulatory, and signal pathways. The BioPAX initiative aims to overcome the heterogeneity... 

Models of pathways exist in many forms but most of these are static representations, not dynamic models of metabolism. They show the network topology of interconnected pathways of enzymes or signalling molecules, but they contain no dynamic information on reaction rates of diffusive encounters. The JWS-online database (http //jjj.biochem.sun.ac.za/database/index.html) on the other hand, is a web-based database containing over 90 dynamics models. Of these however, only a few are approaching what is desired. 

Figure 9.5 Illustration of genes expressed similarly during a time course of somatic cmbryogcnesis in one of the K-mcans cluster sets, set 6, of the microarray data. Adapted from Thibaud-Nissen, e( al The annotations matching clone IDs on the microarray sets represent the top Blastx hit in the public databases at a threshold of K -6. The putative function in cell metabolism is shown oth, other ox, oxidative strcss/dcfcnsc sig, signaling to, transcription u, unknown.

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