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A Comparative Study of Metabolic Networks - An In Silico Systems Biology Tool

  • The "omics" era has thrown open gates for innovative approaches in systems biology for BioInformatics. Metabolome and metabolomics are gaining more and more attention in order to understand the complexity of the underlying cellular networks in organisms. The completion of a long series of genomes has made the comparison of metabolic pathways possible. Shortest path analysis is one of the most comprehensive approaches of understanding the cellular network.

  • Pathway Hunter Tool (PHT) [ 1 , 2 , 3 ,4,5,6] is a robust and user friendly Systems Biology-based BioInformatics tool to process biologically relevant information.

  • Presently we use KEGG [7] and BRENDA [8] databanks but in the near future we intend to integrate other systems biology knowledge banks. Pathway Hunter Tool has more than 300 metabolic networks of various organisms (Eukaryotes: 10+; Bacteria: 200+; Archaea: 20+) from KEGG & BRENDA.

    • Database last updated: 1st September, 2006.
  • Find k-shortest path between a substrate and product metabolite in the model organism(s).
    This module finds all the valid bio-chemical shortest paths that connect two molecules in selected organisms.
    •

  • Generate Load Points and Choke Points information in the metabolic pathways of different organisms.
    This module generates a list of potential drug targets for the selected genomes based on the production/consumption load on metabolites or enzymes. This requires further in vitro/ in vivo verification.
    • Note: This option is time-consuming (3 minutes to 10 minutes depending upon the organism you choose).
    NEW !!
  • Generate statistical information about the metabolic pathways in different organisms.
    This module presents overall connectivity information for the selected organisms.
    • Note: This option is time-consuming (3 minutes to 10 minutes depending upon the organism you choose).

    References

    [1] S.A. Rahman and Dietmar Schomburg: Observing local and global properties of metabolic pathways: "load points" and "choke points" in the metabolic networks Bioinformatics 2006, 22: 1767-1774.

    [2] S.A. Rahman et.al: Metabolic Network Analysis: Implication And Application BMC Bioinformatics 2005, 471-2105-6-S3-S12

    [3] S.A. Rahman et.al: Metabolic pathway analysis web service ( Pathway Hunter Tool at CUBIC ). Bioinformatics 2005 , 21: 1189-1193.

    [4] S.A. Rahman et.al: Pathway Hunter Tool (PHT). Poster in The 5th International conference on Systems Biology - from Bioscience to Medicine 2004, Heidelberg, Germany.

    [5] S.A. Rahman et.al: Revisiting metabolic pathways - Pathway Hunter Tool (PHT). Poster in BioPerspectives 2004, Germany.

    [6] Syed Asad Rahman, Dietmar Schomburg, Rainer Schrader: CUBIC Metabolic Pathway Hunter Tool - CMPHT. Poster in ISMB/ECCB 2004, Glasgow, Scotland, UK.

    [7] Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M: The KEGG resource for deciphering the genome. Nucleic Acids Res 2004 ,32 Database issue:D277-280.

    [8] Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D: BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 2004 ,32 Database issue:D431-433.