Introduction

With the advent of the "omics" era 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 [1][4] analysis is one of the most comprehensive approaches to understand the cellular network.

  • Pathway Hunter Tool (PHT) is a fast, robust, user friendly "Network Biology" tool for reconstruction and dynamic visualization of biochemical pathways using shortest path. Presently we use KEGG [2] and BRENDA [3] databanks but in the near future we tend to integrate other systems biology knowledge banks.

  • Availability
    Pathway Hunter Tool (PHT) is available via internet.

    http://pht.tu-bs.de

    Features in Pathway Hunter Tool (PHT) via internet.

    ChooseOne or more sequenced organisms or build your own virtual organism (Enzymes).

    Options[1] [4]
    • Find k-shortest path between two metabolites in terms of reaction steps.
    • This module finds the all the valid bio-chemical shortest path to connect two molecule in a chosen organism.
    • Find k-shortest path between a substrate and all the other product metabolites in terms of reaction steps.
    • This module finds the all the valid bio-chemical shortest path, which starts with a chosen molecule in an organism.
    • Find k-shortest path between a product and all the other substrate metabolites in terms of reaction steps.
    • This module finds the all the valid bio-chemical shortest path, which produces a chosen molecule in an organism.
    • Statistical information about the network, average path, top 10 hubs etc.
    • This module gives an overall connectivity information about a selected genome.
    Structural Information
    Local similarity: Similarity between substrate and product metabolite of a reaction.
    Global similarity: Similarity between source and product metabolite after some reaction steps in a pathway.

    Constraints
    Via Metabolites, not via Metabolites, via Enzymes, not via Enzymes.
    Minimum number of steps, Maximum number of steps.

    Statistical Analysis
    Organism-Reaction Matrix, Enzyme-Reaction Matrix and Genome Information Matrix.
    Output: Information about enzyme, genes, motifs, disease information.
    Graph: Directed (reversible and irreversible), Undirected (reversible).


    Visualisation/Visualization

    References

    [1] Arita M: The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci U S A 2004, 101(6):1543-1547.
    [2] 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.
    [3] 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.
    [4] Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5(2):101-113.
    [5] yEd - JavaTM Graph Editor URL: http://www.yworks.com/.