Biomolecular Pathway Databases

  • Hong Sain Ooi
  • Georg Schneider
  • Teng-Ting Lim
  • Ying-Leong Chan
  • Birgit Eisenhaber
  • Frank Eisenhaber
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 609)

Abstract

From the database point of view, biomolecular pathways are sets of proteins and other biomacromolecules that represent spatio-temporally organized cascades of interactions with the involvement of low-molecular compounds and are responsible for achieving specific phenotypic biological outcomes. A pathway is usually associated with certain subcellular compartments. In this chapter, we analyze the major public biomolecular pathway databases. Special attention is paid to database scope, completeness, issues of annotation reliability, and pathway classification. In addition, systems for information retrieval, tools for mapping user-defined gene sets onto the information in pathway databases, and their typical research applications are reviewed. Whereas today, pathway databases contain almost exclusively qualitative information, the desired trend is toward quantitative description of interactions and reactions in pathways, which will gradually enable predictive modeling and transform the pathway databases into analytical workbenches.

Key words

biomolecular pathway database pathway KEGG 

Referencess

  1. 1.
    Bader, G.. D., Cary, M.P., Sander, C. (2006) Pathguide: a pathway resource list. Nucleic Acids Res 34, D504–D506.CrossRefPubMedGoogle Scholar
  2. 2.
    Ideker, T., Galitski, T., Hood, L. (2001) A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2, 343–372.CrossRefPubMedGoogle Scholar
  3. 3.
    Wood, L. D., Parsons, D. W., Jones, S., Lin, J., Sjoblom, T., Leary, R. J., Shen, D., Boca, S. M., Barber, T., Ptak, J., et al. (2007) The genomic landscapes of human breast and colorectal cancers. Science 318, 1108–1113.CrossRefPubMedGoogle Scholar
  4. 4.
    Vogelstein, B., Kinzler, K. W. (2004) Cancer genes and the pathways they control. Nat Med 10, 789–799.CrossRefPubMedGoogle Scholar
  5. 5.
    Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., Kanehisa, M. (1999) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27, 29–34.CrossRefPubMedGoogle Scholar
  6. 6.
    Karp, P. D., Riley, M., Paley, S. M., Pelligrini-Toole, A. (1996) EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res 24, 32–39.CrossRefPubMedGoogle Scholar
  7. 7.
    Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36, D480–D484.CrossRefPubMedGoogle Scholar
  8. 8.
    Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., Goto, S., Kanehisa, M. (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 36, W423–W426.CrossRefPubMedGoogle Scholar
  9. 9.
    Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., et al. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37, D619–D622.CrossRefPubMedGoogle Scholar
  10. 10.
    Joshi-Tope, G.., Gillespie, M., Vastrik, I., D’Eustachio, P., Schmidt, E., de, B. B., Jassal, B., Gopinath, G.. R., Wu, G.. R., Matthews, L., et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33, D428–D432.CrossRefPubMedGoogle Scholar
  11. 11.
    Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531.CrossRefPubMedGoogle Scholar
  12. 12.
    Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498–2504.CrossRefPubMedGoogle Scholar
  13. 13.
    Caspi, R., Foerster, H., Fulcher, C. A., Kaipa, P., Krummenacker, M., Latendresse, M., Paley, S., Rhee, S. Y., Shearer, A. G., Tissier, C., et al. (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 36, D623–D631.CrossRefPubMedGoogle Scholar
  14. 14.
    Keseler, I. M., Bonavides-Martinez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R. P., Johnson, D. A., Krummenacker, M., Nolan, L. M., Paley, S., Paulsen, I. T., et al. (2009) EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37, D464–D470.CrossRefPubMedGoogle Scholar
  15. 15.
    Karp, P. D., Paley, S., Romero, P. (2002) The Pathway Tools software. Bioinformatics 18 Suppl 1, S225–S232.PubMedGoogle Scholar
  16. 16.
    Lomax, J. (2005) Get ready to GO! A biologist’s guide to the Gene Ontology. Brief Bioinform 6, 298–304.CrossRefPubMedGoogle Scholar
  17. 17.
    Schaefer, C. F., Anthony, K., Krupa, S., Buchoff, J., Day, M., Hannay, T., Buetow, K. H. (2009) PID: the Pathway Interaction Database. Nucleic Acids Res 37, D674–D679.CrossRefPubMedGoogle Scholar
  18. 18.
    Adriaens, M. E., Jaillard, M., Waagmeester, A., Coort, S. L., Pico, A. R., Evelo, C. T. (2008) The public road to high-quality curated biological pathways. Drug Discov Today 13, 856–862.CrossRefPubMedGoogle Scholar
  19. 19.
    Dahlquist, K. D., Salomonis, N., Vranizan, K., Lawlor, S. C., Conklin, B. R. (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 31, 19–20.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Hong Sain Ooi
    • 1
  • Georg Schneider
    • 1
  • Teng-Ting Lim
    • 1
  • Ying-Leong Chan
    • 1
  • Birgit Eisenhaber
    • 2
  • Frank Eisenhaber
    • 1
  1. 1.Bioinformatics Institute (BII), Agency for science, Technology, and Research (A*STAR)SingaporeSingapore
  2. 2.Experimental Therapeutic Centre (ETC), Bioinformatics Institute (BII), Agency for science, Technology, and Research (A*STAR)SingaporeSingapore

Personalised recommendations