Reactome Knowledgebase of Human Biological Pathways and Processes

  • Peter D’Eustachio
Part of the Methods in Molecular Biology book series (MIMB, volume 694)


The Reactome Knowledgebase is an online, manually curated resource that provides an integrated view of the molecular details of human biological processes that range from metabolism to DNA replication and repair to signaling cascades. Its data model allows these diverse processes to be represented in a consistent way to facilitate usage as online text and as a resource for data mining, modeling, and analysis of large-scale expression data sets over the full range of human biological processes.

Key words

BioMart Data aggregation Gene ontology High-throughput expression data Pathway analysis 


  1. 1.
    Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry. J. M., et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29.PubMedCrossRefGoogle Scholar
  2. 2.
    The Gene Ontology Consortium. (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38, D331–D335.CrossRefGoogle Scholar
  3. 3.
    The UniProt Consortium. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 38, D142–D148CrossRefGoogle Scholar
  4. 4.
    de Matos, P., Alcántara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., et al. (2010) Chemical Entities of Biological Interest: an update. Nucleic Acids Res. 38, D249–D254.PubMedCrossRefGoogle Scholar
  5. 5.
    Leinonen, R., Akhtar, R., Birney, E., Bonfield, J., Bower, L., Corbett, M., et al. (2010) Improvements to services at the European Nucleotide Archive. Nucleic Acids Res. 38, D39–D45.PubMedCrossRefGoogle Scholar
  6. 6.
    Li, L., Stoeckert, C. J. Jr., and Roos, D. S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189.PubMedCrossRefGoogle Scholar
  7. 7.
    Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A., Huber, W. (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21, 3439–3940.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Peter D’Eustachio
    • 1
  1. 1.Department of BiochemistryNew York University School of MedicineNew YorkUSA

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