Chapter 12. Biological Pathway Analysis: An Overview of Reactome and Other Integrative Pathway Knowledge Bases

  1. Gil Alterovitz and
  2. Marco Ramoni
  1. Robin A. Haw1,
  2. Marc E. Gillespie2 and
  3. Michael A. Caudy3

Published Online: 7 JUL 2010

DOI: 10.1002/9780470669716.ch12

Knowledge-Based Bioinformatics: From Analysis to Interpretation

Knowledge-Based Bioinformatics: From Analysis to Interpretation

How to Cite

Haw, R. A., Gillespie, M. E. and Caudy, M. A. (2010) Biological Pathway Analysis: An Overview of Reactome and Other Integrative Pathway Knowledge Bases, in Knowledge-Based Bioinformatics: From Analysis to Interpretation (eds G. Alterovitz and M. Ramoni), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470669716.ch12

Editor Information

  1. Harvard Medical School and Massachusetts Institute of Technology, Boston, USA

Author Information

  1. 1

    Department of Informatics and Bio-computing, Ontario Institute for Cancer Research, Canada

  2. 2

    College of Pharmacy and Allied Health Professions, St. John's University, New York, USA

  3. 3

    Gnomics Web Services, New York, USA

Publication History

  1. Published Online: 7 JUL 2010
  2. Published Print: 16 JUL 2010

ISBN Information

Print ISBN: 9780470748312

Online ISBN: 9780470669716

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Keywords:

  • complex traits;
  • high throughput technologies;
  • biological networks;
  • causal interactions;
  • systems biology;
  • top-bottom approach;
  • gene-disease relationship;
  • drug discovery;
  • expression quantitative trait loci (eQTL);
  • personalized medicine

Summary

This chapter contains sections titled:

  • Biological pathway analysis and pathway knowledge bases

  • Overview of high-throughput data capture technologies and data repositories

  • Brief review of selected pathway knowledge bases

  • How does information get into pathway knowledge bases?

  • Introduction to data exchange languages

  • Visualization tools

  • Use case: pathway analysis in Reactome using statistical analysis of high-throughput data sets

  • Discussion: challenges and future directions of pathway knowledge bases

  • References