Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
PLoS Comput Biol. 2012;8(2):e1002375. doi: 10.1371/journal.pcbi.1002375. Epub 2012 Feb 23.

Ten years of pathway analysis: current approaches and outstanding challenges.

Author information

  • 1Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America. pkhatri@stanford.edu

Abstract

Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces complexity and has increased explanatory power. We discuss the evolution of knowledge base-driven pathway analysis over its first decade, distinctly divided into three generations. We also discuss the limitations that are specific to each generation, and how they are addressed by successive generations of methods. We identify a number of annotation challenges that must be addressed to enable development of the next generation of pathway analysis methods. Furthermore, we identify a number of methodological challenges that the next generation of methods must tackle to take advantage of the technological advances in genomics and proteomics in order to improve specificity, sensitivity, and relevance of pathway analysis.

PMID:
22383865
[PubMed - indexed for MEDLINE]
PMCID:
PMC3285573
Free PMC Article

Images from this publication.See all images (3)Free text

Figure 1
Figure 2
Figure 3
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for Public Library of Science Icon for PubMed Central Icon for Faculty of 1000
    Loading ...
    Write to the Help Desk