Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

Overview

Journal PLoS Comput Biol

Specialty Biology

Date 2012 Mar 3

PMID 22383865

Citations 757

Authors

Purvesh Khatri

Marina Sirota

Atul J Butte

Affiliations

Soon will be listed here.

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.

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