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

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, distinc...

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Autores principales:	Purvesh Khatri, Marina Sirota, Atul J Butte
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/5b956f7070b4449f94613a37ffe2718a
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spelling	oai:doaj.org-article:5b956f7070b4449f94613a37ffe2718a2021-11-18T05:51:34ZTen years of pathway analysis: current approaches and outstanding challenges.1553-734X1553-735810.1371/journal.pcbi.1002375https://doaj.org/article/5b956f7070b4449f94613a37ffe2718a2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22383865/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Pathway 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.Purvesh KhatriMarina SirotaAtul J ButtePublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 2, p e1002375 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Purvesh Khatri Marina Sirota Atul J Butte Ten years of pathway analysis: current approaches and outstanding challenges.
description	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.
format	article
author	Purvesh Khatri Marina Sirota Atul J Butte
author_facet	Purvesh Khatri Marina Sirota Atul J Butte
author_sort	Purvesh Khatri
title	Ten years of pathway analysis: current approaches and outstanding challenges.
title_short	Ten years of pathway analysis: current approaches and outstanding challenges.
title_full	Ten years of pathway analysis: current approaches and outstanding challenges.
title_fullStr	Ten years of pathway analysis: current approaches and outstanding challenges.
title_full_unstemmed	Ten years of pathway analysis: current approaches and outstanding challenges.
title_sort	ten years of pathway analysis: current approaches and outstanding challenges.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/5b956f7070b4449f94613a37ffe2718a
work_keys_str_mv	AT purveshkhatri tenyearsofpathwayanalysiscurrentapproachesandoutstandingchallenges AT marinasirota tenyearsofpathwayanalysiscurrentapproachesandoutstandingchallenges AT atuljbutte tenyearsofpathwayanalysiscurrentapproachesandoutstandingchallenges
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Ten years of pathway analysis: current approaches and outstanding challenges.

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