A comparison of mechanistic signaling pathway activity analysis methods.

TitleA comparison of mechanistic signaling pathway activity analysis methods.
Publication TypeJournal Article
Year of Publication2019
AuthorsAmadoz, A, Hidalgo, MR, Cubuk, C, Carbonell-Caballero, J, Dopazo, J
JournalBrief Bioinform
Volume20
Issue5
Pagination1655-1668
Date Published2019 09 27
ISSN1477-4054
KeywordsAlgorithms; Humans; Postmortem Changes; Signal Transduction; Systems biology; Transcriptome
Abstract

Understanding the aspects of cell functionality that account for disease mechanisms or drug modes of action is a main challenge for precision medicine. Classical gene-based approaches ignore the modular nature of most human traits, whereas conventional pathway enrichment approaches produce only illustrative results of limited practical utility. Recently, a family of new methods has emerged that change the focus from the whole pathways to the definition of elementary subpathways within them that have any mechanistic significance and to the study of their activities. Thus, mechanistic pathway activity (MPA) methods constitute a new paradigm that allows recoding poorly informative genomic measurements into cell activity quantitative values and relate them to phenotypes. Here we provide a review on the MPA methods available and explain their contribution to systems medicine approaches for addressing challenges in the diagnostic and treatment of complex diseases.

DOI10.1093/bib/bby040
Alternate JournalBrief. Bioinformatics
PubMed ID29868818
PubMed Central IDPMC6917216