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Tytuł:
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GSOAP: a tool for visualization of gene set over-representation analysis.
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Autorzy:
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Tokar T; Krembil Research Institute, UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada.
Pastrello C; Krembil Research Institute, UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada.
Jurisica I; Krembil Research Institute, UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada.; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada.; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.; Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-84510, Bratislava, Slovakia.
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Źródło:
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Bioinformatics (Oxford, England) [Bioinformatics] 2020 May 01; Vol. 36 (9), pp. 2923-2925.
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Typ publikacji:
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Journal Article; Research Support, Non-U.S. Gov't
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Język:
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English
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Imprint Name(s):
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Original Publication: Oxford : Oxford University Press, c1998-
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MeSH Terms:
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Gene Ontology*
Software*
Cluster Analysis ; Gene Expression Regulation
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References:
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Oncotarget. 2018 Jan 8;9(10):9137-9155. (PMID: 29507679)
IEEE Trans Neural Netw. 1997;8(1):148-54. (PMID: 18255618)
Nucleic Acids Res. 2017 Jan 4;45(D1):D419-D426. (PMID: 27899558)
OMICS. 2012 May;16(5):284-7. (PMID: 22455463)
Science. 2000 Dec 22;290(5500):2319-23. (PMID: 11125149)
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Entry Date(s):
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Date Created: 20200125 Date Completed: 20201009 Latest Revision: 20220531
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Update Code:
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20240104
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PubMed Central ID:
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PMC7203738
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DOI:
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10.1093/bioinformatics/btaa001
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PMID:
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31977031
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Motivation: Gene sets over-representation analysis (GSOA) is a common technique of enrichment analysis that measures the overlap between a gene set and selected instances (e.g. pathways). Despite its popularity, there is currently no established standard for visualization of GSOA results.
Results: Here, we propose a visual exploration of the GSOA results by showing the relationships among the enriched instances, while highlighting important instance attributes, such as significance, closeness (centrality) and clustering.
Availability and Implementation: GSOAP is implemented as an R package and is available at https://github.com/tomastokar/gsoap.
(© The Author(s) 2020. Published by Oxford University Press.)
