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Status: Bibliographieeintrag

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 Online-Ressource
Verfasst von:Gu, Zuguang [VerfasserIn]   i
 Hübschmann, Daniel [VerfasserIn]   i
Titel:simplifyEnrichment
Titelzusatz:a bioconductor package for clustering and visualizing functional enrichment results
Verf.angabe:Zuguang Gu, Daniel Hübschmann
Jahr:2023
Umfang:13 S.
Illustrationen:Illustrationen
Fussnoten:Gesehen am 13.10.2023 ; Online verfügbar: 6 Juni 2022
Titel Quelle:Enthalten in: Genomics, proteomics & bioinformatics
Ort Quelle:Amsterdam [u.a.] : Elsevier, 2003
Jahr Quelle:2023
Band/Heft Quelle:21(2023), 1, Seite 190-202
ISSN Quelle:2210-3244
Abstract:Functional enrichment analysis or gene set enrichment analysis is a basic bioinformatics method that evaluates the biological importance of a list of genes of interest. However, it may produce a long list of significant terms with highly redundant information that is difficult to summarize. Current tools to simplify enrichment results by clustering them into groups either still produce redundancy between clusters or do not retain consistent term similarities within clusters. We propose a new method named binary cut for clustering similarity matrices of functional terms. Through comprehensive benchmarks on both simulated and real-world datasets, we demonstrated that binary cut could efficiently cluster functional terms into groups where terms showed consistent similarities within groups and were mutually exclusive between groups. We compared binary cut clustering on the similarity matrices obtained from different similarity measures and found that semantic similarity worked well with binary cut, while similarity matrices based on gene overlap showed less consistent patterns. We implemented the binary cut algorithm in the R package simplifyEnrichment, which additionally provides functionalities for visualizing, summarizing, and comparing the clustering. The simplifyEnrichment package and the documentation are available at https://bioconductor.org/packages/simplifyEnrichment/.
DOI:doi:10.1016/j.gpb.2022.04.008
URL:Bitte beachten Sie: Dies ist ein Bibliographieeintrag. Ein Volltextzugriff für Mitglieder der Universität besteht hier nur, falls für die entsprechende Zeitschrift/den entsprechenden Sammelband ein Abonnement besteht oder es sich um einen OpenAccess-Titel handelt.

kostenfrei: Volltext: https://doi.org/10.1016/j.gpb.2022.04.008
 kostenfrei: Volltext: https://www.sciencedirect.com/science/article/pii/S1672022922000730
 DOI: https://doi.org/10.1016/j.gpb.2022.04.008
Datenträger:Online-Ressource
Sprache:eng
Sach-SW:algorithms
 cluster analysis
 clustering
 computational biology
 functional enrichment
 R/bioconductor
 semantics
 simplify enrichment
 software
 visualization
K10plus-PPN:186379817X
Verknüpfungen:→ Zeitschrift

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