Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

BMC Bioinformatics
Ludwig GeistlingerRalf Zimmer

Abstract

Enrichment analysis of gene expression data is essential to find functional groups of genes whose interplay can explain experimental observations. Numerous methods have been published that either ignore (set-based) or incorporate (network-based) known interactions between genes. However, the often subtle benefits and disadvantages of the individual methods are confusing for most biological end users and there is currently no convenient way to combine methods for an enhanced result interpretation. We present the EnrichmentBrowser package as an easily applicable software that enables (1) the application of the most frequently used set-based and network-based enrichment methods, (2) their straightforward combination, and (3) a detailed and interactive visualization and exploration of the results. The package is available from the Bioconductor repository and implements additional support for standardized expression data preprocessing, differential expression analysis, and definition of suitable input gene sets and networks. The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. It combines the advantages of set-based and network-based enrichment analysis in order to der...Continue Reading

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Citations

Apr 28, 2017·International Journal of Molecular Sciences·Enrique Pérez-RiesgoCarlos Villalobos
Feb 7, 2020·Briefings in Bioinformatics·Ludwig GeistlingerLevi Waldron
Nov 11, 2016·PLoS Computational Biology·Lefteris KoumakisGeorge Potamias
Dec 4, 2019·Nature Methods·Robert A AmezquitaStephanie C Hicks
Oct 4, 2016·Bioinformatics·Monther AlhamdooshMatthew E Ritchie
May 14, 2017·BMC Bioinformatics·Joanna ZylaJoanna Polanska
Oct 30, 2020·JCO Clinical Cancer Informatics·Marcel RamosLevi Waldron
Dec 18, 2020·Frontiers in Genetics·Seth JarvisVincent Plagnol
Dec 25, 2021·BMC Bioinformatics·Federico MariniKonstantin Strauch

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

stats
SPIA Signaling Pathway Impact Analysis
Firefox
Unzip
SAFE Significance Analysis of Function and Expression
SBEA
SegMine
GGEA Gene Graph Enrichment Analysis
graphite web
EDASeq

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