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

BMC Bioinformatics

Software

Gergely Csaba¹  Ralf Zimmer¹  Ludwig Geistlinger¹ 

[1] Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 1780333, Munich, Germany;

关键词: Gene expression;    Differential expression;    Pathway analysis;    Gene set enrichment;    Gene network enrichment;   

DOI  :  10.1186/s12859-016-0884-1

 received in 2015-09-07, accepted in 2016-01-08,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundEnrichment 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.ResultsWe 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.ConclusionThe 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 derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.

【 授权许可】

CC BY   
© Geistlinger et al. 2016

【 图 表 】

Fig. 3