BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

Andrea Komljenovic; Julien Roux; Julien Wollbrett; Marc Robinson-Rechavi; Frederic B Bastian

doi:10.12688/f1000research.9973.2

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

F1000Res. 2016 Nov 23:5:2748. doi: 10.12688/f1000research.9973.2. eCollection 2016.

Authors

Andrea Komljenovic^#^{1

2}, Julien Roux^#^{2

3}, Julien Wollbrett^{1

2}, Marc Robinson-Rechavi^{1

2}, Frederic B Bastian^{1

2}

Affiliations

¹ Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
² SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
³ Department of Biomedicine, University of Basel, Basel, Switzerland.

^# Contributed equally.

Abstract

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and re-processed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages. Moreover, BgeeDB includes a new gene set enrichment test for preferred localization of expression of genes in anatomical structures ("TopAnat"). Along with the classical Gene Ontology enrichment test, this test provides a complementary way to interpret gene lists. Availability: https://www.bioconductor.org/packages/BgeeDB/.

Keywords: Bioconductor; Collective Data Access; Gene Enrichment Analysis; Gene expression; R Package.

Grants and funding

This work was supported by SIB Swiss Institute of Bioinformatics project Bgee, Swiss National Science Foundation grant 31003A_153341, SystemsX.ch project AgingX, and Etat de Vaud.