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

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

Andrea Komljenovic #  1   2 , Julien Roux #  2   3 , Julien Wollbrett  1   2 , Marc Robinson-Rechavi  1   2 , Frederic B Bastian  1   2
Affiliations

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

Andrea Komljenovic et al. F1000Res. .

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.

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Conflict of interest statement

Competing interests: No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Standardized expression levels of 16 groups of microarray probesets, clustered according to their expression during mouse early development.
The x-axis displays sample names (column “Chip.ID” of the data.E.MEXP.51 object).
Figure 2.
Figure 2.. Mean-average (MA) plot of differential gene expression between brain and liver in macaque based on RNA-seq data.
Significantly differentially expressed genes (FDR < 1%) are highlighted in red.
See this image and copyright information in PMC

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