Bgee: Database and R Package for Retrieving the Preferred Anatomical Expression Localization of a List of Genes, or of a Single Gene, in Animals.

A wealth of gene expression data is deposited in public repositories, but the problem is how to extract, from this wealth of data, the biologically relevant information about expression patterns of genes. We present here Bgee, a database and R package allowing to identify the preferred anatomical localizations with expression from a list of genes, or for a single gene. The R package also allows to download curated and re-analyzed expression data from Bgee directly into R.

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species. It is based exclusively on curated "normal" healthy expression data, and produces calls of presence/absence of gene expression, in anatomy, life cycles and developmental stages, to allow comparisons between species. Bgee release 14 includes 29 species.

In this demo I will introduce the use of an innovative tool, allowing to discover in which anatomical structures genes from a given set are preferentially expressed: TopAnat. TopAnat analyses are similar to Gene Ontology enrichment tests, but applied to terms from an anatomical ontology, with genes mapped to anatomical terms using the expression calls from Bgee. We hope that TopAnat will prove to be as useful as standard GO enrichment analyses. I will also present how to retrieve from Bgee gene expression ranks, allowing to identify the most relevant anatomical information for each gene. Finally, the Bgee R package also allows to retrieve into R data from thousands of wild-type healthy samples of multiple animal species, curated and re-analyzed in Bgee.