Ensembl and gene set database

In its last version (v5), ASAP incorporates information from the Ensembl (24) ‘vertebrates’ database v54 to v99 and from Ensembl ‘genomes’ v5 to v46. The ASAP_data_v5 database contains 16 734 890 genes with unique Ensembl identifiers for 551 different species. During file parsing, all genes are mapped to the database version chosen by the user (v4 or v5), with the latest stable one always being pre-selected. This mapping is not necessary for most of the steps included in ASAP, but can provide additional information in the result tables, or when hovering on the dynamic plots. It is mostly needed during the last step of the analysis (cell type annotation/functional enrichment), when ASAP needs to relate differentially expressed genes (or marker genes) to gene sets such as GO (25), KEGG (26), Drugbank (27) or cell type annotation databases (28–30).