Get Top Expressed Genes

Find top expressed genes for a specified tissue.

• Returns top expressed genes for a specified tissue in a dataset, sorted by median expression.

• When the optional parameter filterMtGene is set to true, mitochondrial genes will be excluded from the results. By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_top_expressed_genes(
  tissueSiteDetailId,
  datasetId = "gtex_v8",
  filterMtGene = TRUE,
  page = 0,
  itemsPerPage = 250
)

Arguments

tissueSiteDetailId

String. The ID of the tissue of interest. Can be a GTEx specific ID (e.g. "Whole_Blood"; use get_tissue_site_detail() to see valid values) or an Ontology ID.

datasetId

String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

filterMtGene

Logical. Exclude mitochondrial genes.

page

Integer (default = 0).

itemsPerPage

Integer (default = 250).

Value

A tibble.

See also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary()

Examples

# \dontrun{
get_top_expressed_genes(tissueSiteDetailId = "Artery_Aorta")
#> Warning: ! Total number of items (56163) exceeds maximum page size (250).
#> ℹ Try increasing `itemsPerPage`.
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 225
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 56163
#> # A tibble: 250 × 7
#>    tissueSiteDetailId ontologyId     datasetId gencodeId geneSymbol median unit 
#>    <chr>              <chr>          <chr>     <chr>     <chr>       <dbl> <chr>
#>  1 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… MGP        11936. TPM  
#>  2 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… FTL         9196. TPM  
#>  3 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… ACTB        9154. TPM  
#>  4 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… BGN         8167. TPM  
#>  5 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… TAGLN       6099. TPM  
#>  6 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… ACTA2       5736. TPM  
#>  7 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… IGFBP7      5639. TPM  
#>  8 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… MYL9        4275. TPM  
#>  9 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… HSPB1       3780. TPM  
#> 10 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… FLNA        3732. TPM  
#> # ℹ 240 more rows
# }