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GT
Gene expressionGTEx Portal API v2

GTEx

GTEx, the Genotype-Tissue Expression project, measures gene expression across human tissues from donor samples and publishes summary data on the GTEx Portal. Through ScholarMuse, an agent calls search_expression_data with a human gene symbol or Ensembl gene id and gets the median expression in TPM for the 15 highest tissues, the lowest tissue and the release the numbers come from.

ScholarMuse tools: search_expression_data. Each successful call uses credits.

Use in my agent

Ask your agent

In which human tissues is ALB most highly expressed according to GTEx?
Which tissue has the highest median TPM for TTN in GTEx, and what is the value?
Show GTEx tissue expression for ENSG00000141510 and say which release it is from.

What your agent gets back

Every record carries id, source, title, url, license, attribution and retrievedAt. The fields below are the data that comes from GTEx.

search_expression_data

Returned as one record when the `gene` input is given and GTEx knows the gene.

gene
Gene symbol as GTEx names it
gencodeId
Versioned GENCODE gene id
geneDescription
Short gene description
dataset
GTEx release used: gtex_v10 or gtex_v8
unit
Expression unit, TPM
tissuesMeasured
Number of tissues with a median value
topTissues
Top 15 tissues with tissue, tissueId and medianTpm
lowestTissue
Tissue with the lowest median TPM

What it covers

  • Median gene expression in TPM per tissue for human genes, from GTEx release v10, or v8 when the gene is missing from v10.
  • Genes are matched against the GENCODE version of the release: v39 for gtex_v10 and v26 for gtex_v8.
  • The dataset field of every result says which release was used.

Limits

  • Human only. GTEx has no data for other species, and the organism input does not apply to it.
  • Only the 15 highest tissues and the single lowest tissue are returned, not the full tissue table.
  • Medians only. No per-sample values, eQTLs, splicing data, or breakdown by sex or age.
  • One gene per call. A gene GTEx does not recognise returns no record.

How ScholarMuse reaches GTEx

The connector calls the GTEx Portal API v2 directly: reference/gene to resolve the gene, then expression/medianGeneExpression for the per-tissue medians. It asks for release gtex_v10 first and falls back to gtex_v8 if the gene is not found there. No API key is sent.

Responses are cached for up to 30 days. GTEx releases are fixed data sets, so the numbers for a given release do not change in between.

API key: the upstream API can be called without one, so you do not add one.

Licence and attribution

Licence: Open access summary data (GTEx Portal terms; cite the GTEx Consortium)

Expression data from the Genotype-Tissue Expression (GTEx) Project, GTEx Portal (gtexportal.org).

Records that come from GTEx carry this licence and attribution. When you cite the data in a paper, follow GTEx's own citation guidance.

Capabilities that use GTEx

Gene & protein lookupNew

Gene & protein lookup

Life sciences & medicine · NCBI Gene, Ensembl, UniProt +5

Related sources

NCBI GeneEnsemblUniProtInterProReactomeNCBI GEOSTRING

FAQ

ScholarMuse is not an official GTEx product. It is one MCP server for academic data, and its search_expression_data tool queries GTEx. An agent connected to ScholarMuse can use GTEx without a separate server.

No. The GTEx API can be called without a key, and ScholarMuse does not ask you for one. You sign in to ScholarMuse once and your agent calls the tool.

The connector calls the GTEx Portal API v2 directly: reference/gene to resolve the gene, then expression/medianGeneExpression for the per-tissue medians. It asks for release gtex_v10 first and falls back to gtex_v8 if the gene is not found there. No API key is sent. Responses are cached for up to 30 days. GTEx releases are fixed data sets, so the numbers for a given release do not change in between.

Open access summary data (GTEx Portal terms; cite the GTEx Consortium). Attribution: Expression data from the Genotype-Tissue Expression (GTEx) Project, GTEx Portal (gtexportal.org). Records that come from GTEx carry this licence and attribution.

Yes. Each successful call to search_expression_data uses credits, and a call that fails is not charged. Current price: Gene & protein lookup, 1 credit / call.