GTEx Portal through GeneFoundry
Explore tissue-level expression and regulatory associations in open-access GTEx Portal data.
- Research area
- Expression & models
- Namespace
gtex- Listed tools
- 9
- Upstream source
- GTEx Portal
Research tasks
- Compare median expression across tissues
- Resolve genes against the selected GTEx dataset
Start with tool discovery
The catalog lists gtex_get_median_expression_levels as a representative tool. After connecting your client, inspect the tools and input requirements returned by the service before submitting a query.
Identifiers to prepare
- Gene symbol
- Versioned GENCODE/Ensembl gene identifier
- GTEx tissue identifier
All available tools (9)
The router surfaces these tools namespaced under gtex_*:
searchSearch the GTEx Portal genetic expression database for genes. Accepts a natural-language query (e.g. 'UMOD kidney expression'); gene-like terms are matched against the catalog. Returns result documents with id, title, and URL.
Search the GTEx Portal genetic expression database for genes. Accepts a natural-language query (e.g. 'UMOD kidney expression'); gene-like terms are matched against the catalog. Returns result documents with id, title, and URL.
Input parameters
query(string) [required] — A natural-language query or gene symbol; gene-like terms are matched against the GTEx catalog (e.g. 'UMOD kidney expression').
fetchRetrieve full details for a gene from the GTEx Portal database. Use the `id` returned by `search` (`gene:<GENCODE_ID>`); a bare GENCODE ID is also accepted. Expression is listed highest-median tissue first.
Retrieve full details for a gene from the GTEx Portal database. Use the `id` returned by `search` (`gene:<GENCODE_ID>`); a bare GENCODE ID is also accepted. Expression is listed highest-median tissue first.
Input parameters
id(string) [required] — A gene document id from `search` ('gene:<GENCODE_ID>'); a bare GENCODE ID or gene symbol is also accepted (e.g. UMOD).
search_genesSearch the GTEx Portal gene catalog by gene symbol or partial match. Returns a paginated list of genes with GENCODE IDs, symbols, chromosome, and basic metadata. Use this when the user provides a gene name or partial symbol and you need to disambiguate. Pair with `get_gene_information` for full detail.
Search the GTEx Portal gene catalog by gene symbol or partial match. Returns a paginated list of genes with GENCODE IDs, symbols, chromosome, and basic metadata. Use this when the user provides a gene name or partial symbol and you need to disambiguate. Pair with `get_gene_information` for full detail.
Input parameters
limit(integer) — Maximum genes to return per page (1-1000).offset(integer) — Zero-based row offset for pagination (fleet canon).query(string) [required] — Gene symbol or partial symbol to match against the GTEx catalog (e.g. 'BRCA' matches BRCA1, BRCA2).
get_gene_informationRetrieve detailed gene information from GTEx Portal for one or more GENCODE IDs or gene symbols. Returns chromosome, coordinates, gene type, Entrez ID, and description. Use when you already know the gene identifier.
Retrieve detailed gene information from GTEx Portal for one or more GENCODE IDs or gene symbols. Returns chromosome, coordinates, gene type, Entrez ID, and description. Use when you already know the gene identifier.
Input parameters
gencode_version(any) — GENCODE annotation release to resolve against; omit for the server default (v26).gene_id(array) [required] — One or more gene symbols or GENCODE IDs; symbols are auto-resolved (e.g. UMOD or ENSG00000169344.15).genome_build(any) — Genome assembly build; omit for the server default.
get_transcript_informationRetrieve transcript annotations for a single GENCODE ID from GTEx Portal. Returns transcript identifiers, coordinates, and gene linkage. Use for transcript-level analysis or when the user asks about isoforms.
Retrieve transcript annotations for a single GENCODE ID from GTEx Portal. Returns transcript identifiers, coordinates, and gene linkage. Use for transcript-level analysis or when the user asks about isoforms.
Input parameters
gencode_id(string) [required] — A single VERSIONED GENCODE ID (e.g. ENSG00000169344.15). This tool does NOT auto-resolve gene symbols -- resolve a symbol via get_gene_information or search_genes first.gencode_version(any) — GENCODE annotation release; omit for the server default.genome_build(any) — Genome assembly build; omit for the server default.limit(integer) — Maximum transcript rows per page.offset(integer) — Zero-based row offset for pagination.
get_median_expression_levelsGet median GTEx Portal expression (TPM) per tissue for one or more genes (GENCODE IDs or symbols; symbols are auto-resolved). Results are grouped per gene with invariant fields hoisted. Use `sort` + `top_n` to answer 'where is this gene expressed most?' in one call; `response_mode='full'` adds ontologyId; `include_spread=true` adds per-tissue min/max/quartiles/IQR (one extra upstream call).
Get median GTEx Portal expression (TPM) per tissue for one or more genes (GENCODE IDs or symbols; symbols are auto-resolved). Results are grouped per gene with invariant fields hoisted. Use `sort` + `top_n` to answer 'where is this gene expressed most?' in one call; `response_mode='full'` adds ontologyId; `include_spread=true` adds per-tissue min/max/quartiles/IQR (one extra upstream call).
Input parameters
dataset_id(string) — GTEx dataset release to query.gencode_id(array) [required] — One or more gene symbols or GENCODE IDs; symbols are auto-resolved to the dataset's GENCODE release (e.g. UMOD or ENSG00000169344.15). At most 18 genes per call.include_spread(boolean) — Add per-tissue min/max/quartiles/IQR (one extra upstream call).limit(integer) — Genes per page for pagination.offset(integer) — Zero-based gene offset for pagination.response_mode(string) — compact (default; tissue/median/n only) or full (adds ontologyId per tissue).sort(string) — Order tissues by median expression: desc (highest first, default), asc (lowest first), or none (upstream order).tissue_site_detail_id(any) — A single GTEx tissue, or a list of tissues to compare in one call; omit for all tissues.top_n(any) — Keep only the top N tissues after sorting (>=1); omit for all. Pair with sort to answer 'where is this expressed most/least?'.
get_individual_expression_dataGet individual-sample GTEx Portal expression data (TPM) for one or more genes (GENCODE IDs or symbols; symbols are auto-resolved), optionally filtered by tissue and dataset. Returns one row per gene-tissue; each row's `data` is an unlabeled per-sample TPM vector (no sample/donor IDs, upstream order) with `n` = sample count. NOTE: `limit` paginates the gene-tissue ROWS, not samples -- filter by tissue to bound size. Use for variance/distribution analyses where per-sample data is needed.
Get individual-sample GTEx Portal expression data (TPM) for one or more genes (GENCODE IDs or symbols; symbols are auto-resolved), optionally filtered by tissue and dataset. Returns one row per gene-tissue; each row's `data` is an unlabeled per-sample TPM vector (no sample/donor IDs, upstream order) with `n` = sample count. NOTE: `limit` paginates the gene-tissue ROWS, not samples -- filter by tissue to bound size. Use for variance/distribution analyses where per-sample data is needed.
Input parameters
dataset_id(string) — GTEx dataset release to query.gencode_id(array) [required] — One or more gene symbols or GENCODE IDs; symbols are auto-resolved (e.g. UMOD or ENSG00000169344.15).limit(integer) — Maximum gene-tissue rows per page; filter by tissue to bound size.offset(integer) — Zero-based row offset (rows are gene-tissue pairs, not samples).tissue_site_detail_id(any) — Restrict to a single GTEx tissue; omit for all tissues (high volume).
get_top_expressed_genes_by_tissueGet the top expressed genes for a given tissue from GTEx Portal. Use when answering 'what's expressed in this tissue?' rather than 'where is this gene expressed?'. Returns genes ranked by median expression.
Get the top expressed genes for a given tissue from GTEx Portal. Use when answering 'what's expressed in this tissue?' rather than 'where is this gene expressed?'. Returns genes ranked by median expression.
Input parameters
dataset_id(string) — GTEx dataset release to query.filter_mt_gene(boolean) — Exclude mitochondrial genes (default true).limit(integer) — Maximum genes to return per page.offset(integer) — Zero-based row offset for pagination.tissue_site_detail_id(string) [required] — The GTEx tissue to rank genes within (e.g. Whole_Blood).
get_server_capabilitiesReturn supported tools, datasets, the tissue vocabulary, recommended workflows, response modes, error codes, and limits. Compare `capabilities_version` to skip re-fetching when unchanged.
Return supported tools, datasets, the tissue vocabulary, recommended workflows, response modes, error codes, and limits. Compare `capabilities_version` to skip re-fetching when unchanged.
Database & release provenance
- Data mode
none- Attestation
- unhosted
- Release version
v3.1.6
ghcr.io/berntpopp/gtex-link@sha256:388995ec34c12ce6a3dfe004bad535337c95ea1c8a8c3f92e47ba668ea695556Review the response
Keep the source record link and submitted identifiers with your notes. Record the dataset version and retrieval date when available. This page does not contain a captured GTEx Portal response.