RatGTEx REST API (4.0.0)

Download OpenAPI specification:

Daniel Munro: danbmunro@gmail.com URL: https://danmun.ro

This API provides data for the visualizations in the RatGTEx data portal. This version (v4) provides data for RatGTEx data release v4, which uses the GRCr8 genome assembly.

reference

Information on tissues, genes, and variants

Exon annotations for a gene

Fetch a gene's exons

query Parameters

geneId

required

string

Example: geneId=Cd300lf

Gene ID

Responses

Response samples

200

Content type

application/json

{"exon": [{"chromosome": "chr1",
"end": 100875111,
"exonId": "Cd300lf_1",
"exonNumber": 1,
"featureType": "exon",
"geneId": "Cd300lf",
"start": 100874927,
"strand": "-",
"transcriptId": "Cd300lf"
}
]
}

Metadata for one or more genes

Fetch metadata for one or more genes

query Parameters

geneId

required

Array of strings

Example: geneId=Cd300lf,Eno1

One or more gene IDs

Responses

Response samples

200

Content type

application/json

{"gene": [{"chromosome": "chr10",
"description": "Cd300 molecule-like family member F",
"end": 100875111,
"geneId": "Cd300lf",
"hasEqtl": true,
"start": 100858924,
"statusInTissue": [{"eqtl": true,
"expressed": true,
"testedEqtl": true,
"tissueSiteDetailId": "IL"
}
],
"strand": "-",
"tss": 100875111
}
]
}

Metadata for all tissues

Fetch metadata for all tissues

Responses

Response samples

200

Content type

application/json

{"tissueInfo": [{"colorHex": "377eb8",
"colorRgb": "55,126,184",
"dataset": "ratgtex_v4_round11_1",
"datasetId": "ratgtex_v4",
"eGeneCount": 5475,
"expressedGeneCount": 24107,
"hasEgenes": true,
"rnaSeqAndGenotypeSampleCount": 83,
"rnaSeqSampleCount": 83,
"tissueSite": "Brain",
"tissueSiteDetail": "Infralimbic cortex",
"tissueSiteDetailAbbr": "IL",
"tissueSiteDetailId": "IL"
}
]
}

Metadata for one or more variants

Fetch information for one or more variants

query Parameters

variantId

required

Array of strings

Example: variantId=chr10:100826333,chr10:100955984

Variant ID

Responses

Response samples

200

Content type

application/json

{"variant": [{"alt": "T",
"chromosome": "chr10",
"pos": 100826333,
"ref": "C",
"variantId": "chr10:100826333"
}
]
}

expression

Gene expression data

Per-sample expression for a gene across tissues

Fetch per-sample expression (TPM) for a gene across all tissues

query Parameters

geneId

required

string

Example: geneId=Cd300lf

Gene ID

Responses

Response samples

200

Content type

application/json

{"geneExpression": [{"data": [3.33544,
2.679,
4.03568,
2.18627
],
"datasetId": "ratgtex_v4",
"geneId": "Cd300lf",
"geneSymbol": "Cd300lf",
"tissueSiteDetailId": "IL",
"unit": "TPM"
}
]
}

Median expression for genes in selected tissues

Fetch median expression (TPM) for one or more genes in one or more tissues

query Parameters

geneId required	Array of strings Example: geneId=Polr3k,Rtel1,Eno1 One or more gene IDs.
tissueSiteDetailId	Array of strings Example: tissueSiteDetailId=IL,LHb,NAcc One or more tissue IDs. If omitted, all tissues are included.

Responses

Response samples

200

Content type

application/json

{"clusters": {"gene": "((Rtel1:233.244,Polr3k:233.244):1054.57,Eno1:1287.81);",
"tissue": "((IL:12.7061,LHb:12.7061):291.773,NAcc:304.479);"
},
"medianGeneExpression": [{"geneId": "Rtel1",
"median": 22.957,
"tissueSiteDetailId": "IL"
}
]
}

Top 50 genes by median expression in a tissue

Fetch 50 genes with highest median expression in a tissue

query Parameters

filterMtGene	boolean Example: filterMtGene=true Whether mitochondrial genes should be omitted from the top gene list
tissueSiteDetailId required	string Example: tissueSiteDetailId=IL Tissue ID

Responses

Response samples

200

Content type

application/json

{"topExpressedGene": [{"chromosome": "chr11",
"datasetId": "ratgtex_v4",
"geneId": "LOC120093067",
"median": 7700.68,
"tissueSiteDetailId": "IL",
"unit": "TPM"
}
]
}

xQTL

Data on RNA phenotype-variant associations

Dynamic eQTL for one gene-variant pair

Fetch information for one gene-variant pair in one tissue

query Parameters

geneId required	string Example: geneId=Cd300lf Gene ID
tissueSiteDetailId required	string Example: tissueSiteDetailId=IL Tissue ID
variantId required	string Example: variantId=chr10:100826333 Variant ID

Responses

Response samples

200

Content type

application/json

{"alt": "T",
"data": [2.2338,
3.78302,
3.71887,
3.05015,
2.46061
],
"geneId": "Cd300lf",
"genotypes": [1,
1,
null,
1,
0
],
"hetCount": 35,
"homoAltCount": 16,
"homoRefCount": 27,
"maf": 0.42948717948717946,
"pValue": 8.43005e-8,
"pValueThreshold": 0.00172939,
"ref": "C",
"tissueSiteDetailId": "IL",
"variantId": "chr10:100826333"
}

Conditionally independent cis-eQTLs by gene

Fetch conditionally independent cis-eQTLs in any tissue for a gene

query Parameters

geneId

required

string

Example: geneId=Cd300lf

Gene ID

Responses

Response samples

200

Content type

application/json

{"eqtl": [{"alt": "T",
"geneId": "Cd300lf",
"log2aFC": 0.65925,
"pValueBeta": 0.00000805017,
"ref": "C",
"tissueSiteDetailId": "IL",
"variantId": "chr10:100826333"
}
]
}

Significant single-tissue cis-variants for a gene

Fetch all significant cis-variants in all tissues for a gene

query Parameters

geneId

required

string

Example: geneId=Cd300lf

Gene ID

Responses

Response samples

200

Content type

application/json

{"singleTissueEqtl": [{"chromosome": "chr10",
"geneId": "Cd300lf",
"nes": 0.592446,
"pValue": 2.111e-10,
"pos": 99876736,
"tissueSiteDetailId": "BLA",
"variantId": "chr10:99876736"
}
]
}

Conditionally independent cis-xQTLs by gene

Fetch conditionally independent cis-xQTLs in any tissue for a gene

query Parameters

geneId

required

string

Example: geneId=Cd300lf

Gene ID

Responses

Response samples

200

Content type

application/json

{"xqtl": [{"alt": "A",
"geneId": "Cd300lf",
"modality": "splicing",
"pValueBeta": 3.72035e-15,
"phenotypeId": "Cd300lf__chr10_100862967_100866541_clu_7827_-",
"ref": "G",
"tissueSiteDetailId": "pVTA",
"variantId": "chr10:101009133"
}
]
}