get_sqtl_results
Retrieve splicing quantitative trait loci (sQTL) results for a specific gene from GTEx data to identify genetic variants influencing alternative splicing patterns.
Instructions
Get splicing QTL (sQTL) results for a gene
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| datasetId | No | GTEx dataset ID (default: gtex_v8) | gtex_v8 |
| gencodeId | Yes | GENCODE gene ID (e.g., ENSG00000223972.5) | |
| tissueSiteDetailId | No | Tissue site detail ID (optional, for tissue-specific results) |
Implementation Reference
- Main handler function that implements the tool logic for get_sqtl_results. It fetches sQTL genes from the API client for given tissues, groups by tissue, sorts by significance, formats top results and summaries into markdown output.async getSQTLGenes(args: any) { const result = await this.apiClient.getSQTLGenes( args.tissueIds, args.datasetId || 'gtex_v8' ); if (result.error) { return { content: [{ type: "text", text: `Error retrieving sQTL genes: ${result.error}` }], isError: true }; } const sqtlGenes = result.data || []; if (sqtlGenes.length === 0) { return { content: [{ type: "text", text: `No sQTL genes found${args.tissueIds ? ` for tissues: ${args.tissueIds.join(', ')}` : ''}` }] }; } // Group by tissue const tissueGroups: { [key: string]: any[] } = {}; sqtlGenes.forEach(gene => { if (!tissueGroups[gene.tissueSiteDetailId]) { tissueGroups[gene.tissueSiteDetailId] = []; } tissueGroups[gene.tissueSiteDetailId].push(gene); }); let output = `**sQTL Genes (${sqtlGenes.length} results)**\n`; output += `Dataset: ${sqtlGenes[0]?.datasetId}\n`; output += `Tissues: ${Object.keys(tissueGroups).length}\n\n`; Object.entries(tissueGroups).forEach(([tissueId, genes]) => { const tissueDisplayName = this.getTissueDisplayName(tissueId); output += `### ${tissueDisplayName} (${genes.length} sGenes)\n`; // Sort by significance const sortedGenes = genes.sort((a, b) => a.qValue - b.qValue); const topCount = Math.min(10, sortedGenes.length); sortedGenes.slice(0, topCount).forEach((gene, index) => { output += `${(index + 1).toString().padStart(2)}. **${gene.geneSymbol}** (${gene.gencodeId})\n`; output += ` • Phenotype: ${gene.phenotypeId}\n`; output += ` • p-value: ${gene.pValue.toExponential(2)}\n`; output += ` • q-value: ${gene.qValue.toFixed(4)}\n`; output += ` • Empirical p-value: ${gene.empiricalPValue.toExponential(2)}\n`; output += ` • # Phenotypes tested: ${gene.nPhenotypes}\n`; output += ` • p-value threshold: ${gene.pValueThreshold.toExponential(2)}\n`; }); if (sortedGenes.length > topCount) { output += ` ... and ${sortedGenes.length - topCount} more sGenes\n`; } // Tissue summary const qValues = sortedGenes.map(g => g.qValue); output += `\n**Tissue Summary:**\n`; output += ` • Total sGenes: ${genes.length}\n`; output += ` • Most significant q-value: ${Math.min(...qValues).toExponential(2)}\n`; output += ` • Mean phenotypes per gene: ${(genes.reduce((sum, g) => sum + g.nPhenotypes, 0) / genes.length).toFixed(1)}\n\n`; }); if (result.paging_info && result.paging_info.totalNumberOfItems > sqtlGenes.length) { output += `**Note:** Showing ${sqtlGenes.length} of ${result.paging_info.totalNumberOfItems} total results.\n`; } return { content: [{ type: "text", text: output.trim() }] }; }
- src/index.ts:319-341 (schema)Tool schema definition listing the input parameters: gencodeId (required), optional tissueSiteDetailId and datasetId.{ name: "get_sqtl_results", description: "Get splicing QTL (sQTL) results for a gene", inputSchema: { type: "object", properties: { gencodeId: { type: "string", description: "GENCODE gene ID (e.g., ENSG00000223972.5)" }, tissueSiteDetailId: { type: "string", description: "Tissue site detail ID (optional, for tissue-specific results)" }, datasetId: { type: "string", description: "GTEx dataset ID (default: gtex_v8)", default: "gtex_v8" } }, required: ["gencodeId"] } },
- src/index.ts:699-704 (registration)Registration/dispatch logic in CallToolRequestHandler that routes calls to 'get_sqtl_results' to the associationHandlers.getSQTLGenes method, mapping arguments (note: gencodeId from schema is not passed to handler).if (name === "get_sqtl_results") { return await associationHandlers.getSQTLGenes({ tissueIds: args?.tissueSiteDetailId ? [args.tissueSiteDetailId] : undefined, datasetId: args?.datasetId }); }