get_eqtl_genes
Identify genes with expression quantitative trait loci (eQTL) associations within a specified genomic region using GTEx data, optionally filtered by tissue type.
Instructions
Get genes with eQTL associations for a genomic region
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| chr | Yes | Chromosome (e.g., chr1, chr2, chrX) | |
| datasetId | No | GTEx dataset ID (default: gtex_v8) | gtex_v8 |
| end | Yes | End position (1-based) | |
| start | Yes | Start position (1-based) | |
| tissueSiteDetailId | No | Tissue site detail ID (optional, for tissue-specific results) |
Implementation Reference
- MCP tool handler: executes the get_eqtl_genes tool logic, calls API client, formats and groups results by tissue with summaries and top eGenes.async getEQTLGenes(args: any) { const result = await this.apiClient.getEQTLGenes({ tissueSiteDetailId: args.tissueIds, datasetId: args.datasetId || 'gtex_v8', page: args.page || 0, itemsPerPage: args.itemsPerPage || 250 }); if (result.error) { return { content: [{ type: "text", text: `Error retrieving eQTL genes: ${result.error}` }], isError: true }; } const eqtlGenes = result.data || []; if (eqtlGenes.length === 0) { return { content: [{ type: "text", text: `No eQTL genes found${args.tissueIds ? ` for tissues: ${args.tissueIds.join(', ')}` : ''}` }] }; } // Group by tissue for better organization const tissueGroups: { [key: string]: any[] } = {}; eqtlGenes.forEach(gene => { if (!tissueGroups[gene.tissueSiteDetailId]) { tissueGroups[gene.tissueSiteDetailId] = []; } tissueGroups[gene.tissueSiteDetailId].push(gene); }); let output = `**eQTL Genes (${eqtlGenes.length} results)**\n`; output += `Dataset: ${eqtlGenes[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} eGenes)\n`; // Sort by significance (lowest q-value first) const sortedGenes = genes.sort((a, b) => a.qValue - b.qValue); // Show top significant genes 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 += ` • 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 += ` • Log2 allelic fold change: ${gene.log2AllelicFoldChange.toFixed(3)}\n`; output += ` • p-value threshold: ${gene.pValueThreshold.toExponential(2)}\n`; }); if (sortedGenes.length > topCount) { output += ` ... and ${sortedGenes.length - topCount} more eGenes\n`; } // Statistics for this tissue const qValues = sortedGenes.map(g => g.qValue); const foldChanges = sortedGenes.map(g => Math.abs(g.log2AllelicFoldChange)); output += `\n**Tissue Summary:**\n`; output += ` • Total eGenes: ${genes.length}\n`; output += ` • Most significant q-value: ${Math.min(...qValues).toExponential(2)}\n`; output += ` • Mean |fold change|: ${(foldChanges.reduce((sum, fc) => sum + fc, 0) / foldChanges.length).toFixed(3)}\n`; output += ` • Max |fold change|: ${Math.max(...foldChanges).toFixed(3)}\n\n`; }); if (result.paging_info && result.paging_info.totalNumberOfItems > eqtlGenes.length) { output += `**Note:** Showing ${eqtlGenes.length} of ${result.paging_info.totalNumberOfItems} total results.\n`; } return { content: [{ type: "text", text: output.trim() }] }; }
- src/index.ts:672-676 (registration)Tool registration/dispatch: routes callTool requests for 'get_eqtl_genes' to the AssociationHandlers.getEQTLGenes method.if (name === "get_eqtl_genes") { return await associationHandlers.getEQTLGenes({ tissueIds: args?.tissueSiteDetailId ? [args.tissueSiteDetailId] : undefined, datasetId: args?.datasetId });
- src/index.ts:219-247 (schema)MCP tool schema: defines input schema for listTools response (note: schema params chr/start/end not used in dispatch).name: "get_eqtl_genes", description: "Get genes with eQTL associations for a genomic region", inputSchema: { type: "object", properties: { chr: { type: "string", description: "Chromosome (e.g., chr1, chr2, chrX)" }, start: { type: "integer", description: "Start position (1-based)" }, end: { type: "integer", description: "End position (1-based)" }, tissueSiteDetailId: { type: "string", description: "Tissue site detail ID (optional, for tissue-specific results)" }, datasetId: { type: "string", description: "GTEx dataset ID (default: gtex_v8)", default: "gtex_v8" } }, required: ["chr", "start", "end"] }
- src/utils/api-client.ts:459-475 (helper)API client helper: performs HTTP request to GTEx Portal /association/egene endpoint to fetch eQTL genes data.async getEQTLGenes(params: GetEQTLGenesParams): Promise<GTExApiResponse<EQTLGene[]>> { try { const queryParams = this.buildQueryParams({ tissueSiteDetailId: params.tissueSiteDetailId, datasetId: params.datasetId || 'gtex_v8', page: params.page || 0, itemsPerPage: params.itemsPerPage || 250 }); const response = await this.axiosInstance.get(`/association/egene?${queryParams}`); return { data: response.data.data, paging_info: response.data.paging_info }; } catch (error) { return error as GTExApiResponse<EQTLGene[]>; } }
- src/types/gtex-types.ts:402-407 (schema)TypeScript interface defining parameters for getEQTLGenes API call (matches actual usage).export interface GetEQTLGenesParams { tissueSiteDetailId?: string[]; datasetId?: string; page?: number; itemsPerPage?: number; }