get_tissue_expression

Retrieve tissue-specific protein expression data from the Human Protein Atlas to analyze where genes are active in the human body.

Instructions

Get tissue-specific expression data for a protein

Input Schema

TableJSON Schema

Name	Required	Description	Default
`gene`	Yes	Gene symbol
`format`	No	Output format (default: json)

Implementation Reference

src/index.ts:893-919 (handler)

The main handler function that executes the 'get_tissue_expression' tool. Validates input using isValidGeneArgs, fetches tissue expression data via fetchTissueExpression, formats as JSON text response, and handles errors.

private async handleGetTissueExpression(args: any) {
  if (!isValidGeneArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid gene arguments');
  }

  try {
    const result = await this.fetchTissueExpression(args.gene);
    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(result, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error fetching tissue expression: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:748-751 (helper)

Helper function that performs the actual API query for tissue expression data by calling searchProteins with specific tissue-related columns.

private async fetchTissueExpression(gene: string): Promise<any> {
  const columns = ['g', 'eg', 'rnats', 'rnatd', 'rnatss', 't_RNA_adipose_tissue', 't_RNA_adrenal_gland', 't_RNA_brain', 't_RNA_breast', 't_RNA_colon', 't_RNA_heart_muscle', 't_RNA_kidney', 't_RNA_liver', 't_RNA_lung', 't_RNA_ovary', 't_RNA_pancreas', 't_RNA_prostate', 't_RNA_skeletal_muscle', 't_RNA_skin_1', 't_RNA_spleen', 't_RNA_stomach_1', 't_RNA_testis', 't_RNA_thyroid_gland'];
  return this.searchProteins(gene, 'json', columns, 1);
}

src/index.ts:485-495 (registration)

Tool registration entry in the tools array passed to server.setTools(), including name, description, and input schema.

  name: 'get_tissue_expression',
  description: 'Get tissue-specific expression data for a protein',
  inputSchema: {
    type: 'object',
    properties: {
      gene: { type: 'string', description: 'Gene symbol' },
      format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
    },
    required: ['gene'],
  },
},

src/index.ts:676-677 (registration)
Switch case in the CallToolRequest handler that routes 'get_tissue_expression' calls to the handleGetTissueExpression method.
```
case 'get_tissue_expression':
  return this.handleGetTissueExpression(args);
```

src/index.ts:487-494 (schema)

Input schema defining parameters for the tool: required 'gene' string and optional 'format' enum.

inputSchema: {
  type: 'object',
  properties: {
    gene: { type: 'string', description: 'Gene symbol' },
    format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
  },
  required: ['gene'],
},

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