human-protein-atlas-database

Retrieve protein expression and subcellular localization data from the Human Protein Atlas API.

Updated Sep 9, 2026
One-click install
npx skills add https://github.com/xlinh2301/EditCTC --skill human-protein-atlas-database-xlinh2301
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: human-protein-atlas-database
Source: https://github.com/xlinh2301/EditCTC/tree/main/.agents/skills/human-protein-atlas-database
Command: npx skills add https://github.com/xlinh2301/EditCTC --skill human-protein-atlas-database-xlinh2301

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires polite-http, and includes scripts (resource) and references (resource) components.

What problem does it solve? RNA-seq data alone cannot confirm whether a gene's protein product actually exists, where it localizes in the cell, or how abundant it is across human tissues. This Skill queries the Human Protein Atlas (HPA) to retrieve immunohistochemistry-based protein expression levels, subcellular locations, and RNA-protein agreement data for human genes. ## Core Features & Use Cases - Gene ID Resolution: Map common gene symbols (e.g., TP53, ERBB2) to the Ensembl IDs required by HPA endpoints. - Expression & Localization Queries: Fetch semi-quantitative IHC tissue expression levels (High/Medium/Low/Not Detected), subcellular locations, and full atlas entries including RNA-seq consensus. - Attribute Search: Filter genes by criteria such as brain region enrichment, protein class, or chromosome using the HPA search query syntax. - Use Case: A researcher validating a candidate drug target checks whether the protein is actually expressed in the tissue of interest and confirms its subcellular localization before designing experiments. ## Quick Start Ask the assistant to look up the tissue protein expression and subcellular location of a gene such as ERBB2 using the Human Protein Atlas skill.

Frequently Asked Questions about human-protein-atlas-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I get protein expression data from the Human Protein Atlas?▼

Run the hpa_cli.py script with the get-tissue-expression subcommand and an Ensembl gene ID. It returns IHC-based expression levels (High, Medium, Low, or Not Detected) across normal human tissues, optionally filtered by a comma-separated tissue list.

How to convert a gene symbol to an Ensembl ID for HPA queries?▼

Use the resolve-ensembl-id subcommand with the gene symbol, for example TP53 or ERBB2. HPA endpoints are strictly Ensembl-based, so this mapping step is required before querying expression or localization data.

Can I search HPA for genes elevated in a specific brain region?▼

Yes, use the search-hpa subcommand with a query like brain_category_rna:Amygdala;Region enriched. The references/search-api.md document describes the full query syntax including Boolean operators, specificity categories, and protein class filters.

Does the Human Protein Atlas support non-human species or QTL queries?▼

No, HPA is strictly limited to human proteins and provides wild-type expression data only. It cannot answer eQTL, pQTL, or variant-level association questions, and purely quantitative RNA expression is better served by GTEx.

Why does my HPA search return no results?▼

Queries may fail if they are not detailed enough or use incorrect field syntax. Consult references/search-api.md for valid fields and operators, avoid quoting terms with spaces, and try example queries from the HPA website to refine the search.