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human-protein-atlas-database

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

1|Updated Aug 31, 2026
Search Tags:#bioinformatics#genomics#ensembl#protein expression#human protein atlas#subcellular localization#immunohistochemistry
One-click install
npx skills add https://github.com/nguyenhungtran18/skill-and-tool-tracker --skill human-protein-atlas-database-nguyenhungtran18
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: human-protein-atlas-database
Source: https://github.com/nguyenhungtran18/skill-and-tool-tracker/tree/main/skills/human_protein_atlas_database
Command: npx skills add https://github.com/nguyenhungtran18/skill-and-tool-tracker --skill human-protein-atlas-database-nguyenhungtran18

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 within the cell, or how abundant it is across human tissues. This Skill queries the Human Protein Atlas (HPA) to retrieve semi-quantitative protein expression data based on immunohistochemistry (IHC) across normal tissues and cancer types. ## Core Features & Use Cases - Gene Symbol Resolution: Map common gene symbols like TP53 or ERBB2 to Ensembl IDs required by HPA endpoints. - Expression & Localization Queries: Retrieve tissue-level protein abundance (High, Medium, Low, Not Detected) and subcellular locations such as nucleoplasm or mitochondria. - Attribute-Based Search: Filter genes by criteria like brain region enrichment, protein class, or antibody validation level using the HPA search syntax. - Use Case: A researcher studying ERBB2 can resolve its Ensembl ID, confirm its membrane localization, and check protein levels across breast tissue and cancer samples to validate RNA-seq findings. ## Quick Start Ask the AI to resolve the gene symbol TP53 to its Ensembl ID and then retrieve its tissue protein expression levels 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 for a gene from the Human Protein Atlas?▼

First resolve the gene symbol to an Ensembl ID with the resolve-ensembl-id command, then run get-tissue-expression with that ID. Results are written as JSON containing IHC-based levels of High, Medium, Low, or Not Detected per tissue.

How to find the subcellular location of a protein using HPA?▼

Run the get-subcellular-location command with the gene's Ensembl ID. It returns main and additional subcellular locations such as nucleoplasm, mitochondria, or vesicles based on immunocytochemistry staining data.

What is the difference between HPA protein data and GTEx RNA-seq data?▼

HPA confirms whether the protein product exists and where it localizes using immunohistochemistry, while GTEx measures RNA transcription levels. Use HPA for protein-level validation and GTEx when only transcript expression matters.

Can I use the Human Protein Atlas for non-human species or variant-level QTL queries?▼

No. HPA is strictly limited to human proteins and provides wild-type expression data only. It contains no eQTL, pQTL, or variant-level association information, so other databases are required for those queries.

Why does my HPA search query return no results?▼

Queries may fail if the field syntax is wrong or terms are quoted unnecessarily, since HPA search is case-insensitive and space-containing values need no quotes. Consult the search-api reference and test simpler field:value pairs first.

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