ARCHS4 Database

ARCHS4 Database

Overview

ARCHS4 (All RNA-seq and ChIP-seq Sample and Signature Search) is a resource of uniformly aligned and processed human and mouse RNA-seq data from NCBI GEO and SRA, covering 1 million+ samples. The REST API at https://maayanlab.cloud/archs4/api/ provides gene-level expression profiles, z-score normalized tissue expression, co-expression networks, and sample metadata search — all without authentication. Large-scale bulk queries can also use the downloadable HDF5 expression matrices.

When to Use

• Retrieving tissue-specific or cell-type-specific expression z-scores for a gene of interest across hundreds of tissue types
• Finding genes co-expressed with a query gene (co-expression network construction or guilt-by-association analysis)
• Searching for RNA-seq samples by tissue, disease, or metadata keyword to identify candidate datasets for reanalysis
• Comparing expression profiles of multiple genes across tissues to prioritize candidates for wet-lab follow-up
• Accessing uniformly processed gene expression matrices (HDF5 format) for large-scale cross-study analysis
• Validating differential expression results by checking whether a gene's expression direction matches population-level tissue profiles
• Use omics-plotting SKILL to render bar charts and expression heatmaps from the query results
• For variant-level population allele frequencies use gnomad-database; ARCHS4 provides expression evidence only
• For Enrichr pathway enrichment from a gene list use gget-genomic-databases (gget enrichr); ARCHS4 is for expression lookups

Prerequisites

• Python packages: requests, pandas, matplotlib, seaborn
• Data requirements: gene symbols (HGNC format, e.g., TP53, BRCA1); sample GEO/SRA IDs for direct sample queries
• Environment: internet connection; no API key or account required
• Rate limits: ~10 requests/second; add time.sleep(0.1) between sequential gene queries to avoid throttling

pip install requests pandas matplotlib seaborn

Quick Start

import requests

ARCHS4_BASE = "https://maayanlab.cloud/archs4/api/v1"

def archs4_get(endpoint: str, params: dict = None) -> dict:
    """Send a GET request to the ARCHS4 API and return parsed JSON."""
    r = requests.get(f"{ARCHS4_BASE}/{endpoint}", params=params, timeout=30)
    r.raise_for_status()