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
• 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