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()
    return r.json()

# Quick check: top tissues expressing TP53
data = archs4_get("meta/genes/TP53/zscore")
tissues = data.get("values", [])
print(f"TP53 tissue expression entries: {len(tissues)}")
top5 = sorted(tissues, key=lambda x: x.get("zscore", 0), reverse=True)[:5]
for t in top5:
    print(f"  {t['tissue']:<40}  z={t['zscore']:.2f}")
# TP53 tissue expression entries: 200
#   thymus                                   z=2.81
#   testis                                   z=2.44

Core API

Query 1: Gene Expression Z-Scores Across Tissues

Retrieve z-score normalized expression for a gene across all available tissue types. Z-scores are computed per-sample relative to the population distribution; positive values indicate above-average expression.

import requests
import pandas as pd

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

def get_gene_tissue_zscore(gene_symbol: str, species: str = "human") -> pd.DataFrame:
    """Return tissue z-score expression profile for a gene.

    Parameters
    ----------
    gene_symbol : str
        HGNC gene symbol (e.g., 'TP53').
    species : str
        'human' or 'mouse' (default: 'human').
    """
    endpoint = f"meta/genes/{gene_symbol}/zscore"
    r = requests.get(
        f"{ARCHS4_BASE}/{endpoint}",
        params={"species": species},
        timeout=30
    )
    r.raise_for_status()
    data = r.json()
    records = data.get("values", [])
    df = pd.DataFrame(records)
    return df.sort_values("zscore", ascending=False).reset_index(drop=True)

df = get_gene_tissue_zscore("MYC")
print(f"MYC tissue z-scores: {len(df)} tissue types")
print(df[["tissue", "zscore"]].head(10).to_string(index=False))
# MYC tissue z-scores: 200
#                     tissue  zscore
#                      colon    3.12
#             small intestine    2.98
#                    placenta    2.74

# Query mouse tissues for a gene
df_mouse = get_gene_tissue_zscore("Myc", species="mouse")
print(f"Mouse Myc: top 5 tissues")
print(df_mouse[["tissue", "zscore"]].head(5).to_string(index=False))

Query 2: Co-expressed Genes

Find genes whose expression is most correlated with a query gene across all ARCHS4 samples. Useful for identifying pathway partners, regulators, or candidate targets.

import requests
import pandas as pd

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

def get_coexpressed_genes(gene_symbol: str, top_n: int = 50,
                           species: str = "human") -> pd.DataFrame:
    """Return genes co-expressed with the query gene.

    Parameters
    ----------
    gene_symbol : str
        HGNC gene symbol.
    top_n : int
        Number of correlated genes to return (default: 50).
    species : str
        'human' or 'mouse' (default: 'human').
    """
    r = requests.get(
        f"{ARCHS4_BASE}/meta/genes/{gene_symbol}/correlations",
        params={"species": species, "limit": top_n},
        timeout=30
    )
    r.raise_for_status()
    data = r.json()
    records = data.get("values", [])
    df = pd.DataFrame(records)
    return df.sort_values("correlation", ascending=False).reset_index(drop=True)

coexp = get_coexpressed_genes("PCNA", top_n=20)
print(f"Top co-expressed genes with PCNA (n={len(coexp)}):")
print(coexp[["gene", "correlation"]].head(10).to_string(index=False))
# Top co-expressed genes with PCNA (n=20):
#   gene  correlation
#   RFC4         0.91
#   RFC2         0.89
#   MCM6         0.87

# Extract gene list for downstream enrichment
gene_list = coexp["gene"].tolist()
print(f"Co-expression gene list: {gene_list[:10]}")
# Pass gene_list to Enrichr or pathway analysis tools

Query 3: Sample Search

Search for RNA-seq samples by metadata keyword (tissue, disease condition, cell type, treatment). Returns GEO/SRA sample identifiers with metadata fields.

import requests
import pandas as pd

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

def search_samples(keyword: str, species: str = "human",
                   limit: int = 100) -> pd.DataFrame:
    """Search ARCHS4 samples by metadata keyword.

    Parameters
    ----------
    keyword : str
        Search term (e.g., 'breast cancer', 'liver', 'HeLa').
    species : str
        'human' or 'mouse'.
    limit : int
        Maximum number of samples to return.
    """
    r = requests.get(
        f"{ARCHS4_BASE}/samples/search",
        params={"query": keyword, "species": species, "limit": limit},
        timeout=30
    )
    r.raise_for_status()
    data = r.json()
    records = data.get("samples", [])
    return pd.DataFrame(records)

samples = search_samples("pancreatic cancer", limit=50)
print(f"Samples matching 'pancreatic cancer': {len(samples)}")
if len(samples) > 0:
    print(samples[["sample_id", "series_id", "title"]].head(5).to_string(index=False))
# Samples matching 'pancreatic cancer': 50
#   sample_id  series_id  title
#   GSM2345678  GSE123456  Pancreatic ductal adenocarcinoma - sample 1

Query 4: Gene-Level Metadata Summary

Retrieve summary statistics and metadata for a gene including the number of samples expressing it, expression percentile, and available annotation.

import requests

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

def get_gene_metadata(gene_symbol: str, species: str = "human") -> dict:
    """Return metadata and expression summary for a gene."""
    r = requests.get(
        f"{ARCHS4_BASE}/meta/genes/{gene_symbol}",
        params={"species": species},
        timeout=30
    )
    r.raise_for_status()
    return r.json()

meta = get_gene_metadata("GAPDH")
print(f"Gene: {meta.get('gene_symbol', 'N/A')}")
print(f"Species: {meta.get('species', 'N/A')}")
print(f"Ensembl ID: {meta.get('ensembl_gene_id', 'N/A')}")
print(f"Description: {meta.get('description', 'N/A')[:80]}")

# Compare metadata for a panel of housekeeping genes
import time

housekeeping = ["GAPDH", "ACTB", "B2M", "HPRT1", "RPLP0"]
for gene in housekeeping:
    meta = get_gene_metadata(gene)
    print(f"  {gene:<8}  {meta.get('ensembl_gene_id', 'N/A')}")
    time.sleep(0.1)

Query 5: Visualization — Tissue Expression Barplot

Fetch the top-tissue z-scores, then read skills/data-visualization/omics-plotting/SKILL.md and follow its "Box / Violin / Bar" recipe on the exported CSV (→ figures/BRCA1_tissue_expression.png).

import requests
import pandas as pd

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

def tissue_zscores(gene_symbol: str, top_n: int = 20, species: str = "human") -> pd.DataFrame:
    """Fetch top tissue z-scores for a gene and save for plotting."""
    r = requests.get(
        f"{ARCHS4_BASE}/meta/genes/{gene_symbol}/zscore",
        params={"species": species},
        timeout=30,
    )
    r.raise_for_status()
    df = pd.DataFrame(r.json().get("values", [])).sort_values("zscore", ascending=False).head(top_n)
    df.to_csv(f"{gene_symbol}_tissue_zscores.csv", index=False)
    return df

df = tissue_zscores("BRCA1", top_n=15)
print(f"Top tissues for BRCA1: {len(df)} -> BRCA1_tissue_zscores.csv")
# Render with the omics-plotting SKILL (`skills/data-visualization/omics-plotting/SKILL.md`) "Box / Violin / Bar" recipe (horizontal bar of zscore by tissue).

Query 6: HDF5 Bulk Data Access

Download or stream from ARCHS4's precomputed HDF5 expression matrices for large-scale cross-sample analysis. The HDF5 files contain gene × sample count matrices for human and mouse.

import requests

# HDF5 files are available for bulk download from the ARCHS4 data portal
# URL pattern: https://maayanlab.cloud/archs4/download#expression
# Human gene-level: human_gene_v2.6.h5
# Mouse gene-level: mouse_gene_v2.6.h5

def get_h5_download_urls() -> dict:
    """Return download URLs for ARCHS4 HDF5 expression matrices."""
    base = "https://maayanlab.cloud/archs4"
    return {
        "human_gene": f"{base}/files/human_gene_v2.6.h5",
        "mouse_gene": f"{base}/files/mouse_gene_v2.6.h5",
        "human_transcript": f"{base}/files/human_transcript_v2.6.h5",
        "mouse_transcript": f"{base}/files/mouse_transcript_v2.6.h5",
    }

urls = get_h5_download_urls()
for key, url in urls.items():
    print(f"  {key:<22}  {url}")

# To work with a downloaded HDF5 file:
try:
    import h5py
    import numpy as np

    h5_path = "human_gene_v2.6.h5"   # after download

    def extract_gene_from_h5(h5_path: str, gene_symbol: str,
                              n_samples: int = 1000) -> dict:
        """Extract expression values for a gene from the HDF5 matrix."""
        with h5py.File(h5_path, "r") as f:
            genes = [g.decode() for g in f["meta"]["genes"]["gene_symbol"][:]]
            if gene_symbol not in genes:
                raise ValueError(f"{gene_symbol} not found in HDF5")
            idx = genes.index(gene_symbol)
            expr = f["data"]["expression"][idx, :n_samples]
            sample_ids = [s.decode() for s in f["meta"]["samples"]["geo_accession"][:n_samples]]
        return {"gene": gene_symbol, "expression": expr, "sample_ids": sample_ids}

    result = extract_gene_from_h5(h5_path, "TP53", n_samples=500)
    print(f"TP53 expression: mean={result['expression'].mean():.2f},"
          f" max={result['expression'].max():.2f} (n={len(result['expression'])} samples)")
except ImportError:
    print("h5py not installed. Install with: pip install h5py")
except FileNotFoundError:
    print("HDF5 file not downloaded yet. Use the URLs above to download first.")

Key Concepts

Z-Score Normalization

ARCHS4 reports gene expression as z-scores computed relative to all samples for that gene. A z-score of 0 means expression at the population mean; a z-score of 2.0 means expression 2 standard deviations above the mean. Z-scores are more interpretable across datasets than raw counts because they account for library size differences and batch effects introduced by uniform alignment across studies.

# Example: Positive z-score = above-average expression for that gene
# z > 2.0 → top ~2.5% of samples for that gene
# z < -2.0 → bottom ~2.5% of samples for that gene
# Use absolute z-score thresholds consistently when comparing across genes

HDF5 vs REST API

Species and Gene Symbol Conventions

ARCHS4 indexes human samples using HGNC gene symbols (uppercase, e.g., TP53) and mouse samples using MGI symbols (first letter uppercase, e.g., Trp53). The species parameter accepts "human" or "mouse". Mixed-case or ensemble IDs will return empty results.

Common Workflows

Workflow 1: Multi-Gene Tissue Expression Heatmap

Goal: Compare tissue expression profiles of a gene panel and visualize as a heatmap to identify tissue-specific vs ubiquitous expression patterns.

import requests, time
import pandas as pd

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

gene_panel = ["MYC", "TP53", "BRCA1", "EGFR", "KRAS", "CDK4"]
top_n_tissues = 25

def get_tissue_zscores(gene: str) -> pd.Series:
    r = requests.get(
        f"{ARCHS4_BASE}/meta/genes/{gene}/zscore",
        params={"species": "human"},
        timeout=30
    )
    r.raise_for_status()
    records = r.json().get("values", [])
    df = pd.DataFrame(records).set_index("tissue")["zscore"]
    return df

# Build expression matrix (genes × tissues)
all_data = {}
for gene in gene_panel:
    try:
        all_data[gene] = get_tissue_zscores(gene)
        print(f"  Fetched {gene}")
    except Exception as e:
        print(f"  Warning: {gene} failed — {e}")
    time.sleep(0.1)

matrix = pd.DataFrame(all_data).T   # genes × tissues
# Select top tissues by max absolute z-score
tissue_importance = matrix.abs().max(axis=0).sort_values(ascending=False)
top_tissues = tissue_importance.head(top_n_tissues).index
matrix_subset = matrix[top_tissues]

# Save the gene × tissue matrix; render with the omics-plotting SKILL (`skills/data-visualization/omics-plotting/SKILL.md`) "Expression heatmap"
# recipe (RdBu_r, center=0) -> figures/archs4_panel_heatmap.png
matrix_subset.to_csv("archs4_panel_matrix.csv")
print(f"Panel matrix ready: {matrix_subset.shape} -> archs4_panel_matrix.csv")

Workflow 2: Co-expression Network Seed Expansion

Goal: Start from a seed gene, retrieve co-expressed partners, then query their co-expressed genes in turn to build a two-hop co-expression neighborhood.

import requests, time
import pandas as pd

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

def get_coexp(gene: str, top_n: int = 20, species: str = "human") -> list:
    r = requests.get(
        f"{ARCHS4_BASE}/meta/genes/{gene}/correlations",
        params={"species": species, "limit": top_n},
        timeout=30
    )
    r.raise_for_status()
    return [rec["gene"] for rec in r.json().get("values", [])]

seed_gene = "PCNA"
min_correlation = 0.80

# Hop 1: direct co-expressed partners
hop1_genes = get_coexp(seed_gene, top_n=30)
print(f"Hop 1 partners of {seed_gene}: {len(hop1_genes)}")
time.sleep(0.1)

# Hop 2: co-expressed genes of each partner
edges = set()
for gene in hop1_genes[:10]:   # limit for demonstration
    partners = get_coexp(gene, top_n=20)
    for partner in partners:
        if partner != seed_gene:
            edges.add((gene, partner))
    time.sleep(0.1)

# Summarize the network
network_df = pd.DataFrame(list(edges), columns=["source", "target"])
hub_counts = network_df["source"].value_counts()
print(f"\nTwo-hop network: {len(edges)} edges")
print(f"Top hub genes:")
print(hub_counts.head(5))

network_df.to_csv(f"{seed_gene}_coexp_network.csv", index=False)
print(f"\nSaved {seed_gene}_coexp_network.csv")

Workflow 3: Sample Discovery and Dataset Summary

Goal: Search for samples by disease keyword, summarize how many GEO series are available, and export sample metadata for downstream reanalysis selection.

import requests, time
import pandas as pd

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

def search_and_summarize(keyword: str, species: str = "human",
                          limit: int = 200) -> pd.DataFrame:
    """Search samples and return a tidy metadata DataFrame."""
    r = requests.get(
        f"{ARCHS4_BASE}/samples/search",
        params={"query": keyword, "species": species, "limit": limit},
        timeout=30
    )
    r.raise_for_status()
    records = r.json().get("samples", [])
    return pd.DataFrame(records)

keyword = "colorectal cancer"
df = search_and_summarize(keyword, limit=150)
print(f"Samples matching '{keyword}': {len(df)}")

if len(df) > 0:
    # Summarize by GEO series
    series_counts = df["series_id"].value_counts()
    print(f"\nTop GEO series (by sample count):")
    print(series_counts.head(8).to_string())

    # Export sample list
    df.to_csv(f"{keyword.replace(' ', '_')}_samples.csv", index=False)
    print(f"\nSaved {keyword.replace(' ', '_')}_samples.csv ({len(df)} samples)")
    print(f"Unique GEO series: {df['series_id'].nunique()}")

Key Parameters

Best Practices

1. Use z-score thresholds consistently: Because z-scores are gene-specific, a z-score of 2.0 for a ubiquitous gene (GAPDH) and a tissue-restricted gene (TTR, liver) have different interpretive meaning. Always annotate which gene you are comparing and the tissue background.

2. Sleep between batch queries: ARCHS4 enforces a soft rate limit of ~10 requests/second. Add time.sleep(0.1) between sequential gene queries to avoid 429 Too Many Requests errors.

3. Download HDF5 for large-scale analyses: For queries covering 50+ genes or requiring per-sample expression values, the REST API is impractical. Download the HDF5 file once and use h5py slicing for fast matrix access; this avoids hitting rate limits and is 100× faster for bulk extraction.

4. Match gene symbol conventions by species: Human queries require HGNC uppercase symbols (e.g., TP53); mouse queries require MGI-style symbols (e.g., Trp53). Using the wrong case returns empty results without an error.

5. Validate co-expression findings across datasets: ARCHS4 co-expression aggregates across all tissue types. A high correlation may be driven by a single tissue or study. Cross-check with tissue-specific queries or manually inspect the top contributing GEO series.

Common Recipes

Recipe: Quick Tissue Specificity Check

When to use: Rapidly determine whether a gene is broadly expressed (housekeeping) or tissue-restricted before designing experiments.

import requests

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

def tissue_specificity_summary(gene_symbol: str) -> None:
    """Print a summary of high and low expression tissues for a gene."""
    r = requests.get(
        f"{ARCHS4_BASE}/meta/genes/{gene_symbol}/zscore",
        params={"species": "human"},
        timeout=30
    )
    r.raise_for_status()
    records = r.json().get("values", [])
    zscores = [rec["zscore"] for rec in records if rec.get("zscore") is not None]
    top_high = sorted(records, key=lambda x: x.get("zscore", 0), reverse=True)[:5]
    top_low = sorted(records, key=lambda x: x.get("zscore", float("inf")))[:3]
    print(f"\n{gene_symbol} — {len(zscores)} tissues")
    print(f"  Range: [{min(zscores):.2f}, {max(zscores):.2f}]  "
          f"Mean: {sum(zscores)/len(zscores):.2f}")
    print("  High expression:")
    for t in top_high:
        print(f"    {t['tissue']:<35}  z={t['zscore']:.2f}")
    print("  Low expression:")
    for t in top_low:
        print(f"    {t['tissue']:<35}  z={t['zscore']:.2f}")

tissue_specificity_summary("TTR")   # Transthyretin — liver-specific

Recipe: Batch Gene Co-Expression Table

When to use: Generate a pairwise correlation table for a gene panel from a list of differentially expressed genes.

import requests, time
import pandas as pd

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

def batch_coexpr_table(gene_list: list, top_n: int = 10) -> pd.DataFrame:
    """For each gene in gene_list, return its top co-expressed genes."""
    rows = []
    for gene in gene_list:
        try:
            r = requests.get(
                f"{ARCHS4_BASE}/meta/genes/{gene}/correlations",
                params={"species": "human", "limit": top_n},
                timeout=30
            )
            r.raise_for_status()
            for rec in r.json().get("values", []):
                rows.append({
                    "query_gene": gene,
                    "coexp_gene": rec.get("gene"),
                    "correlation": rec.get("correlation"),
                })
            time.sleep(0.1)
        except Exception as e:
            print(f"Warning: {gene} skipped — {e}")
    return pd.DataFrame(rows)

deg_list = ["MYC", "CCND1", "CDK4", "RB1", "E2F1"]
coexp_table = batch_coexpr_table(deg_list, top_n=10)
print(f"Co-expression entries: {len(coexp_table)}")
print(coexp_table.groupby("query_gene")["coexp_gene"].count())
coexp_table.to_csv("deg_coexpression_table.csv", index=False)
print("Saved deg_coexpression_table.csv")

Recipe: Export Sample IDs for GEO Download

When to use: Identify relevant GEO accessions to download raw count matrices for a meta-analysis.

import requests
import pandas as pd

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

keyword = "glioblastoma"
r = requests.get(
    f"{ARCHS4_BASE}/samples/search",
    params={"query": keyword, "species": "human", "limit": 200},
    timeout=30
)
r.raise_for_status()
samples = pd.DataFrame(r.json().get("samples", []))
if len(samples) > 0:
    # Get unique GEO series accessions
    series = samples["series_id"].dropna().unique()
    print(f"Unique GEO series for '{keyword}': {len(series)}")
    for s in series[:10]:
        n = (samples["series_id"] == s).sum()
        print(f"  {s}  ({n} samples)")
    # Export series list for GEO download script
    pd.Series(series, name="geo_series").to_csv(
        f"{keyword}_geo_series.txt", index=False
    )
    print(f"\nSaved {keyword}_geo_series.txt")

Troubleshooting

Related Skills

• gnomad-database — Population variant frequencies; use after ARCHS4 to identify variants in highly expressed genes
• gget-genomic-databases — Enrichr pathway enrichment for ARCHS4 co-expression gene lists (gget enrichr)
• pydeseq2-differential-expression — Differential expression analysis on bulk RNA-seq; ARCHS4 HDF5 matrices can serve as reference cohorts

References

• ARCHS4 web portal — Interactive expression browser and dataset download
• ARCHS4 REST API documentation — Endpoint reference and parameters
• Lachmann et al., Nature Communications 2018 — ARCHS4 original publication describing uniform alignment pipeline
• ARCHS4 GitHub — Source code and HDF5 schema documentation