name: Expression Atlas
description: Expression Atlas is EMBL-EBI's open science resource that provides information about gene and protein expression across species and biological conditions. It aggregates, processes, and visualizes gene expression data from thousands of manually curated experiments spanning multiple species, tissue types, developmental stages, diseases, and experimental perturbations. Both bulk RNA-sequencing and single-cell RNA-sequencing datasets are supported, offering baseline expression profiles and differential gene expression analysis results through standardized processing pipelines.
contacts: []
products: [{"category": "GraphicalInterface", "description": "Main web portal for searching and exploring gene expression data across species, tissues, and experimental conditions with interactive heatmaps and visualizations", "format": "http", "id": "expressionatlas.portal", "name": "Expression Atlas Portal", "product_url": "https://www.ebi.ac.uk/gxa/home"}, {"category": "GraphicalInterface", "description": "Single Cell Expression Atlas portal for exploring single-cell RNA-seq data with interactive t-SNE/UMAP plots, cell type annotations, and marker gene analysis", "format": "http", "id": "expressionatlas.single-cell", "name": "Single Cell Expression Atlas", "product_url": "https://www.ebi.ac.uk/gxa/sc"}, {"category": "ProgrammingInterface", "description": "REST API for programmatic access to expression data, experiment metadata, and differential expression results", "format": "http", "id": "expressionatlas.api", "name": "Expression Atlas REST API", "product_url": "https://www.ebi.ac.uk/gxa/help/api.html"}, {"category": "Product", "description": "FTP archive containing processed expression data files, experiment metadata, and analysis results for bulk RNA-seq experiments", "format": "http", "id": "expressionatlas.ftp-bulk", "name": "Expression Atlas FTP (Bulk Data)", "product_url": "https://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/"}, {"category": "Product", "description": "FTP archive containing single-cell RNA-seq processed data, cell metadata, and clustering results", "format": "http", "id": "expressionatlas.ftp-single-cell", "name": "Expression Atlas FTP (Single Cell Data)", "product_url": "https://ftp.ebi.ac.uk/pub/databases/single-cell/", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-10-15_ HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 404 error when accessing file"]}, {"category": "Product", "description": "Individual experiment data downloads in TSV format containing expression matrices and statistical results", "format": "tsv", "id": "expressionatlas.experiment-downloads", "name": "Expression Atlas Experiment Downloads", "product_url": "https://www.ebi.ac.uk/gxa/download"}, {"category": "Product", "description": "Normalized gene expression data and raw count matrices in R data object format for computational analysis", "format": "mixed", "id": "expressionatlas.r-objects", "name": "Expression Atlas R Data Objects", "product_url": "https://www.ebi.ac.uk/gxa/help/r-data-objects.html", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 500 error when accessing file", "File was not able to be retrieved when checked on 2025-10-15_ HTTP 500 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 500 error when accessing file"]}, {"category": "Product", "description": "Baseline expression summary data across human tissues and cell types from GTEx, Human Protein Atlas and other major studies", "format": "tsv", "id": "expressionatlas.baseline-summary", "name": "Expression Atlas Baseline Summary", "product_url": "https://www.ebi.ac.uk/gxa/baseline/experiments"}, {"category": "Product", "description": "Differential gene expression results across diseases, perturbations, and comparative studies with statistical significance metrics", "format": "tsv", "id": "expressionatlas.differential-results", "name": "Expression Atlas Differential Results", "product_url": "https://www.ebi.ac.uk/gxa/experiments?experimentType=differential"}, {"category": "DocumentationProduct", "description": "Comprehensive help documentation covering data access, analysis methods, API usage, and interpretation guidelines", "format": "http", "id": "expressionatlas.documentation", "name": "Expression Atlas Help Documentation", "product_url": "https://www.ebi.ac.uk/gxa/help/index.html"}, {"category": "GraphicalInterface", "description": "Web portal for searching and browsing ncRNA sequences, structures, and annotations", "format": "http", "id": "rnacentral.portal", "name": "RNAcentral Portal", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/"}, {"category": "ProgrammingInterface", "description": "REST API for programmatic access to RNAcentral data", "format": "http", "id": "rnacentral.api", "name": "RNAcentral REST API", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/api"}, {"category": "Product", "description": "FTP archive with current and archived release files (sequences and annotations)", "format": "http", "id": "rnacentral.ftp", "name": "RNAcentral FTP Archive", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://ftp.ebi.ac.uk/pub/databases/RNAcentral"}, {"category": "DataModelProduct", "description": "Public PostgreSQL database for direct SQL access to RNAcentral data", "format": "postgres", "id": "rnacentral.public-db", "name": "RNAcentral Public Postgres Database", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/help/public-database"}]
raw_data: {"activity_status": "active", "category": "Aggregator", "creation_date": "2025-09-09T00:00:00Z", "description": "Expression Atlas is EMBL-EBI's open science resource that provides information about gene and protein expression across species and biological conditions. It aggregates, processes, and visualizes gene expression data from thousands of manually curated experiments spanning multiple species, tissue types, developmental stages, diseases, and experimental perturbations. Both bulk RNA-sequencing and single-cell RNA-sequencing datasets are supported, offering baseline expression profiles and differential gene expression analysis results through standardized processing pipelines.", "domains": ["genomics", "biological systems", "organisms"], "homepage_url": "https://www.ebi.ac.uk/gxa/home", "id": "expressionatlas", "last_modified_date": "2025-10-09T00:00:00Z", "layout": "resource_detail", "license": {"id": "https://creativecommons.org/licenses/by/4.0/", "label": "CC-BY-4.0", "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png"}, "name": "Expression Atlas", "products": [{"category": "GraphicalInterface", "description": "Main web portal for searching and exploring gene expression data across species, tissues, and experimental conditions with interactive heatmaps and visualizations", "format": "http", "id": "expressionatlas.portal", "name": "Expression Atlas Portal", "product_url": "https://www.ebi.ac.uk/gxa/home"}, {"category": "GraphicalInterface", "description": "Single Cell Expression Atlas portal for exploring single-cell RNA-seq data with interactive t-SNE/UMAP plots, cell type annotations, and marker gene analysis", "format": "http", "id": "expressionatlas.single-cell", "name": "Single Cell Expression Atlas", "product_url": "https://www.ebi.ac.uk/gxa/sc"}, {"category": "ProgrammingInterface", "description": "REST API for programmatic access to expression data, experiment metadata, and differential expression results", "format": "http", "id": "expressionatlas.api", "name": "Expression Atlas REST API", "product_url": "https://www.ebi.ac.uk/gxa/help/api.html"}, {"category": "Product", "description": "FTP archive containing processed expression data files, experiment metadata, and analysis results for bulk RNA-seq experiments", "format": "http", "id": "expressionatlas.ftp-bulk", "name": "Expression Atlas FTP (Bulk Data)", "product_url": "https://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/"}, {"category": "Product", "description": "FTP archive containing single-cell RNA-seq processed data, cell metadata, and clustering results", "format": "http", "id": "expressionatlas.ftp-single-cell", "name": "Expression Atlas FTP (Single Cell Data)", "product_url": "https://ftp.ebi.ac.uk/pub/databases/single-cell/", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-10-15_ HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 404 error when accessing file"]}, {"category": "Product", "description": "Individual experiment data downloads in TSV format containing expression matrices and statistical results", "format": "tsv", "id": "expressionatlas.experiment-downloads", "name": "Expression Atlas Experiment Downloads", "product_url": "https://www.ebi.ac.uk/gxa/download"}, {"category": "Product", "description": "Normalized gene expression data and raw count matrices in R data object format for computational analysis", "format": "mixed", "id": "expressionatlas.r-objects", "name": "Expression Atlas R Data Objects", "product_url": "https://www.ebi.ac.uk/gxa/help/r-data-objects.html", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 500 error when accessing file", "File was not able to be retrieved when checked on 2025-10-15_ HTTP 500 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 500 error when accessing file"]}, {"category": "Product", "description": "Baseline expression summary data across human tissues and cell types from GTEx, Human Protein Atlas and other major studies", "format": "tsv", "id": "expressionatlas.baseline-summary", "name": "Expression Atlas Baseline Summary", "product_url": "https://www.ebi.ac.uk/gxa/baseline/experiments"}, {"category": "Product", "description": "Differential gene expression results across diseases, perturbations, and comparative studies with statistical significance metrics", "format": "tsv", "id": "expressionatlas.differential-results", "name": "Expression Atlas Differential Results", "product_url": "https://www.ebi.ac.uk/gxa/experiments?experimentType=differential"}, {"category": "DocumentationProduct", "description": "Comprehensive help documentation covering data access, analysis methods, API usage, and interpretation guidelines", "format": "http", "id": "expressionatlas.documentation", "name": "Expression Atlas Help Documentation", "product_url": "https://www.ebi.ac.uk/gxa/help/index.html"}, {"category": "GraphicalInterface", "description": "Web portal for searching and browsing ncRNA sequences, structures, and annotations", "format": "http", "id": "rnacentral.portal", "name": "RNAcentral Portal", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/"}, {"category": "ProgrammingInterface", "description": "REST API for programmatic access to RNAcentral data", "format": "http", "id": "rnacentral.api", "name": "RNAcentral REST API", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/api"}, {"category": "Product", "description": "FTP archive with current and archived release files (sequences and annotations)", "format": "http", "id": "rnacentral.ftp", "name": "RNAcentral FTP Archive", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://ftp.ebi.ac.uk/pub/databases/RNAcentral"}, {"category": "DataModelProduct", "description": "Public PostgreSQL database for direct SQL access to RNAcentral data", "format": "postgres", "id": "rnacentral.public-db", "name": "RNAcentral Public Postgres Database", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/help/public-database"}], "publications": [{"authors": ["Nancy George", "Silvie Fexova", "Alfonso Munoz Fuentes", "Pedro Madrigal", "Yalan Bi", "Haider Iqbal", "Upendra Kumbham", "Nadja Francesca Nolte", "Lingyun Zhao", "Anil S Thanki", "Iris D Yu", "Jose C Marugan Calles", "Karoly Erdos", "Liora Vilmovsky", "Sandeep R Kurri", "Anna Vathrakokoili-Pournara", "David Osumi-Sutherland", "Ananth Prakash", "Shengbo Wang", "Marcela K Tello-Ruiz", "Sunita Kumari", "Doreen Ware", "Damien Goutte-Gattat", "Yanhui Hu", "Nick Brown", "Norbert Perrimon", "Juan Antonio Vizca\u00edno", "Tony Burdett", "Sarah Teichmann", "Alvis Brazma", "Irene Papatheodorou"], "doi": "10.1093/nar/gkad1021", "id": "https://doi.org/10.1093/nar/gkad1021", "journal": "Nucleic Acids Research", "preferred": true, "title": "Expression Atlas update: insights from sequencing data at both bulk and single cell level", "year": "2024"}, {"authors": ["Irene Papatheodorou", "Nancy George", "Silvie Fexova", "Alfonso Munoz-Fuentes", "Pedro Madrigal", "Haider Iqbal", "Upendra Kumbham", "Nadja F Nolte", "Lingyun Zhao", "Anil S Thanki", "David Osumi-Sutherland", "Ananth Prakash", "Shengbo Wang", "Marcela K Tello-Ruiz", "Sunita Kumari", "Doreen Ware", "Juan Antonio Vizca\u00edno", "Tony Burdett", "Sarah A Teichmann", "Alvis Brazma"], "doi": "10.1093/nar/gkz947", "id": "https://doi.org/10.1093/nar/gkz947", "journal": "Nucleic Acids Research", "title": "Expression Atlas update: from tissues to single cells", "year": "2020"}], "repository": "https://github.com/ebi-gene-expression-group"}