Human Protein Atlas

Human Protein Atlas
Name	Human Protein Atlas
Type	Research resource
Established	2003
Founder	Knut and Alice Wallenberg Foundation
Headquarters	Stockholm

Human Protein Atlas is a large-scale proteomics project mapping protein expression and localization across human tissues, cells, and organs. It integrates data from antibody-based imaging, transcriptomics, and mass spectrometry to produce an open-access resource used in biomedical research, clinical studies, and drug discovery. The project links to global initiatives and institutions and contributes to standards in proteomics, histology, and bioinformatics.

Overview

The project provides annotated protein expression profiles for human genes, linking proteomic observations to resources such as Ensembl, UniProt, GenBank, European Bioinformatics Institute, and National Center for Biotechnology Information. Databases and portals interoperate with platforms like ProteomeXchange, PRIDE Archive, ArrayExpress, Gene Ontology annotations, and KEGG pathway maps. The resource is widely cited in publications from institutions including Karolinska Institutet, University of Cambridge, Harvard University, Massachusetts Institute of Technology, and Stanford University.

History and development

The initiative began in the early 2000s with funding from organizations such as the Knut and Alice Wallenberg Foundation and partnerships with universities and research institutes including Uppsala University, Karolinska Institutet, and industrial collaborators like AbbVie and Pfizer. Early methodological developments drew on technologies developed at places such as European Molecular Biology Laboratory, Cold Spring Harbor Laboratory, and Broad Institute. Milestones include integration of antibody profiling with transcriptomics influenced by consortia like the ENCODE Project and the 1000 Genomes Project, and later expansion aligning with efforts by Human Cell Atlas and International Cancer Genome Consortium.

Data and methodology

Data modalities include immunohistochemistry, immunofluorescence, RNA sequencing, and mass spectrometry. Protocols reference guidelines from World Health Organization laboratories, standards promoted by Human Proteome Organization, and quality frameworks used by Clinical Laboratory Improvement Amendments-compliant facilities. Antibody validation strategies build on practices from European Medicines Agency submissions and are cross-referenced with antibody registries maintained by Thermo Fisher Scientific and Abcam. Computational pipelines integrate tools developed at European Bioinformatics Institute, Wellcome Sanger Institute, and software from EMBL-EBI collaborators for image analysis and expression quantification.

Main components and resources

The resource consists of tissue atlases, cell atlases, subcellular localization data, pathology atlases, and blood protein maps. Tissue and cell datasets are linked to specimen sources such as Karolinska University Hospital and tissue banks affiliated with Uppsala University Hospital and Sahlgrenska University Hospital. Subcellular localization draws on microscopy platforms from Zeiss, Leica Microsystems, and imaging centers at University of Oxford. Pathology integrations reference standards from American Society of Clinical Oncology and diagnostic criteria from World Health Organization tumor classifications. Proteomics outputs are deposited to repositories like PRIDE Archive and cross-referenced with identifiers from UniProt and Ensembl.

Applications and impact

Researchers use the resource to prioritize targets in translational projects at pharmaceutical companies such as AstraZeneca, Novartis, Roche, and GlaxoSmithKline. Clinicians and pathologists from Mayo Clinic, Cleveland Clinic, and Johns Hopkins Hospital have applied the atlases in biomarker discovery and diagnostic validation. The project informs cancer research linked to The Cancer Genome Atlas analyses, immunology studies collaborating with groups at National Institutes of Health, and single-cell biology aligning with the Human Cell Atlas. Educational uses include integration into curricula at Karolinska Institutet, Uppsala University, University of Cambridge, and workshops organized with European Molecular Biology Organization.

Governance, funding, and collaborations

Governance and oversight involve academic leadership from laboratories at KTH Royal Institute of Technology, Karolinska Institutet, and institutional partners such as Uppsala University. Major funding sources include the Knut and Alice Wallenberg Foundation, national research councils like the Swedish Research Council, and collaborative grants with agencies including the European Commission and foundations such as the Bill & Melinda Gates Foundation. International collaborations bring together consortia including Human Cell Atlas, Human Proteome Organization, and partnerships with repositories at European Bioinformatics Institute and National Center for Biotechnology Information.

Category:Proteomics Category:Biological databases