The Human Protein Atlas background and history

The Human Protein Atlas (HPA) journey started in 2000, the same year as the announcement of the completion of the Human Genome Project. In 2003, the program received generous support from the Knut and Alice Wallenberg Foundation (KAW), and the program was changed to an exclusively academic endeavor. The aim of the program has been to map the human proteins in cells, tissues, organs and blood, using integration of various 'omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, proximity extension assay (PEA)-based protein profiling and systems biology.

Primarily based in Sweden, the Human Protein Atlas project involves the joint efforts of the Royal Institute of Technology in Stockholm, Uppsala University, Uppsala Akademiska University Hospital, and more recently also Science for Life Laboratory based in both Uppsala and Stockholm. Formal collaborations are with groups in India, South Korea, Japan, China, Germany, France, Switzerland, USA, Canada, Denmark, Finland, The Netherlands, Spain, and Italy.

The first version of the Human Protein Atlas website was launched in 2005 and consisted of protein expression data based on approximately 700 antibodies. Since then, each new release has included more data and new functionalities and features to the website.

Important additions include:

Version Year released Feature
1 2005 The launch of the Human Protein Atlas. 700 antibodies.
2 2006 Inclusion of cell-line data and confocal images showing subcellular localizations.
3 2007 A new search function that allowed advanced query based searches was included.
4 2008 The overall database structure was shifted from a previously antibody-centric structure, to a gene-centric structure in order to include information on all genes predicted by Ensembl.
7 2010 A major restructure accompanying the introduction of the concept of annotated protein expression for paired antibodies (two independent antibodies directed against different, non-overlapping epitopes on the same protein).
12 2013 The protein atlas database was complemented with transcriptomics profiles from 27 normal tissues, and the format with four sub-atlases was introduced.
13 2014 An analysis of all major organ and tissues in the human body using transcriptomics and antibody-based profiling was included. The results were summarized on interactive knowledge-pages divided into 7 human proteomes and 27 tissues and organs.
14 2015 A new mouse brain atlas was introduced.
15 2016 Inclusion of RNA-seq data from the Genotype-Tissue Expression (GTEx) consortium.
16 2016 A new Cell Atlas was launched with subcellular localization corresponding to over 12,000 protein-coding genes, together with a new approach for visualization of antibody validation and the inclusion of transcriptomics data from the FANTOM5 program.
17 2017 The Pathology Atlas was launched, where a systems-level approach based on genome-wide transcriptomics data and clinical meta data of almost 8000 patients was used in order to analyze the proteome of 17 major cancer types.
19 2019 Three new Atlases were introduced; a Blood Atlas, a Brain Atlas and a Metabolic Atlas.
21 2021 The resource now includes 10 separate sections including the new additions Single Cell Type, Tissue Cell Type and Cell line.
22 2022 Two new sections were introduced; the Structure section and the Disease Blood Atlas section
23 2023 The Interaction section was introduced. It was built on the former Metabolic section and includes protein-protein interaction networks as well as metabolic networks

A 20-year journey into the body

In an expansive supplement published by Science, a journey is taken through the 20 years since the establishment of the Human Protein Atlas (HPA) consortium, to underscore milestones reached and to celebrate releases of updates and additions to the atlas. For the reader’s convenience, reprints of the relevant journal articles associated with the most important of these milestones are provided. You can download the pdf version here.

Together with Science, the microsite has been produced to show some of HPA's hightlighs.

Below, the 39 most significant milestones in the history of the HPA consortium are outlined. Click on any milestone and read about key facts and publications related to each milestone.

Scientific Milestones
Year No Title Year No Title
1985 1 Affinity tags for protein purification 2015 21 The Tissue Atlas
1989 2 Solid phase sequencing 2016 22 Correlation of RNA and protein levels
1993 3 Next generation sequencing 2016 23 Human secretome resource
1996 4 First concept of antibody-based proteomics 2016 24 Antibody validation
2000 5 The Human Genome Project 2017 25 The Subcellular Atlas
2000 6 Chromosome 21 pilot 2017 26 The Pathology Atlas
2003 7 Start of the Human Protein Atlas program 2017 27 Systems medicine
2004 8 Tissue microarrays 2018 28 Wellness profiling and precision medicine
2004 9 The HPA data management system 2018 29 Deep learning and citizen science
2005 10 Launch of the Human Protein Atlas portal 2019 30 Human secretome annotation
2006 11 Creation of an antibody resource 2019 31 The Blood Atlas
2007 12 Protein arrays 2019 32 The HPA Kaggle Challenge
2008 13 Web-based pathology annotation 2020 33 The Brain Atlas
2008 14 Epitope mapping of antibodies 2020 34 The Metabolic Atlas
2008 15 Antibodypedia antibody portal 2020 35 The fight against the novel coronavirus
2009 16 Antibody-based biomarker discovery 2021 36 The Single Cell Type Atlas
2010 17 Knowledge-based portal 2022 37 The Disease Blood Atlas
2011 18 Therapeutic antibodies and Affibodies 2022 38 Protein 3D structures
2012 19 Targeted proteomics 2023 39 Interaction section
2014 20 Integration of RNA and protein profiles