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 |
24 |
2024 |
The 12 sections have been reorganized into 8 resource with ample new data, including the launch of a Pan-Disease Blood Atlas and spatial transcriptomics data. |
Significant milestones
Below, the 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.
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 hpajourney.proteinatlas.org has been produced to show some of HPA's highlights.