First major analysis of Human Protein Atlas published

27 January 2015

An image of dyed proteins from the Human Protein Atlas.

An image of dyed proteins from the Human Protein Atlas.

A research article published today in Science presents the first major analysis based on the Human Protein Atlas, including a detailed picture of the proteins that are linked to cancer, the number of proteins present in the bloodstream, and the targets for all approved drugs on the market.

The Human Protein Atlas, a major multinational research project supported by the Knut and Alice Wallenberg Foundation, recently launched an open source tissue-based interactive map of the human proteins. Based on 13 million annotated images, the database maps the distribution of proteins in all major tissues and organs in the human body, showing both proteins restricted to certain tissues, such as the brain, heart, or liver, and those present in all. As an open access resource, it is expected to help drive the development of new diagnostics and drugs, but also to provide basic insights in normal human biology.

In the Science article, ‘Tissue-based Atlas of the Human Proteome’, the approximately 20,000 protein-coding genes in humans have been analysed and classified using a combination of genomics, transcriptomics, proteomics, and antibody-based profiling.

‘This has been an incredible team effort where researchers with different backgrounds and knowledge have contributed to continuously moving the project in the right direction. I'm especially pleased that pathology has become the focal point, and that we have been able to collaborate around and use the clinical pathology resources available’, says Professor Fredrik Pontén at Uppsala University’s Department of Immunology, Genetics and Pathology.

The analysis shows that almost half of the protein-coding genes are expressed in a ubiquitous manner and thus found in all analysed tissues.

Approximately 15 per cent of the genes show an enriched expression in one or several tissues or organs, including well-known tissue-specific proteins, such as insulin and troponin. The testes, or testicles, have the most tissue-enriched proteins followed by the brain and the liver.

The analysis suggests that approximately 3,000 proteins are secreted from the cells and an additional 5,500 proteins are located to the membrane systems of the cells.

‘This is important information for the pharmaceutical industry. We show that 70 per cent of the current targets for approved pharmaceutical drugs are either secreted or membrane-bound proteins’, says the article’s lead author, Mathias Uhlén, professor of microbiology at the Royal Institute of Technology and director of the Human Protein Atlas program. ‘Interestingly, 30 per cent of these protein targets are found in all analysed tissues and organs. This could help explain some side effects of drugs and thus might have consequences for future drug development.’

The analysis also contains a study of the metabolic reactions occurring in different parts of the human body. The most specialised organ is the liver with a large number of chemical reactions not found in other parts of the human body.

More information, including a copy of the paper, can be found online at the Science press package at You will need your user ID and password to access this information.

The study has been carried out by researchers in Sweden at Uppsala University, the Royal Institute of Technology, Karolinska Institutet, Chalmers University of Technology, Lund University, and Stockholm University.

Full article: Tissue-based map of the human proteome