The Human Protein Atlas
A 20-year journey into the body
The Human Protein Atlas is a free, open-access database hosting over 10 million annotated images and associated information, including mass spectrometry-based proteomics, transcriptomics, and systems biology.
Scroll down to learn more about the human proteome and the Human Protein Atlas project. Take a journey into the body through 3D videos that transport you deep inside the brain, liver, and muscles.
Human beings consist of...
Proteins are responsible for...
Each cell contains...
Human beings consist of approximately 30 trillion (3x10¹³) cells
Proteins are responsible
for the majority of all biological functions, including:
Catalysis (enzymes)
Defense (immune proteins)
Structure
Signaling
Reproduction
Cell replication and renewal
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Each cell contains about 3 billion base pairs of DNA, only 1.1% of which represent the approximately 20,000 known protein-encoding genes
The Human Proteome
Building the Human Protein Atlas
Journey into the body
Additional resources
Acknowledgements
The Human Proteome
Building the Human Protein Atlas
Journey into the body
Additional resources
Acknowledgements
The Human Proteome
Exploring our proteome enables us to better understand health and disease.
Discoveries
Facts
HPA-generated discoveries
From the Human Protein Atlas program, we have learned that
10%
of proteins are “housekeeping” and thus needed in all dividing cells.
15%
of proteins are “specific” (tissue-enriched) and present in only one tissue.
13%
of proteins are in the human secretome, but only one-third of these are secreted into the blood.
~750
proteins are targets for pharmaceutical drugs on the market today.
~1,000
enzymes make up the proteins responsible for human metabolism.
unique proteins detected in testis (largest number in humans).
Many proteins are localized to several compartments in the cell.
The levels of many proteins in cancer cells may influence the survival of a patient.
The protein profiles in the brain of different mammalian species (mouse, pig, and human) show similarities, but there are many examples showing distinct differences.
HPA facts
Hundreds of thousands of researchers visit the Human Protein Atlas portal every month, making the database one of the most used biological databases in the world.
55,000+
antibodies generated in-house.
21,000
antibodies passed the stringent requirements of the HPA program for use in immunohistochemistry.
10+ million
tissue and cell images generated using this antibody resource.
70,000
analyses carried out on in-house generated microarrays to validate the antibodies.
Building the Human Protein Atlas
In 1996, the original concept for antibody-based proteomics was described by HPA researchers. Over the next two decades, the HPA database has helped the world visualize the important work of proteins.
Explore some of its biggest milestones
2000
2003
2005
2008
2010
2015
2016
2017
2018
2019
2020
The HPA pilot project is launched with the goal of analyzing all proteins encoded by chromosome 21.
2000
The HPA first receives funding from the Knut and Alice Wallenberg Foundation. Support has continued to the present day.
2003
The first version of the Human Protein Atlas portal is released. The portal has been updated annually.
2005
The Antibodypedia portal is launched to allow sharing of information on antibody validation. The portal now contains information on more than 4 million antibodies.
2008
A major milestone is reached: inclusion of 50% of human protein-coding genes in the atlas.
2010
The Tissue Atlas is launched, providing expression profiles of human tissues and organs. The article describing this atlas, published in the journal Science, has been cited thousands of times.
2015
The International Working Group for Antibody Validation (IWGAV), chaired by an HPA researcher, proposes guidance for reproducible validation of antibodies.
2016
The Subcellular Atlas (also called the HPA Cell Atlas) is published in Science, providing information on high-resolution spatial distribution of proteins within cells.
2017
The Pathology Atlas is released (Science), offering insights regarding the influence of protein expression on patient survival for 17 major cancer types. A new data visualization concept is described called “survival scatter plots.”
The HPA database of images is used for deep learning, utilizing a citizen-science approach involving 32 million image classifications based on input from more than 300,000 gamers.
2018
Analysis of the proteins secreted from human cells (the secretome) is published, including genome-wide annotation of the proteins that are predicted to be actively secreted into the blood.
The Blood Atlas published in Science, providing single-cell–level information on expression profiles in B cells, T cells, monocytes, granulocytes, and dendritic cells.
2019
Based on the HPA Cell Atlas image collection, a computational competition with 2,200 teams is organized to identify deep-learning solutions for classification of protein patterns.
Also in 2020, The Metabolic Atlas is published (Science Signaling), showing more than 120 manually curated metabolic pathway maps visualizing each individual protein's participation in different metabolic processes.
Additionally, the HPA consortium is engaged in various ways to support the fight against the coronavirus pandemic, including the development of diagnostics and therapeutic applications.
2020
The Brain Atlas released and published in Science, showing expression profiles in the different parts of the mammalian brain by comparing data from humans, pigs, and mice.
Journey into the body
3D movies were generated using resources from the HPA program to visualize different structures in mammalian tissue. Follow the links below to join our journey of discovery.
Use the hotspots to look
inside the body
Pancreas
The pancreas produces enzymes to facilitate the digestion of food. It is also responsible for regulating blood sugar levels through insulin. Malfunction in insulin production leads to diabetes. Insulin, shown in green, is stored in the pancreatic Islets of Langerhans. The nerve fibers (red) form a fine network dispersed throughout the whole pancreas, surrounding the blood vessels and the islets. The 3D image enables detailed investigation of the islets and nerves, their interaction, and detailed localization in space.
Heart
The heart provides our entire body with life-giving oxygen via the blood. It requires a constant supply of energy, delivered by the coronary artery network (red). The heart also harbors extensive networks of nerves (green), signaling to the heart muscle when to beat. Cardiovascular diseases are one of the leading causes of death worldwide. By studying the heart in 3D, we can learn more about the coronary artery and nerve fibers.
Nerves
The peripheral nervous system is immensely complex, with millions of nerves wired throughout the body. The nerves are vital for the processing of sensory input, giving us the ability to see, hear, feel, and function. Here, visualizing the nerves (white and red) provides detailed information on how they are organized. During embryonic development, nerves grow from cell bodies close to the spinal cord, extending to the skin and other organs such as the eyes, which include a large number of neurons. By understanding how the nervous system is formed and wired, we can untangle the secrets of many diseases.
Brain
The brain controls virtually everything required to be human. The primary signaling unit is the neuron, which sends messages via neurotransmitters and receptors. An example of an uncharacterized receptor, known as an orphan receptor, is shown in red. It has been detected exclusively in the thalamus of the brain. The brain also contains glial cells (green), such as astrocytes, which support the work of the neuronal cells, as well as protecting the brain at the blood-brain barrier. The blood vessels (red) and are a crucial part of the blood-brain barrier, which protects the brain from unwanted chemicals or infections. However, the blood-brain barrier also hinders drugs from entering the brain, making drug development for diseases inside the brain more difficult.
Muscles
The combined mass of all skeletal muscle makes it one of the largest organs in our body. Contraction of muscles is controlled by neurons. Nerve signals sent from the brain travel to the motor end plates, signaling muscle fibers to contract. The alpha neurons of the muscle, stained in blue, show the intricate network of nerves. In te case of amyotrophic lateral sclerosis, or ALS, the motor neurons start to degenerate, and when the signal is lost, the muscle fibers atrophy, leading to weakness and paralysis.
Liver
The liver produces biochemicals necessary for digestion and growth. We are inside one of the portal veins that run in parallel with the hepatic artery and the bile duct. Here, the blood flows from the intestine to the liver.
Journeys into human neurological diseases
When proteins don’t function properly, disease results. Follow these journeys into brain regions afflicted by various neurological diseases.
Alzheimer’s disease
Parkinson’s disease
Narcolepsy
Alzheimer’s disease
Alzheimer's disease is a chronic neurodegenerative disease that usually starts slowly and gradually worsens over time. Here we explore the early stage of the disease in the locus coeruleus, showing both healthy neurons as well as those with an accumulation of tau protein (red). Alzheimer’s disease has been identified as a protein-misfolding disease, caused by the accumulation of abnormally folded proteins that form plaques made up of amyloid beta peptide and tangles of tau protein. In the second part of the movie, we see the combination of tau (red) and amyloid plaques (green) in the cerebral cortex of the brain. Finally, we look at the amyloid plaques in detail, this time in red, together with neuronal cell bodies (green). The presence of vast amounts of amyloid plaques is evident in this Alzheimer’s patient.
Parkinson’s disease
Parkinson’s disease is a long-term degenerative disorder of the central nervous system that mainly affects the motor system. This disease involves the neurotransmitter dopamine, which is integral to the brain’s reward system and motor function. The dopamine neurons (green) degenerate during the disease and in the advanced stages eventually die.
Narcolepsy
We know that almost all parts of our brain are somehow involved in our sleep, but there is one peptide that is key: orexin. If orexin-producing cells die, and the switch mechanism between sleep and wakefulness is disabled, it will lead to the disease narcolepsy. Here, the part of the brain involved in narcolepsy is explored using 3D imaging. We can see how the cell projections have gone from the hypothalamus all the way down to the lower brainstem and work closely with the locus coeruleus neurons (red).
Additional Resources
We have created a free digital booklet that details the exciting two-decade journey of the Human Protein Atlas, from the chromosome 21 pilot in 2000 to the release of the latest data, The Metabolic Atlas, in 2020. Click the button to get your personal copy.
Download booklet
Digital booklet
HPA posters
Click on a poster to download it
In partnership with Science, HPA created four visually stunning educational posters about different aspects of the Human Protein Atlas. Flip through them here and click on the links to download a PDF copy.
The Tissue Atlas (2015)
The Cell Atlas (2017)
The Blood Atlas (2019)
The Brain Atlas (2019)
The HPA tutorial videos
A number of tutorial videos have been produced to show different aspects of the Human Protein Atlas and its content. These can be accessed at the HPA video channel.
Watch our tutorials
Acknowledgements
We acknowledge all of the HPA teams for their hard work during the 20 years since the start of the HPA effort. Special thanks to Dr. Csaba Adori for creating the 3D movies using light-sheet microscopy.
We are grateful to the Knut and Alice Wallenberg Foundation for being the main funder of the HPA program.
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Background and rotator images: © Mikael Wallerstedt
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