HPA 21 Launch Webinar

AI-based efforts facilitate the mapping of the human building-blocks

A new version of the open access Human Protein Atlas has been launched (version 22). Two new sections are introduced, both relying heavily on AI-based prediction modelling and machine learning. First, a new Human Disease Blood Atlas is launched using next generation blood profiling, initially aimed to facilitate research in the field of Cancer Prediction Medicine. Secondly, a new Structure resource section is launched using an AI-based prediction model (AlphaFold), to show the 3D structures for all human proteins. In addition, a major update of the Tissue Atlas section is released with detailed multiplex spatial profiling of proteins specific for single cell types in human testis or kidney. More data is also provided on single cell analysis of tissues and organs as well as data from an extensive catalogue of human cell lines.

The Human Protein Atlas consortium has today launched the version 22 of the open access resource for profiling of the human proteins (www.proteinatlas.org). The resource explores different aspects of all proteins and contains 12 major sections, including two new sections; the Disease Blood Atlas section and the Protein 3D Structure section. In addition, all 5 million web pages in this open access resource have been updated.

Disease Blood Atlas
This new section presents the result of a novel pan-cancer strategy to explore the proteome signature in blood from cancer patients. Plasma profiles of 1,463 proteins from more than 1,400 cancer patients representing 12 major cancer types were measured in minute amounts of blood plasma collected at the time of diagnosis and before treatment. Protein levels are based on analysis with proximity extension assay (Olink Explore) and targeted proteomics (mass spectrometry). We highlight proteins associated with each of the analyzed cancer types based on differential expression analysis as well as a machine-learning based disease prediction strategy. By combining the results from all cancer types, a panel of proteins suitable for the identification of individual cancer types based on a drop of blood is presented. Learn about in the new Disease Blood Atlas:
    • comprehensive and accurate protein levels in blood covering 12 different cancer types
    • the levels of proteins in blood using targeted proteomics and proximity extension assay
    • proteins associated with each of the analyzed cancers

Structure section
This new section presents the three-dimensional structures of all human proteins based on the prediction model developed by the AlphaFold algorithm. AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet (Google), which performs prediction of protein structures. The program is designed as a deep learning system. In addition, experimentally verified structures from the Protein Data Bank (PDB) are also visualized. The binding site for the various antibodies used in the Human Protein Atlas can also be visualized for the individual proteins. Additionally, the amino acid positions of population variants and variants with known clinical relevance in are shown. Learn about in the new Structure section:
    • the experimental and predicted 3D structure of human proteins
    • the known missense variants with clinical significance
    • the known missense variants in the population
    • the antigen structure for a majority of antibodies

Tissue Atlas section
The revised section has in this version implemented multiplex immunohistochemistry based on fluorescence high-resolution imaging, to study protein localization in single cell types of human testis or kidney. By combining deep annotation data and single-cell transcriptomics, three antibody panels have been developed to further characterize the spatial expression of proteins during testicular germ cell development (spermatogenesis), and highlight tubular and glomerular proteins in kidney. In the first version launched today, more than 500 protein targets have been analyzed in human testis or kidney. Learn about in the revised Tissue section:
    • in-depth protein localization in testis and kidney based on multiplex profiling
    • protein localization in tissues at a single-cell level
    • a catalogue of genes enriched in a particular tissue (specificity)
    • which genes have a similar expression profile across tissues (expression cluster)

Cell Line section
The revised section now includes genome-wide data covering more than 1000 human cell lines analyzed either "in-house" or by the Cancer Cell Line Encyclopedia (CCLE). The data allows for researchers to select best cell lines for a particular application based on similarity to cancers, the presence or absence of various biological pathways and/or the presence of immunological molecules (cytokines). Learn about in the revised Cell Line section:
    • a catalogue of genes enriched or lacking expression in a particular cell line (specificity)
    • which cell line has the most consistent expression profile to its corresponding cancer tissue
    • cancer-related pathway and cytokine activity of each cell line

Version 22 also contains a vast amount of new information within the various parts of the Human Protein Atlas, including revised summary pages for all human protein-coding genes and a new Methods Summary for the 12 sections with information how the data in each section have been generated, analyzed and visualized. The strategies for dimensionality reduction and density-based clustering of co-expression patterns have been extended to explore the gene expression landscape and we present Expression UMAP clustering of all protein-coding genes.

"We believe that the new sections of the open access Human Protein Atlas with large amounts of novel data covering all human proteins provide new dimensions of valuable information for researchers interested in human biology and disease", says Mathias Uhlén, Director of the Human Protein Atlas consortium. The work was funded by the Knut and Alice Wallenberg Foundation.
Press release (PDF) | News article

New version 21 of the Human Protein Atlas

A new version 21 of the open access Human Protein Atlas has been launched. A lot of new data and content have been added and the resource now includes 10 separate sections exploring the human proteins from different angels. All data has been updated on the approximately 15 million individual web pages.

A single cell type map of human tissues.

In a study published today in the US journal Science Advances, a single cell type map of human tissues is presented. An open access atlas has been launched with more than 250,000 interactive plots to allow researchers to explore the expression in individual single cell types for all protein-coding genes in these tissues.
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Towards a Cell Cycle Atlas

Today researchers within the Human Protein Atlas (HPA) publish a study of single-cell RNA and protein expression in relation to cell cycle progression in the journal of Nature. At the same time, the dataset is made publicly available as an integrated part of the Cell Atlas, providing a new resource for researchers around the globe to explore in the quest to further understand the human cell cycle and proliferative diseases such as cancer.
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A 20-year journey with the Human Protein Atlas

 20 years ago, the Human Protein Atlas initiative started and to celebrate this event, the journal Science has today published a booklet "The Human Protein Atlas - a 20-year journey into the body".
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New findings on enzymes with an important role for SARS-CoV-2 infection

Researchers within the Human Protein Atlas have described the presence of the enzyme ACE2 in the entire human body, which is suggested to be the key protein used by the SARS-CoV-2 virus for host cell entry and development of the disease COVID-19. In contrast to previous studies, the study shows that none or only very low levels of ACE2 protein is present in the normal respiratory system.
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HPA in the fight against Covid-19

The Human Protein Atlas (HPA) consortium is engaged in the corona epidemic in various ways to aid in the fight against the health consequences of this pandemic outbreak.
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What is the role of human protein ACE2 for SARS-CoV-2 infection of the human lung?

Today, an article was published in bioRxiv (Hikmet et al) describing the presence in the human body of the enzyme Angiotensin I converting enzyme 2 (ACE2), suggested to be the target for coronavirus attachment to the surface of human cells. The results raise questions regarding the role of ACE2 for infection of human lungs and highlights the need to further explore the route of transmission during SARS-CoV-2 infection.
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An atlas of human metabolism

Published today in the journal Science Signaling, Metabolic Atlas (metabolicatlas.org) enables exploration of the most extensive mapping of human metabolism to date. Biochemical information and connectivity for thousands of reactions, compounds, and genes comprising human metabolism is presented with over 150 manually curated 2D maps and automatically generated 3D networks.
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One step closer to understanding the human brain

Published today in the journal Science, the Brain Atlas resource is the latest database to be released by the Human Protein Atlas program, which is based at the Science for Life Laboratory (SciLifeLab).

The brain is the most complex organ of our body both in structure and function, and a dedicated brain atlas has therefore been created combining data from the human brain with corresponding information about the brain of pig and mouse.

Immune cell map arms researchers with new tool to fight deadly diseases

A first-ever map of the human body's immune cells has been created by scientists in Sweden, providing medical research with a detailed description of the proteins in human blood. The open-access database offers medical researchers an unprecedented resource in the search for treatments for diseases.
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Horizon Discovery partners with the Human Protein Atlas

Today it is announced that Horizon Discovery and the Human Protein Atlas have entered into partnership. The HPA Cell Atlas program will integrate Horizon's HAP1 cell line and has selected Horizon's CRISPR-edited knockout cell models to further expand the knowledge available in the Cell Atlas program.
Press release (PDF) | News article

The Human Secretome defined - a novel map of all proteins actively secreted to blood

Today, a novel map of all proteins secreted to human blood is described. The paper by Uhlen et al. entitled "The Human Secretome" is published in the journal Science Signaling and provides a first comprehensive annotation of all proteins secreted by the human cells. In addition, an analysis of the concentrations of the proteins circulating in the human blood is described. This map provides a unique resource to study human biology and diseases, in particular for immune-based research and efforts to develop new, effective treatments in oncology and autoimmune diseases.
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The Human Blood Atlas launched - a resource for exploration of blood cells and proteins

A new Blood Atlas has been launched, as part of the open access Human Protein Atlas, in which the proteins in human blood cell types are described together with a comprehensive analysis of all proteins predicted to be secreted from human cells ("the secretome"). The new atlas provides a unique resource for the study of human biology and diseases, in particular for immune-based research and efforts to develop new, effective treatments in oncology and autoimmune diseases.
Press release (PDF) | News article

A new Brain Atlas launched to allow the exploration of proteins in the different regions of the brain

Today, as part of the Human Protein Atlas program, a new Brain Atlas is launched showing for the first time an integrated view of the proteins located to the different regions of the human, mouse and pig brain. The regional expression in these three mammalian brains have been profiled and the analysis includes 1,710 human brain samples, 119 pig brain samples and 67 mouse brain samples. The new database provides many insights of biological relevance for human brain biology and disease.
Press release (PDF) | News article

A new Metabolic Atlas launched to explore human metabolism

A new Metabolic Atlas has been launched as part of the open access Human Protein Atlas program (www.proteinatlas.org/metabolic), allowing researchers to explore the expression of biochemical pathways across human tissues. The new resource leverages the most extensive mapping of human metabolism to date, with biochemical information and connectivity for more than 13,000 reactions, 4,000 unique compounds, and 3,500 genes.
Press release (PDF) | News article

New version of the Human Protein Atlas launched with a focus on validation of antibodies

A new version of the Human Protein Atlas is launched today implementing the strategy for enhanced validation of antibodies suggested by the International Working Group for Antibody Validation (IWGAV). More than 10,540 antibodies directed to a total of 6,787 human protein targets have passed the criteria of enhanced validation.
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Chan Zuckerberg Initiative teams up with Swedish researchers to map all cells in human body

The Human Protein Atlas and Cell Atlas projects at KTH Royal Institute of Technology's Science for Life Laboratory (SciLifeLab) are teaming up with the Chan Zuckerberg Initiative to strengthen research in cell biology and proteomics.
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New Pathology Atlas maps the genes involved in cancer to accelerate progress in personalized cancer medicine

A new Pathology Atlas is launched today with an analysis of all human genes in all major cancers showing the consequence of their corresponding protein levels for overall patient survival. The difference in expression patterns of individual cancers observed in the study strongly reinforces the need for personalized cancer treatment based on precision medicine. In addition, the systems level approach used to construct the Pathology Atlas demonstrates the power of "big data" to change how medical research is performed.
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The Human Protein Atlas selected as European core resource in life science by ELIXIR

Today, the organization ELIXIR selected the Human Protein Atlas (HPA) as a European core resource in life science. HPA was selected for its fundamental importance to the wider life-science community and as an important international resource of biological data. The Human Protein Atlas contains information for a large majority of all human protein-coding genes, including a Tissue Atlas showing the location of the proteins in human tissues and organs and a Cell Atlas showing the subcellular location in human cells at the single cell level.
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The Human Cell Atlas selected as one of ten emerging technologies to make a change to society

This week, Scientific American announced ten emerging technologies with innovations that are on the verge of changing society. One of the technologies selected was the Human Cell Atlas, which aims to integrate research exploring the building-blocks of human cells using new emerging technologies. One of the projects underlying the Human Cell Atlas is the Human Protein Atlas with the ultimate aim to provide a spatial map of all human proteins using a combination of "big data technologies".
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The first comprehensive map of the subcellular localization of human proteins reveals new insights in human biology

The first analysis of how proteins are arranged in a cell was published today in Science, revealing that a large portion of human proteins can be found in more than one location in a given cell.
Press release (PDF)

HPA 16 - The Cell Atlas Launched At 2016 ASCB Meeting

After the completion of the human genome in 2001, another major milestone was reached with the launch of the Cell Atlas at the 2016 American Society of Cell Biology Meeting. An open-access interactive database with unparalleled high-resolution images, the Cell Atlas visualizes for the first time the location of over 12,000 proteins in cells opening the way to "spatial proteomics", an exciting new discipline predicted to lead to a fundamental increase in our understanding of human health and disease.
Press release (PDF) | News article

Important link between genomics and proteomics

Several previous reports have concluded that RNA levels cannot be used to predict protein levels. However, in a new study from KTH Royal Institute of Technology published in the journal Molecular Systems Biology, scientists show that protein levels can be predicted from RNA levels if a gene-specific RNA-to-protein factor is used.
Press release (PDF)

HPA 15 - New version of the human proteins atlas with extensive transcriptomics data

Today, the Human Protein Atlas consortium launched version 15 of the database including extensive transcriptomics data and a new display view to allow comparisons of human tissue profiles on both the RNA and protein level. The launch is accompanied with an article in Molecular Systems Biology describing transcriptome resources with a focus on the comparison between the datasets generated from the Broad Institute, Boston, US (GTEx) and the Human Protein Atlas consortium at Science for Life Laboratory, Sweden.
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HPA 14 - New version of the human proteins atlas

The Human Protein Atlas today launched a new version of the database. The major new additions to version 14 are a new Mouse Brain Atlas and a new approach for antibody validation.
Press release (PDF) | News article

HPA 13 - Launch of the tissue-based map of the human proteins

A decade after the completion of the human genome, the Human Protein Atlas program today launched a tissue-based atlas covering the protein complement of the human genome. Based on 13 million annotated images, an interactive database has been created to show the distribution of proteins in all major tissues and organs in the human body.
Press release broadcasted live on Nov 6, 2014 at 3 p.m. CET
Press release (PDF)