HPA 22 Launch Webinar

A new version 24 of the open access Human Protein Atlas resource has been released at the HUPO meeting in Dresden, Germany

A new version of the open access Human Protein Atlas has been launched (version 24) including many new features. The data is summarized in eight resources harboring information about all human protein-coding genes. Altogether 5 million web pages and over 10 million manually annotated high-resolution bioimages are presented, including 16 knowledge summaries in which various aspects of the human proteome is reported. A new Blood Disease Atlas containing open access next generation blood profiling data from 59 diseases, including patients with cancers, autoimmune, infectious, neurobiology and cardiovascular diseases is launched. New features include multiplex profiling of human tissues and a new section presenting spatial transcriptomics of the human brain (cerebral cortex). AlphaFold source code has been used to predict the 3D structures of more than 80,000 protein isoforms and variant data from AlphaMissense has been integrated. In the Interaction resource the protein interaction data from the IntAct database has now been complemented with data from BioGRID, Bioplex and OpenCell. 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 24 of the open access resource for profiling of the human proteins (www.proteinatlas.org). The resource explores different aspects of all proteins and contains eight major resources

The Blood resource

This new resource combines the data from the former Blood and Disease sections together with extensive novel information on blood profiles in patients with various diseases. The resource presents the result of a novel pan-disease approach to explore the proteome signatures in blood in patients from various major disease areas (Autoimmune, Infection, Metabolic, Cardiovascular, Psychiatric, and Pediatric). Plasma profiles of 1162 proteins, from more than 6,121 patients representing 59 diseases, were measured in minute amounts of blood plasma collected at the time of diagnosis and most often before treatment. Protein levels are based on analysis with proximity extension assay (Olink Explore) and targeted proteomics with spike in of stable isotope labeled standards (mass spectrometry). Based on differential expression analysis, we highlight proteins associated with each disease type analyzed. By combining the results from all cancer types, a panel of proteins suitable for identifying individual cancer types based on a drop of blood is presented.

Learn about:
• comprehensive and accurate protein levels in blood covering patients from 59 diseases
• the levels of proteins in blood using targeted proteomics and proximity extension assays
• proteins associated with elevated levels for each of the analyzed diseases

The Brain resource

The Brain resource is dedicated to the central nervous system with a focus on comparison between regions and cell-types of the brain. Over the years the Brain resource has increased completeness by providing the most extended overview of protein expression in 200 micro-dissected areas of the brain based on bulk RNA-sequencing data. In the current version, the first high-resolution spatial transcriptomics data of the human cerebral cortex is launched. With a capture resolution of 0.5 micrometer, a both cellular and spatial information on protein expression is provided for the first time, using tools to quantify, impute and visualize protein expression in the human cerebral cortex.

Learn about:
• proteins expression in different regions of the brain
• protein expression in different cell-types of the human cerebral cortex
• single cell analysis of cortex using spatial transcriptomics

The Subcellular resource

The Subcellular resource has in this version launched a major update in terms of a Cilia Atlas. The proteome and its subcellular organization have been systematically mapped in primary cilia across different cell lines, and in the flagellum of human sperm. With the help of high-throughput immunofluorescence imaging, we have been able to identify hundreds of proteins localized to these compartments and subcompartment localization.

The primary cilium, an antenna-like organelle with sensory capabilities, extending as a solitary unit from the surface of nearly all vertebrate cell types. We have identified 653 proteins within the primary cilium and its substructures. Intriguingly, the primary cilium stands out for exhibiting the highest degree of proteome heterogeneity among subcellular structures and organelles. This heterogeneity manifests in multiple features including cell type heterogeneity, single-cell heterogeneity, and multi-localization, indicating the fundamental role of the primary cilium in receiving and conveying cell-specific signals.

The sperm cell is the male reproductive cell, highly specialized in motility and fertilization of the female egg. To achieve this, sperm cells contain several unique subcellular structures, including a long motile cilium called the flagellum, promoting high motility and aiding egg penetration, and a sac containing enzymes crucial for penetrating the egg called the acrosome. We have identified 645 proteins to localize to specific substructures of the human sperm cell. Interestingly, we observe extensive single-cell heterogeneity for these proteins underscoring the importance of functional diversity within a sperm population.

Learn about:
• proteins localized to the primary cilia
• proteins localized to the flagellum and other sperm-specific subcellular compartments
• single-cell heterogeneity of the metabolic proteome

The Single cell resource

The new Single Cell Resource consolidates the previously separate sections-Single Cell Type, Tissue Cell Type, and Immune Cell-into a unified structure. Additionally, it now includes Single Nuclei Brain data, representing expression profiles of 2.5 million brain cells. This resource offers a comprehensive single-cell overview of all protein-coding genes. The Tissue Cell Type dataset has been expanded to include new cell type enrichment data for the spleen, salivary glands, adrenal glands, and pituitary gland. Furthermore, the resource now incorporates external cluster data from the Tabula Sapiens project, allowing users to compare their findings with the clustering and cell annotation provided by the Human Protein Atlas (HPA) pipeline. With the inclusion of the brain single nuclei data, users can explore cell clusters across 11 distinct brain regions and compare these results with the cell type specificity across other datasets within the resource.

Learn about:
• the Single cell type data, providing the expression profiles across 81 cell types from 31 human tissues, and cell type specificity based on gene expression.
• the Tissue cell type section, providing the predicted cell-type expression specificity based on bulk RNAseq
• the Single nuclei brain section, providing more details regarding cell type specificity within the brain, based on single nuclei RNAseq
• the Immune cell section, providing expression comparison between sorted immune cells

The Structure and interaction resource

This new resource contains data from the former Structure and Interaction sections. The Structure resource presents the three-dimensional structures of most human proteins, and now also their related isoforms, based on in-house predictions generated using the AlphaFold source code. The ProteinBrowser tool can be used to highlight features such as antigen sequences for HPA antibodies, InterPro domains and membrane regions in the structures. The positions of experimental and predicted clinical and population missense variants from Ensembl Variant and AlphaMissense can also be explored. The Interaction resource presents data on protein-protein interactions and metabolic networks. The interaction networks presented are now based on data from four different sources, IntAct, BioGRID, BioPlex and OpenCell, that have been integrated with data regarding protein expression, location and classification.

Learn about:
• the predicted 3D structure for more than 83,000 protein isoforms
• the structure of selected protein features and the position of missense variants
• the interaction partners of more than 15,000 proteins
• the expression, location and other features of all proteins in the interaction networks
• the pathways related to 2,900 metabolic genes and the expression profiles of the genes in each metabolic pathway

The Tissue resource

The Tissue resource has in this version launched a major update of multiplex tissue profiling using immunohistochemistry-based fluorescence high-resolution imaging. With the help of single-cell transcriptomics and an iterative staining-stripping method, seven antibody panels have been developed to study protein localization in single-cell types, cell states and subcellular structures in eight different human tissue types. Based on overlap of antibody staining with cell-specific markers, the dataset launched today shows the detailed spatial location of 612 proteins during germ cell development in testis, 178 proteins in different structures of motile ciliated cells, 162 proteins in different tubular and glomerular cells in kidney and 121 proteins in glandular and ductal cells in salivary gland.

Learn about:
• in-depth protein localization of 1,021 proteins using multiplex tissue profiling
• protein localization in tissues, single-cell types, cell states and subcellular structures
• a catalogue of genes enriched in a particular tissue (specificity)
• which genes have a similar expression profile across tissues (expression cluster)

The Cancer resource

The Cancer resource includes the analysis of the expression profiles of 6,918 patients across 21 cancer types using the gene annotations. The refined approach enabled us to offer an updated list of prognostic genes for several of the major human cancers. To strengthen the reliability of the cancer resource, data from 10 independent cancer cohorts were integrated, creating a cross-validated, reliable collection of prognostic genes. The updated resource lays the foundation for precision oncology and the development of personalized treatment strategies.

Learn about:
• the updated correlations between gene expression and survival outcomes using global gene expression profiling.
• independent datasets from 10 different cancer types were compiled to identify a robust set of confidence prognostic genes (CPGs).
• a substantial portion (53.6%) of protein-coding genes were expressed in all cancers analysed, while an additional 12.1% of genes were not detected in any of the cancer types.

The Cell Line resource

The resource now includes genome-wide data covering more than 1,200 human cell lines analyzed either "in-house" or through external resources such as the Cancer Cell Line Encyclopedia (CCLE). The data enables for researchers to identify the best cell lines for particular applications based on similarity to cancers, the presence or absence of various biological pathways and/or the presence of immune signalling molecules (cytokines). The new version complements the data with protein analysis from the CCLE covering 511 cell lines.
Learn about:
• 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

The Knowledge Summaries

Version 24 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 8 resources 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. In addition, we provide 15 knowledge summaries in which the HPA team has assembled data covering topics of high biological or medical interest:

1. The Disease Blood Atlas - explore the proteins profiles in blood from patients with various diseases
2. 3D-structures of proteins - explore the structures of human proteins isoforms
3. The cell and tissue specific proteome - explore all proteins elevated in tissues and cell types
4. The human secretome - explore all proteins predicted to be secreted from human cells
5. The human membrane proteome - explore all proteins predicted to be membrane-bound
6. The house-keeping proteome - explore the proteins essential for all cells
7. The human protein classes - explore the profiles of various protein classes
8. Evidence of the human protein-coding genes - explore the evidence for each of the proteins
9. The right cell line for your experiment - explore the protein profiles in human cell lines
10. The druggable proteome - explore the protein profiles of targets for human pharmaceuticals
11. The cancer proteome - explore the expression of proteins involved in human cancers
12. Transcription factor landscape - explore the cell specificity of all human transcription factors
13. Multiplex tissue profiling - explore the single-cell type-specific spatial location of proteins expressed in testis, kidney, salivary gland and ciliated cells
14. Spatial transcriptomics of the brain - explore the expression in the human cerebral cortex
15. Cilia and basal bodies - explore the detailed subcellular localization of proteins in these cells
16. Sperm and flagella - explore the detailed subcellular localization of proteins in these cells

"The HPA team is proud to launch a lot of new data in the new version of the open access Human Protein Atlas to provide extended knowledge about the building-blocks of humans; the proteins", says Mathias Uhlen, Director of the Human Protein Atlas consortium.

The work was funded by the Knut and Alice Wallenberg Foundation
Link to the new version of the Human Protein Atlas: www.proteinatlas.org

For more information, contact: Mathias Uhlen (email: mathias.uhlen@scilifelab.se) or Åsa Sivertsson (email: asa.sivertsson@scilifelab.se) or Gustav Ceder (email: gustav.ceder@gmail.com).

Data availability
All data in the Human Protein Atlas is publicly available and to further increase and simplify access we have now summarized and structured the data available for each resource and included downloadable files with related meta data. The complete data is available in XML format and in collaboration with BioImage archive also >10M raw images, corresponding to about 300TB of data, are now available and can be used as a resource for bioimage analysis.

About
Human Protein Atlas. The Human Protein Atlas (HPA) is a program based at SciLifeLab (Science for Life Laboratory), Stockholm, that started in 2003 with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource are open access to allow scientists, both in academia and industry, to freely access the data for exploration of the human proteome. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease, and it has been selected by the organization ELIXIR (www.elixir-europe.org) as a European core resource due to its fundamental importance for the wider life science community and by the GCBR as a Global Core Biodata Resource. The HPA consortium is funded by the Knut and Alice Wallenberg Foundation. For more information, see: www.proteinatlas.org

Knut and Alice Wallenberg Foundation. The Knut and Alice Wallenberg Foundation is the largest private financier of research in Sweden and also one of Europe's largest. The Foundation's aim is to benefit Sweden by supporting basic research and education, mainly in medicine, technology, and the natural sciences. The Foundation can also initiate grants to strategic projects and scholarship programs. For more information, see: https://kaw.wallenberg.org/en Press release (PDF)

The version 23 of the Human Protein Atlas is based on an updated genome assembly and features a new Interaction section

The Human Protein Atlas consortium has today launched the version 23 of the open access knowledge resource covering human protein profiles in cells, tissues, organs and blood (www.proteinatlas.org). A new Interaction section is introduced containing data for human protein-protein interaction networks that adds new aspects in terms of protein function. In addition, all five million web pages in the resource have been updated based on a new genome assembly (Ensembl v109), thus reflecting the new consensus genome containing 20,162 protein-coding genes.

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.

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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".
Press release (PDF) | News article

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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.
Press release (PDF) | News article

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".
Press release (PDF) | News article

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.
Press release (PDF) | News article

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)