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Summary of data presented in the Tissue section, with a representative image of protein expression (left) and an interactive chart showing the tissue-specific mRNA expression (right). The image and the chart are clickable and will redirect to more Tissue data. This section contains information regarding the expression profiles of protein-coding genes in normal human tissue, both on the mRNA and protein level. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry.
Tissue expression clusteri
The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.
Not detected - no cluster assigned
Tissue specificityi
The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected.
A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation.
"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.
Summary of data presented in the Brain Atlas and a representative image of mRNA expression in the human brain. The image is clickable and will redirect to more Brain Atlas data. The Brain Atlas explores the protein expression in the mammalian brain by visualization and integration of data from three mammalian species (human, pig and mouse). Transcriptomics data combined with affinity-based protein in situ localization down to single cell level is available in a brain-centric sub atlas of the Human Protein Atlas.
Human regional specificityi
The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category.
Not detected
SINGLE CELL TYPEi
Summary of data presented in the Single cell type section, with an interactive chart showing the cell type-specific mRNA expression. The chart is clickable and will redirect to more Single cell type data. This section contains information about single cell type RNA expression based on scRNAseq of human tissues. The data also covers transcriptomics analysis of human blood and cultured cell lines.
Single cell type expression clusteri
The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.
Plasma cells - Protein processing (mainly)
Cell type specificityi
The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.
Cell type enriched (Plasma cells)
TISSUE CELL TYPEi
Summary of cell specificity data from the tissue cell type section. Listed below are the cell types in which the selected gene has predicted specificity, and images of the tissues in which they reside. Clicking here will redirect to more detailed data on the selected gene's predicted cell type specificity in different tissues.
The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
Genes can have enriched specificity in different cell types in one or several tissues, or be enriched in a core cell type that appears in many different tissues.
Core cell type enriched
PATHOLOGYi
Summary of data presented in the Pathology section, with representative images of protein expression in cancer (left) and correlation between mRNA expression and patient survival (right). Images are clickable and redirect to pages with more Pathology data. This section contains mRNA and protein expression data from 17 different forms of human cancer, as well as correlation analysis of mRNA expression and patient survival. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry.
Prognostic marker in head and neck cancer (favorable) and breast cancer (favorable)
Cancer specificityi
Specificity of RNA expression in 17 cancer types is categorized as either cancer enriched, group enriched, cancer enhanced, low cancer specificity and not detected.
Cancer enhanced (stomach cancer)
Cancer distributioni
Distribution of RNA expression in 17 cancer types is categorized as either detected in single, detected in some, detected in many, detected in all, or not detected.
Detected in many
DISEASE
Upregulated in diseasei
A gene is classified as upregulated in a disease if the average concentration of all samples of that disease is significantly higher (adj P-value<0.05) than the average concentration of samples of all diseases as measured by PEA . For gender specific diseases the analysis includes only samples corresponding to the same gender from the other diseases.
Not available
Disease prediction modeli
The disease(s) the gene is associated with and able to predict according to glmnet prediction models. To be included the gene has to be upregulated according to differential expression analysis and have more than 50% overall importance as indicated by the prediction models.
Summary of data presented in the Immune Cell section and a representative image of mRNA expression in immune cells in the blood. The image is clickable and will redirect to more immune cell related data. The Immune Cell section contains information regarding single cell type mRNA expression profiles of protein-coding genes in various immune cells in the blood, e.g. B-cells and granulocytes.
Immune cell expression clusteri
The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.
B-cells - Immunoglobulins (mainly)
Immune cell specificityi
The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.
Group enriched (memory B-cell, naive B-cell)
BLOOD PROTEINi
Summary of data presented in the Blood proteins section and a representative image of the concentration in plasma and related function for the protein in plasma. The image is clickable and will redirect to more data. The Blood proteins section contains plasma levels of proteins detected in human blood and an analysis of the human secretome (including annotation of the genes predicted to be actively secreted to human blood) is also presented.
Detected in blood by immunoassayi
The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search.
No (not applicable)
Detected in blood by mass spectrometryi
Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.
Yes
Detected in blood by proximity extension assayi
Detection or not of the gene in blood, based on proximity extension assays (Olink) for a longitudinal wellness study covering 76 individuals with three visits during two years.
No
SUBCELLULARi
Summary of data presented in the Cell Atlas and a representative image of subcellular localization. The Cell Atlas provides RNA expression data derived from RNA sequencing of a large panel of cell lines and protein localization data derived from antibody-based profiling by immunofluorescence confocal microscopy, using a subset of cell lines selected based on RNA expression.
Main locationi
Main subcellular location(s) and reliability score(s) for the encoded protein(s) in human cells. The main location(s) may be characterized by presence in all tested cell lines and/or ihigher staining intensity compared to the potential additional location(s). If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively.
Not available
CELL LINEi
Summary of data presented in the Cell Line section and a representative image of mRNA expression across different human cell lines. The image is clickable and will redirect to more cell line data. This section contains information regarding mRNA expression profiles of human protein-coding genes for a large variety of cell lines.
Cell line expression clusteri
The RNA data was used to cluster genes according to their expression across cell lines. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.
Myeloma - Immunoglobulins (mainly)
Cell line specificityi
RNA specificity category based on RNA sequencing data from cancer cell lines in the Human Protein Atlas grouped according to type of cancer. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines.
Cancer enriched (Myeloma)
Cell type distributioni
The RNA distribution category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: detected in all, detected in many, detected in some, detected in single and not detected.
The Human Protein Atlas project is funded
