The tissue section - Tissue-based map of the human proteome

This section of the Human Protein Atlas focuses on the expression profiles in human tissues of genes both on the mRNA and protein level. The protein expression data from 44 normal human tissue types is derived from antibody-based protein profiling using conventional and multiplex immunohistochemistry. All underlying images of immunohistochemistry stained normal tissues are available together with knowledge-based annotation of protein expression levels. The protein data covers 15303 genes (76%) for which there are available antibodies. The mRNA expression data is derived from deep sequencing of RNA (RNA-seq) from 40 different normal tissue types.

More information about the specific content and the generation and analysis of the data in the section can be found on the Methods Summary.

Learn about:

protein localization in tissues at a single-cell level
if a gene is enriched in a particular tissue (specificity)
which genes have a similar expression profile across tissues (expression cluster)

MULTIPLEX TISSUE PROFILINGⁱ

Explore the proteomes of cell types and cell states

The Tissue section has implemented a novel protocol for multiplex immunohistochemistry based on fluorescence high-resolution imaging, to study protein localization in single-cell types. 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 the kidney. In version 23.0, 742 proteins have been analyzed using multiplex tissue profiling, including 592 for testis and 162 for kidney. By using an iterative staining-stripping method and a robust 5-plex antibody panel, proteins expressed in spermatogonia, spermatocytes, spermatids, and Sertoli cells were characterized.

Kidney

Testis

THE TISSUE AND ORGAN PROTEOMESⁱ Tissues and organs are divided into groups according to functional features they have in common. Each tissue name is clickable and redirects to the selected proteome. If you hold your mouse over a symbol, the corresponding organ will be highlighted in the human figure. The colored bars represent number of genes with elevated expression in the associated tissue divided into tissue enriched (red), group enriched (orange) or tissue enhanced (purple) categories according to the transcriptomics based specificity classification. Mouse-over reveals the number of genes in each of the three categories. The length of the bars visualizes the number of elevated genes in each tissue compared to the tissue with the maximum amount of elevated genes (brain). Explore the proteomes of specific tissues and organs
The expression for all protein-coding genes in all major tissues and organs in the human body can be explored in this interactive database, including numerous catalogs of proteins expressed in a tissue-restricted manner.
Eye Retina Heart Skeletal muscle Smooth muscle Adrenal gland Parathyroid gland Thyroid gland Pituitary gland Lung Bone marrow Lymphoid tissue Liver Gallbladder Testis Epididymis Prostate Seminal vesicle Adipose tissue Brain Choroid plexus Salivary gland Esophagus Tongue Stomach Intestine Pancreas Kidney Urinary bladder Breast Vagina Cervix Endometrium Fallopian tube Ovary Placenta Skin
Based on transcriptomics analysis across all major organs and tissue types in the human body, all putative 20162 protein coding genes have been classified with regard to abundance and distribution of transcribed mRNA molecules, including 10930 proteins showing a significantly elevated level of expression in a particular tissue or a group of related tissues and 8899 proteins detected in all organs and tissues. Read more about the different categories of elevated expression here. Specificity Distribution

TISSUE EXPRESSIONⁱ

The RNA data was used to cluster genes according to their expression across tissues. The clustering of 18492 genes expressed in tissues resulted in 83 expression clusters, which have been manually annotated to describe common features in terms of function and specificity. The result of the cluster analysis is presented as a UMAP based on gene expression, where each cluster has been summarized as colored areas containing most of the cluster genes.

Go to interactive expression cluster page

THE ENRICHED GENES ⁱ A description about the classification of genes into the tissue enriched and group enriched categories is found here. The red circles connected to each tissue name indicates the number of tissue enriched genes associated with that particular tissue. The orange circles indicate the number of genes with enriched expression in a group of tissues, connected by lines.
An interactive network plot of the numbers of enriched and group enriched genes in all major organs and tissue types in the human body, connected to their respective enriched tissues. Click to obtain the corresponding list of genes.

HUMAN SUBPROTEOMES

Explore the various proteomes

The various subproteomes can be explored in this interactive database including numerous catalogs of protein-coding genes with detailed information regarding expression and localization of the corresponding proteins.

The Tissue-
specific Proteome

The Housekeeping
Proteome

The Regulatory
Proteome

The Secretome and
Membrane Proteome

The Isoform Proteome

The Cancer Proteome

The Druggable Proteome