How to Use the Tissue Atlas
Discover how you can use the Tissue Atlas section on the Human Protein Atlas for your research. We guide you through the information you can find on the atlas.
The Tissue Atlas is part of the Human Protein Atlas database, a tissue-based map of the complete human proteome based on RNA seq data and antibody-based profiling.
Discover the Tissue Atlas
On the Tissue Atlas, you find protein expression data such as IHC stainings from 44 normal tissues created using antibodies against the human proteome. You can also compare protein expression to RNA expression. If you find antibodies on the Human Protein Atlas you would like to use, the antibodies developed for the atlas are available from Atlas Antibodies as Triple A Polyclonals.
Here we have created a guide for you on how to explore the Tissue Atlas. We'll show how to discover in which tissues the human proteins are expressed, and how to explore antibody stainings from both normal tissues and cancers. All images below are example images from the Human Protein Atlas website.
If you are also interested in the Cell Atlas, take a look at the Cell Atlas user guide.
Step-by-step guide: explore the Tissue Atlas for a specific protein
In this guide, we will use Aquaporin 4, coded by the gene AQP4, as an example. We will show all the data available in the Tissue Atlas for the Aquaporin 4 protein and the antibody stainings using Aquaporin 4 antibodies. Follow the same steps for your protein of interest.
Step 1. Find your protein
Start by searching for your protein or gene on the Human Protein Atlas start page.
When you have found your protein, click on the Tissue Atlas tab in the upper right corner. At the top of this page, you will find general information about the target gene. See the example below for Aquaporin 4. The page also shows Human Protein Atlas data based on antibody stainings and RNA-seq values.
Step 2. View the RNA and protein expression summary
This section presents the RNA expression (left) and protein expression (right) of AQP4 illustrated as horizontal bars. The 44 normal human tissues analyzed are divided into color-coded groups according to functional features. For each group, a list of included tissues is accessed by clicking either on the text, the symbol or on the bars.
To access all images for a specific tissue, click on the tissue name or on the bar (illustrated in yellow below). This will take you to the image data page for that specific tissue.
Step 3. Explore all staining images
When visiting a specific tissue page, antibody stainings are presented from tissue samples from three different patients. The Aquaporin 4 cerebral cortex page is chosen here as an example. The whole core images can be viewed in high-resolution by clicking on the images. The image below shows one of the cerebral cortex stainings for Aquaporin 4 in high-resolution. Information about the samples is presented in the table to the left.
RNA-seq data of the individual samples that have been used for the transcript profiling are shown in the lower section of this page. TPM (transcripts per million) values give a quantification of the gene abundance which is comparable between different genes and samples.
Step 4. Primary data section with stainings from 44 tissues
Clicking on the Primary data section brings you directly to the IHC images from 44 normal human tissues, including 76 different cell types. Pathology-based annotation of protein expression has been performed for all tissues and images. The IHC images can be viewed in high resolution by clicking on the different tissues.
Step 5. View stainings from extended tissue profiling
Extended tissue profiling has been performed on a number of tissues that have not been shown on the Human Protein Atlas before; eye, lactating breast, full section adrenal gland and extended brain (hypothalamus, pituitary gland) and skin (hair follicle sweat glands) samples. If a specific antibody has been used for these extended analyses, the results can be reached from the same view as for the 44 "standard" tissues. For illustrating retina expression, PDE6B was chosen as an example below.
Step 6. Get details of RNA expression
For each gene, RNA-data from three different sources are presented: Internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project. In addition, consensus RNA data combining the three datasets is presented.
Step 7. Find the antigen position on the target gene
Following the gene/protein link in the left side menu, you will reach a page containing general gene and protein information. In the protein browser section of the page, the green horizontal bar represents the exact amino acid position of the antigen on the target protein used for antibody production. The different isoforms of AQP4 are clickable in the different tabs.
Step 8. Explore cancer stainings in the pathology atlas
On top of the page, clicking on the Pathology tab takes you to the Pathology Atlas entry for Aquaporin 4. The antibodies have been used for staining tumor samples from up to 12 patients from 20 human cancers. The Pathology Atlas can be used to study differential expression between different patients, or between normal versus cancerous tissues. As in previous sections, you can click on each tissue and view the whole cores in high-resolution.
Step 9. Antibody validation
Clicking on the Antibodies and Validation symbol takes you to a separate page describing the antibodies and antigens used and the validation in more detail. On this page, you can see all antibodies against the protein. The links in the Provider field takes you to the product pages to purchase the antibodies. See the example for Aquaporin 4 below. The antibodies developed by the Human Protein Atlas and used for the stainings are available from Atlas Antibodies as Triple A Polyclonals.
All Triple A Polyclonals have been approved on protein arrays for specifically recognizing their corresponding antigens. The antibody staining results are compared to RNA-seq data and literature about the target protein, as well as to other antibodies against the same target.
A concept of antibody validation on the Human Protein Atlas has been introduced, Enhanced Validation. The Enhanced Validation complements the standard validation. The concept is based on the guidelines proposed by a group of distinguished researchers in an article published in Nature Methods 2016 (Uhlén et al; A proposal for antibody validation). Learn more about the Enhanced Validation methods and how our antibodies are validated here.