How to Use the Cell Atlas

Discover how you can use the Cell Atlas section on the Human Protein Atlas for your research. We guide you through the information you can find on the atlas.

The Cell Atlas is a section of the Human Protein Atlas, a fantastic tool if you're working with cell biology research.

Discover the Cell Atlas

The Cell Atlas visualizes the spatial distribution of proteins in the human cell. For each protein you can find immunofluorescent stainings from target specific antibodies in several human cell lines, annotated subcellular locations and target gene RNA expression in a vast number of cell lines. For many of the proteins, you can also see the results of different validation assays performed, such as siRNA knockdown, GFP co-localization and cell cycle dependency analyses. 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 produced for the atlas are available from Atlas Antibodies as Triple A Polyclonals.

Here we have created a guide for you on how to use the Cell Atlas. All images below are from the Cell Atlas on the Human Protein Atlas portal. If you are interested in the Tissue Atlas, take a look at the Tissue Atlas guide. 

Step-by-step guide: Explore the Cell Atlas for a specific protein

In this guide, we will use the Cyclin B1 protein as example, and present the data available in the Cell Atlas. 

Step 1. Find your protein

Start by searching for your protein or gene on the Human Protein Atlas.

Search for your gene or protein
Search for your gene or protein, image from the Human Protein Atlas website.

When you have found your protein, click on the Cell Atlas icon in the upper right corner. In the top of the gene page you will find general information about the target gene, see the example below for Cyclin B1. The page also shows Human Protein Atlas data based on antibody stainings. The subcellular localization of the target protein is visualized in green in the schematic cell image.

Cell Atlas entry for Cyclin B1
Image from the Human Protein Atlas showing the top of the gene page in the Cell Atlas entry for Cyclin B1.

Step 2. RNA expression overview

Below the general information you will find results from the different assays performed. The first assay section shows RNA expression of the target gene in 56 cell lines. The cell lines are divided into 12 color-coded groups according to the organ they were obtained from. By clicking on the toolbars in the top right corner you can sort the cell lines in the chart by different criteria.

 

RNA expression of Cyclin B1 in 56 cell lines
Image from the Human Protein Atlas showing RNA expression of Cyclin B1 in 56 cell lines.

Step 3. Human cells

Further down on the Cell Atlas page for your gene is the Human Cell section. Here you can see antibody stainings using immunofluorescence in three human cell lines; U2-OS and two additional cell lines selected based on RNA expression.
Click on an image to view it in high resolution. You can change the visualization of the staining by selecting different color channels visualizing probes or antibody staining only.

Antibody staining using immunofluorescence in three human cell lines
Antibody staining using immunofluorescence in three human cell lines, image from the Human Cells section of the Cyclin B1 entry in the Cell Atlas.

Step 4. Custom data

Cell cycle dependency information of protein expression is shown in the custom data section. It includes co-localization experiments with known organelle markers or stainings of proteins in the cell cycle marker cell line U-2 OS FUCCI (Fluorescence Ubiquitination Cell Cycle Indicator).

Cell cycle dependency information of protein expression
Cell cycle dependency information of protein expression is shown in the custom data section. Image from the custom data section of the Cyclin B1 entry on the Cell Atlas.

Step 5. siRNA

The siRNA validation is performed in siRNA transfected U-2 OS cells immunofluorescently stained with the target antibody. The boxplot and images from one or two siRNA-assays show the downregulation in the siRNA treated cells compared to the negative control (scrambled) samples. The images below are from the Cyclin B1 siRNA assay in the Human Protein Atlas.

siRNA downregulation of Cyclin B1 in U-2 OS Cells
siRNA downregulation of Cyclin B1 in U-2 OS Cells. Image from the siRNA section of the Cyclin B1 entry on the Cell Atlas. Image from the Human Protein Atlas

Step 6. GFP

The GFP (Green Fluorescent Protein) section shows overlap between antibody staining and GFP-tagged target protein in HeLa cells. The antibody staining (green) and GFP (purple) and two organelle probes are displayed as different channels.

ICC-IF stainings showing overlap between Cyclin B1
ICC-IF stainings showing overlap between Cyclin B1 staining and GFP-tagged Cyclin B1 in HeLa cells. Image from the GFP section of the Cyclin B1 entry on the Cell Atlas on the Human Protein Atlas..

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, the green horizontal bars represent the positions of the PrEST antigens on the target protein used for antibody production. The exact positions are presented if you hover the mouse over the green horizontal bars.

Image from the Gene and Protein section of the Cyclin B1 entry of the Human Protein Atlas.
In the protein browser, you see the positions of the antigen sequences for the available antibodies against the protein. Image from the Gene and Protein section of the Cyclin B1 entry of the Human Protein Atlas.

Step 8. 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 Cyclin B1 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.

Antibody Validation tab for the protein on the Human Protein Atlas.
Information on individual antibodies against a protein are available on the Antibody Validation tab for the protein on the Human Protein Atlas. Image from the Human Protein Atlas

Enhanced Validation

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). Discover more about the Enhanced Validation methods and how our antibodies are validated here.