All search results are displayed on this page.
- The search box & how to search. There are three ways to search the database: by entering a query in the search box, by viewing the antibodies by chromosome or by advanced search. The chromosome link named "other" lists the antibodies where the EnsEMBL information is lacking or in any other way does not fit into the 24 chromosomes.
The database can be queried with any part of a gene name, description, EnsEMBL gene id or antibody id. In order to list all available antibodies, empty the query field and press the search button.
The advanced search can be queried based on protein expression levels in all the included normal and cancerous tissues. Multiple criteria can be entered in order to find proteins with a high expression level in one tissue but low or negative expression level in another tissue. In addition, the “tissue search” can be combined with search strings representing gene name, description and words from text summaries of annotated antibodies (“free search”).
- Number of hits. The amount of hits is counted by gene name or by antibody id. You can change the counted entity by clicking on either the "Antibody ID" or "Gene name" link, both residing in the table header. The default view is to sort by gene name.
- The result table & interpretation of the results
- The gene name is either the HUGO id (collected from EnsEMBL), the name of the gene given by the provider of the antibody or, in some rare cases, the EnsEMBL gene id.
- The descriptions are collected from NCBI by using the id provided by EnsEMBL.
- The chromosome data are provided by EnsEMBL.
- There are currently three link icons in the "links" column:
 is a link to Uniprot
 is a link to NCBI
 is a link to EnsEMBL.
- The Antibody ID shows the HPA or CAB id (HPA generated or a "Collaborator" AntiBody) and by clicking on the link you enter the pages for the chosen antibody.
- The validation score can be high, medium, low, very low or N/A:
"High" indicates that the quality assurance supports the specificity of the antibody towards the expected human target protein with high confidence.
"Low" shows that the antibody probably is specific to the expected target, but the validation is less clear and cross-reactivity cannot be excluded.
The validation score is further discussed on the quality assurance page.
- There are three ways to sort the results: by gene name, by chromosome or by antibody id. By clicking once on either of these links in the table header the results will be sorted in alphabetically descending order. By clicking once more on the same link the table will be sorted in reverse order.
- If there are more than 50 hits, the result set will be divided into pages of 50 hits each. You can navigate through the result set by clicking on the links to the right below the search box.
This page shows an overview of the annotations of all tissues and cells for the selected antibody.
The validation score is shown in the header. The annotations are represented by colored circles and listed in sections according to stained tissue- and cell types.
- Sections:
- Gene data. This section contains information from external sources about the targeted gene.
- Normal tissues. This section shows an overview of the annotations of the normal tissues. Normal tissues are listed together with their annotated cell types. Each normal tissue type is represented by three images from unique patients.
- Annotation summary. This section contains a short summary of the general staining pattern of the antibody.
- Cancer tissues. This section shows an overview of the annotations of all cancer tissues. Most cancer types are represented by duplicate samples from 12 patients. Three cancer types are represented by duplicate samples from 4 patients.
- Cell lines – IHC. This section shows an overview of the TMAx generated annotations of all cell lines. Each cell line is represented by duplicate samples.
- Cells. This section shows an overview of the TMAx generated annotations of all cells. Each cell type is represented by duplicate samples.
- Cell lines – IF. This section shows an overview of the annotations of all cell lines stained with immunofluorescence. Each cell line is represented by duplicate samples.
- The color codes. Four colors are used to represent the intensity of the protein expression. Black is used to mark the number of images considered not representative:
 Red represents strong expression.
 Orange represents moderate expression.
 Yellow represents weak expression.
 White represents negative cells or tissues.
 Black represents not representative images.
The combinations with black represent the number of images that are invalid in some way. These images are marked with black. An example:
 A strongly stained tissue with one invalid and one representative image.
- Sort order. Normal tissues and cancer tissues can be sorted in two ways: by alphabetic order or by histogenic order (the tissues are sorted based on cellular origin). Clicking on the sort order text in the section header changes the sort order.
- Expand/collapse section. The minus sign to the left in the section headers can be used to collapse the current section. When collapsed the plus sign expands the section.
- Navigation. The navigation box can be used to navigate between the different sections of this page and to other pages showing relevant information about the antibody. When more than one antibody directed against one protein is published in the protein atlas it is possible to navigate to the other antibody/antibodies through this box.
- Search. This search box can be used to make a new search.
This page shows the annotation for the selected tissue and the commonly found cell types. Click on an image to view a higher magnification. Below the images patient information (age and sex) is displayed.
- The annotation.
The evaluation is based on three images. The intensity, quantity and localization of the staining of each (if more than one) cell type is annotated. Further information is available on the annotation description page.
This page summarizes the staining pattern and intensity of an antibody for a selected cancer type.
- This page shows all images of this cancer type stained with the selected antibody. Most cancer types are represented by duplicate samples from 12 patients (24 images). Three cancer types are represented by duplicate images from 4 patients (8 images).
Clicking on an image in this view will bring you to a more detailed page showing the image pair in a higher magnification.
- Selecting sets of annotated tissues. On the left side, three blocks show the annotation and tissue parameters. Clicking on one parameter will highlight the representative images. Clicking on multiple parameters will narrow the selection down to the images having all the selected parameters. Clicking on the Clear-button will reset the parameter selection.
- Annotation Data. Within this block the number of positively stained tumors is shown.
- Tumor cells. Within this block the specific annotation parameters are given.
- Tissue data. Within this block information about the gender and age of the patients is given.
This page shows one annotation unit: an evaluation of the tumor cells in the cancer tissue. Click on an image to view a larger version. Below the images is information about the gender and age of the patient (age and gender are identical for both images since the samples are retrieved from the same patient).
- The annotation.
Normally the evaluation is made on both images. The intensity, quantity and subcellular localization of the staining of the tumor cells are annotated. Some more information is available on the annotation description page.
This page shows TMAx generated annotations of a primary cell or cell line. Click on an image to view a larger version. Below the images is information about the gender and age of the patient (age and gender are identical for both images since the samples are retrieved from the same patient).
Output parameters from the software always displayed in conjunction with the annotated images are:
- number of objects defined as cells in the image
- staining intensity (negative, weak, moderate and strong)
- fraction (%) of positive cells
In addition, two overlay images with additional numerical information are presented to facilitate interpretation. The information displayed includes:
- object based view representing fraction (%) of immunostained cells. The color code for each cell represents a range of immunoreactivity, blue (negative/very weak), yellow (weak/moderate), orange (moderate/strong) and red (strong) cells. This classification is based on areas of different intensities within each object (cell). This differs slightly from the subjective classification provided by manual annotation of cells in normal and cancer tissue.
- area based view representing immunostained areas (%) within cells. The color code represents a range of immunoreactivity, yellow (weak/moderate), green (moderate/strong) and red (strong). Negative/very weak areas are transparent. The intensity score is generated from this area based analysis.
- The annotation.
Normally the evaluation is made on both images. The intensity and subcellular localization of the staining of the tumor cells are annotated. Some more information is available on the annotation description page.
This page shows the annotation for the selected cell line. Click on an image to view a larger version. Besides the HPA antibodies, the cells are also stained with cellular probes targeting specific compartments in the cells. The different organelle probes are displayed as different colors/channels in the multicolor images; the HPA antibody staining is shown in green, nuclear stain in blue, micro-tubules in red and ER in yellow. By clicking the buttons below the images the different channels can be turned on and off. In the default view all layers except ER are on.
- The annotation.
Normally the evaluation is made on both images. The intensity and subcellular localization of the staining of the tumor cells are annotated. Some more information is available on the annotation description page.
Antibody information
This page summarizes the gene, protein, PrEST (Protein Epitope Signature Tag, the selected protein fragment) and validation data for the antibodies.
- Gene data. All features and links within this section are from external sources and describe numerous data about the targeted gene.
- Protein data. All features within this section are from external sources where the chosen PrEST sequence has been mapped towards the EnsEMBL database. The features from the perfect mapped protein are displayed. Collaborator antibodies are mapped on their gene name or supplied EnsEMBL id.
- PrEST Data. All features within this section are concerning the PrEST. The PrEST has been mapped to EnsEMBL and the three best hits are displayed.
- Antibody data. All features within this section are from the production system. The immunohistochemistry retrieval method and dilution are shown. The antibody provider and product name are also shown.
- Validation summary. The validation of the antibody is shown as a score from high to very low. A validation comment explains why a certain score was set. For antibodies supplied through commercial or other academic sources (CAB-antibodies) we refer to internal quality controls provided by respective company.
- Antibody specificity. This section shows the results from the PrEST-array analysis of the specificity of the antibody.
- Western blot. This section shows the Western blot results and score for the antibody.
- Where can I order the antibodies?
The antibody provider and product name (for CAB-antibodies) can be found in the antibody data section of the antibody info page for each antibody.
- What’s the difference between CAB-antibodies and HPA-antibodies?
CAB is short for Collaborator Antibody. CAB-antibodies are submitted by both commercial and academic external antibody providers. HPA-antibodies are produced by the HPA-program.
Since CAB-antibodies are supplied through commercial or other academic sources we refer to internal quality controls provided by respective company.
- How can I download data from the database?
Our general policy is to not provide downloadable data. We hope to be able to provide this service in the future.
- Can I use your images?
The Protein Atlas imaged can be used under certain conditions. Read our image usage policy for more information.
- When is the next release?
The main release is planned to the HUPO Annual World Congress every autumn but there may be smaller releases throughout the year.
- Why doesn’t the antibody I am interested in have Western blot data?
In the earliest versions of the protein atlas this validation was not done for CAB-antibodies and there are no current plans of supplying such data for those antibodies. In many cases Western blot data is available from the external antibody supplier. From version 2.0 all antibodies in the protein atlas should have Western blots.
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