All search results are displayed on this page.
- The search box & how to search.
There are four ways to search the database: by entering a query in the search box, by browsing a chromosome, by browsing a protein class 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. When browsing by protein classes, a list of all protein classes is found via the link named "More…".
The database can be queried with any part of a gene name, description, EnsEMBL gene id or antibody id. At least 3 characters are required for free text search. In order to list all genes and 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 protein class search, chromosome search and search strings representing gene name, description and words from text summaries of annotated antibodies ("free search").
- Number of hits.
The number of hits is by default counted by gene name. You can change the counted entity by clicking on the "Antibody ID" link residing in the table header. You can also filter all searches to only show genes with tissue profiles (antibodies) by checking the filter box adjacent to the search box.
- 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 Uniprot 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.
- There are currently 82 protein classes in the atlas:
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Blood group antigen proteins. A summary of the human proteins that are responsible for the molecular basis of the blood group antigens. |
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Candidate cancer biomarkers. A List of Candidate Cancer Biomarkers for Targeted Proteomics |
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Candidate cardiovascular disease genes. Candidate-based proteomics in the search for biomarkers of cardiovascular disease |
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CD markers. Human cell differentiation molecules |
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Mutated genes in cancer. Genes for which mutations have been causally implicated in cancer |
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Hydrolases. Enzymes that catalyse the hydrolysis of various bonds |
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Isomerase. Enzymes that catalyse changes within one molecule |
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Ligase. Enzymes that catalyse the joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate |
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Oxidoreductases. Enzymes catalysing oxido-reductions. The substrate oxidized is regarded as hydrogen or electron donor |
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Transferases. Enzymes transferring a group, for example, the methyl group or a glycosyl group, from one donor compound to another acceptor compound |
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Lyases. Enzymes cleaving C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation |
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Adenosine and adenine nucleotide receptors |
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Chemokines and chemotactic factors receptors |
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Odorant/olfactory and gustatory receptors |
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GPCRs excl olfactory receptors |
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G-protein coupled receptors. 7-transmembrane G-linked receptors - also known as GPCRs |
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Family T2R receptors (taste receptor GPCRs) |
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Voltage-gated ion channels. IUPHAR Voltage-gated Ion Channels |
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Calcium-Activated Potassium Channels. IUPHAR Voltage-gated Ion Channels |
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CatSper and Two-Pore Channels. IUPHAR Voltage-gated Ion Channels |
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Cyclic Nucleotide-Regulated Channels. IUPHAR Voltage-gated Ion Channels |
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Inwardly Rectifying Potassium Channels. IUPHAR Voltage-gated Ion Channels |
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Transient Receptor Potential Channels. IUPHAR Voltage-gated Ion Channels |
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Two-P Potassium Channels. IUPHAR Voltage-gated Ion Channels |
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Voltage-Gated Calcium Channels. IUPHAR Voltage-gated Ion Channels |
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Voltage-Gated Potassium Channels. IUPHAR Voltage-gated Ion Channels |
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Voltage-Gated Sodium Channels. IUPHAR Voltage-gated Ion Channels |
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Atypical kinases. Atypical kinases; ADCK, Alpha-type, FAST, PDK/BCKDK, PI3/PI4-kinase, RIO-type |
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CAMK Ser/Thr protein kinases. CAMK; calcium/calmodulin-dependent protein kinases |
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AGC Ser/Thr protein kinases. AGC; containing the PKA, PKG and PKC subfamilies |
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Kinases. Protein kinases mediate signal transduction in eucaryotic cells through phosphorylation of substrate proteins,
thereby controlling many cellular processes including metabolism, transcription, cell cycle progression, differentiation and
apoptosis |
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CK1 Ser/Thr protein kinases. CK1; casein kinase 1 |
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TKL Ser/Thr protein kinases. TKL; tyrosine protein kinase-like |
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CMGC Ser/Thr protein kinases. CMGC; containing the CDK, MAPK, GSK3 and CLK sufamilies |
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NEK Ser/Thr protein kinases. NEK; |
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RGC receptor guanylate cyclase kinases. RGC; adenylyl cyclase class-4/guanylyl cyclase |
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STE Ser/Thr protein kinases. STE; |
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Tyr protein kinases. Tyr; tyrosine protein kinase |
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Potential transmembrane proteins |
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Membrane proteins predicted by MDM. Transmembrane protein predictions based on a majority decision method |
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MEMSAT3 predicted membrane proteins. Transmembrane proteins predictions based on the method MEMSAT3 |
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MEMSAT-SVM predicted membrane proteins. Transmembrane proteins predictions based on the method MEMSAT-SVM |
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Phobius predicted membrane proteins. Transmembrane proteins predictions based on the method Phobius |
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SCAMPI predicted membrane proteins. Transmembrane proteins predictions based on the method SCAMPI (multi version) |
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SPOCTOPUS predicted membrane proteins. Transmembrane proteins predictions based on the method SPOCTOPUS |
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THUMBUP predicted membrane proteins. Transmembrane proteins predictions based on the method THUMBUP |
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TMHMM predicted membrane proteins. Transmembrane proteins predictions based on the method TMHMM2.0 |
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GPCRHMM predicted membrane proteins. Transmembrane proteins predictions based on the method TMHMM2.0 |
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>9TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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1TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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2TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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3TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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4TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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5TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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6TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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7TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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8TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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9TM proteins predicted by MDM. Transmembrane proteins predictions based on a majority decision method |
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Peptidases. Peptidases (also termed proteases, proteinases and proteolytic enzymes) |
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Plasma proteins. A Non-Redundant List of Proteins Present in Plasma |
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Threonine-type peptidases |
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SH3-domain containing proteins. Src-Homology-3 domain containing proteins |
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SH2-domain containing proteins. Src-Homology-2 domain containing proteins |
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Accessory Factors Involved in Transport. Auxiliary transport proteins |
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Transporter channels and pores. Channel-type facilitators |
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Electrochemical Potential-driven transporters. Secondary carrier-type facilitators. |
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Transcription factors. Predicted transcription factors in genomes based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries |
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Primary Active Transporters |
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Transporters. Membrane transport proteins |
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Transport Electron Carriers. Transmembrane electron flow systems |
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UniProt - no evidence at protein level. Proteins without evidence at protein level |
- 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 is divided into 4 columns representing the 4 different internal validation methods; Protein array, Western blot, Immunohistochemistry and Immunofluorescence. The different methods have different scoring systems but the scores have been color coded as follows:
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Supportive |
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Uncertain |
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Not supportive |
The validation scores are further discussed on the quality assurance page.
For antibodies supplied through commercial or other academic sources we provide our Western blot and Immunohistochemistry validation scores. For further validation we refer to quality controls provided by respective company.
- 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.
This page shows an overview of the annotations of all tissues and cells for the selected antibody.
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. For HPA antibodies there is also an image representative of the immunohistochemistry staining pattern. By holding your mouse cursor over the image you can see a explanatory text.
- 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 - IHC. This section shows an overview of the TMAx generated annotations of all primary cells. Each cell type is represented by duplicate samples.
- Cell Expression Diagram - IHC. This section shows the normalised protein expression relative to the size of the different cells and cell lines.
- 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. There are also an annotation summary, a validation score and a representative image.
- 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.
The color codes are translated from the IHC annotation parameters "intestity" and "quantity" using the following lookup table:
| Intensity | Quantity | Color (Score) |
| Strong | >75% |  |
| Strong | 25-75% | |
| Strong | <25% |  |
| Strong | rare | |
| Moderate | >75% | |
| Moderate | 25-75% | |
| Moderate | <25% |  |
| Moderate | rare | |
| Weak | >75% | |
| Weak | 25-75% | |
| Weak | <25% |  |
| Weak | rare | |
| Negative | >75% | |
| Negative | 25-75% | |
| Negative | <25% | |
| Negative | rare | |
- 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. The 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, sex, SNOMED classification numbers and patient id) 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, age, SNOMED classification numbers and patient id of the patient (the information is 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.
This page summarizes the gene and protein data for the genes and 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. Collaborator antibodies are mapped on their gene name or supplied EnsEMBL id. The features from the proteins with more than 80% homology are displayed. You can see the number of transcripts matching the PrEST in the Protein data bar. By default only the protein view from the perfect mapped protein is shown. To view the protein views for all matching transcripts, click on the show protein view link.
- The protein view. The protein view displays the following features:
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A. | Antigen used for antibody generation. |
| B. | Maximum sequence identity (%) for 10 aa sliding window to all other proteins from other genes. Dark red - 100% identity, Red - 90% identity, Orange - 80% identity. |
| C. | Maximum sequence identity (%) for 50 aa sliding window to all other proteins from other genes. |
| D. | MDM, GPCR-HMM, MEMSAT-SVM, MEMSAT3, THUMBUP, SCAMPI_m, SPOCTOPUS, TMHMM and Phobius: membrane protein topology prediction. Turquoise - signal peptide, blue - outside loop, orange - transmembrane region, yellow - reentrant region, red - inside loop. |
| E. | Signal peptide prediction (turquoise). |
| F. | Common (purple) and unique (grey) regions between alternative processed transcripts from the same gene. |
| G. | Low complexity region. |
| H. | InterPro regions. |
| I. | Restriction sites used in cloning. |
| J. | Protein amino acid scale. |
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Further information about the features |
Antigen/Antibody information
This page summarizes the PrEST (Protein Epitope Signature Tag, the selected protein fragment) and validation data for the antibodies.
- PrEST Data. This section shows the size and sequence of the PrEST. Also the PrEST has been mapped to EnsEMBL and the proteins corresponding to the three best gene hits are displayed.
- Antibody data. This sections shows the immunohistochemistry retrieval method and dilution. The product name and a direct link to the antibody provider are also shown.
- Validation: IHC. This sections shows the immunohistochemistry validation score and a validation comment.
- Validation: IF. This sections shows the immunofluorescence validation.
- Validation: Protein Array. This section shows the results from the PrEST-array analysis of the specificity of the antibody.
- Validation: Western blot. This section shows the Western blot results and score for the antibody.
Further information on the validation can be found on the quality assurance page.
- Where can I order the antibodies?
HPA-antibodies can be ordered from Atlas Antibodies (within Europe) or Sigma (world-wide). External antibodies (CAB-antibodies) have different providers. The product name and a direct link to the antibody provider can be found in the antibody data section of the Antigen/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 images 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.
- What part of the protein has been used for immunization?
The sequence of the PrEST (Protein Epitope Signature Tag) used for immunization can be found on the Antigen/Antibody info page for each HPA antibody.
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