Help texts are available for all data pages via the "?" in the table headlines.
If you do not find the answer to your question in the available help text or the FAQ below, do not hesitate to contact us: contact@proteinatlas.org
FAQ
Data questions
General questions
Submission questions
How can I download your data?
There are numerous ways you can download data:
- Most of the data (complete or subset) is available as CSV/TSV, RDF or XML files in the downloadable data section.
- Obtain a subset of the data as XML, RDF and TAB files containing data from the result of a search. Use the links located at the far right in the table header of the search result.
- Fetch a single entry of data/images as a TSV, RDF or XML file for one gene by URL: for instance http://www.proteinatlas.org/ENSG00000121410.xml
See the downloadable data section for more details.
Is any of the quantitative data underlying your protein 'scores' available for analysis?
The protein scores of the specific cell types of the tissues in the tissue atlas are available in the xml files.
Is there a way to save the result of a search?
The best way to save or download a specific search result from the Protein Atlas is to use the TAB-file option located at the far right in the table header of the search result list.
Is it possible to extract a list of a certain protein class such as all secreted proteins?
The list of specific protein classes as for instance predicted secreted proteins, can be found by using the protein atlas search: protein_class:Predicted+secreted+proteins. From the search result page you can then download the list of genes as tab separated values by clicking "TAB" located at the far right in the table header.
Is there an efficient way to download the subcellular images for a set of proteins?
There are some ways you can download the images (only jpg) and all of them depend on that you write a script or setup some tool to parse the XML files that we provide on the site.
First obtain an XML file from any of the ways as described in the downloadable data section.
The image link for subcellular images resides in the element for each antibody in the subAssay/data/cellLine and subAssay/data/assayImage/imageUrl elements.
The image in the element is named after which channels that are toggled on and may include nucleus (blue), microtubuli (red), antibody (green) and endoplasmatic reticulum (yellow), in this order. Toggled off channels are left out of the filename according to this naming scheme.
Example:
<imageUrl size="large">
http://www.proteinatlas.org/images/21616/193_D2_1_blue_red_green.jpg
</imageUrl>
Do you provide a parser script that we can use to convert the XML file into a more readable format?
No, unfortunately not. The easiest way to extract the information is probably to use XML transformation such as XSLT.
Can we look at your RNAseq raw data?
What if our purpose is commercial, can we still use your data?
I would like to have more patient data, is that possible?
Unfortunately not, the available data is already listed on the homepage (gender, age, diagnosis and grade, if known) and since all material is anonymized there is no possibility to find further information then what we are already showing.
I am interested in buying one of the antibodies you have tested, where can I find it?
Start by looking at the antibodies used in the "antibody/antigen" tag; Provider and product name are listed there, follow the provider-link and search for the product name (HPA antibodies are directly linked).
Can I get the protocol used for staining the antibody?
Yes, you can download the protocol for both IHC and IF.
What does the star mean?
The star is used as an indicator for Supportive reliability.
What is the definition for uncertain vs supportive?
The guidelines for supportive vs uncertain are specific for each sub atlas and you can read more about this here, it is mainly based on support from external sources (Uniprot/swissprot), internal RNAseq data as well as similarity to paired antibody staining pattern.
We would like to include images (results) from the protein atlas in our publication, is that possible?
Yes, the use of data and images from the protein atlas in publications and presentations is permitted as long as the following conditions are met:
- The publication and/or presentation are solely for informational and non-commercial purposes.
- The source of the data and/or image is referred to the site (www.proteinatlas.org) and/or one or more of our publications are cited, listed here.
What is the best way to cite the protein atlas?
We prefer that you use either of the publications listed here
Are you able to provide tissue sample for testing?
The gene that I am interested in is still missing information, when can that data be expected to be included in the database?
We usually release new data 1-2 times every year and are trying our best to continue exploring the uncharacterized targets, but some are very tricky and takes longer time. Please email contact@proteinatlas.org and we might be able to tell you if there is any results waiting in the pipeline.
My company is interested in submitting antibodies, how should we proceed?
Can researchers submit their antibodies for validation?
Yes, also research teams are welcome to submit their in house antibodies for testing. Academic collaborators are also able to ask for delayed release of the data and images on the public Human Protein Atlas portal if publication based on the results are being prepared. The decision will be made by the Human Protein Atlas priority committee and is normally not granted for longer than one year.
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