There are numerous ways you can download data:

• Most of the data (complete or partial) 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

The protein scores of the specific cell types are available in the xml files.

The best way to save or download a specific search result from the Human Protein Atlas is to use the TAB-file option located at the far right in the table header of the search result list.

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.

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>

No, unfortunately not. The easiest way to extract the information is probably to use XML transformation such as XSLT.

You can find the raw counts of the tissue samples at ArrayExpress:
http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1733/

and the raw counts of the cell lines here:
http://www.ncbi.nlm.nih.gov/bioproject/PRJNA183192

Yes, please see the licence & citation page for full details.

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 than what we are already showing.

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).

Yes, you can download the protocol for both IHC and IF.

The guidelines for the reliability scores are specific for each sub-atlas. You can read more about the guidelines for the Tissue Atlas here and the Cell Atlas here. The reliability score is based on consistency with internal RNA-seq data, support from external sources (UniprotKB/Swiss-Prot), as well as staining pattern similarity between independent antibodies.

Protein expression score is based on immunohistochemical data manually scored with regard to staining intensity (negative, weak, moderate or strong) and fraction of stained cells (<25%, 25-75% or >75%). Each combination of intensity and fractions is automatically converted into an protein expression level score as follows: negative - not detected; weak <25% - not detected; weak combined with either 25 - 75% or 75% - low; moderate <25% - low; moderate combined with either 25 - 75% or 75% - medium; strong <25% - medium, strong combined with either 25 - 75% or 75% - high. In addition to this, protein expression values are manually adjusted as necessary when evaluated by our expert annotators. More information about knowledge-based annotation is available in the Assays & annotation section.

The images on the atlas are the raw data that show the immunohistochemical staining of each antibody. The expression score describes a knowledge-based best estimate of the true protein expression. This means that an expert has manually analyzed all images and assessed if the staining is likely to be the true protein expression or not. If the expert determined that the staining seen is not the true protein expression, the score will be set to "not detected".

More information about annotation of antibody staining is available in the assays & annotation section Immunohistochemistry - tissues: Annotation.

More information about knowledge-based annotation of protein expression is available in the assays & annotation section Immunohistochemistry - tissues: Knowledge-based annotation.

Yes, the use of data and images from the Human Protein Atlas in publications and presentations is permitted as long as the licence & citation conditions are met.

Please cite one of our publications as stated in the Data usage policy.

No, we are not.

We usually release new data 1-2 times every year and are trying our best to continue exploring the uncharacterized targets.All genes have general gene information and RNA expression data . If you have questions regarding a specific gene please email contact@proteinatlas.org and we might be able to tell you if there are any unpublished results.

Please read the Antibody submission section for details on how to submit antibodies. If you have any additional questions, please email contact@proteinatlas.org

Yes, researchers and 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.