Downloadable data Tissue Brain Single cell type Single nuclei brain Immune cell Subcellular Cancer Blood disease Blood protein Cell line Interaction Protein atlas data

Downloadable data

Programmatic access

If you want to programmatically access a subset of the data more information can be found on the help page

Search results

The data files represented here includes data available in the Human Protein Atlas version 24.0. A subset of this data can also be downloaded from the Search page with the genes corresponding to the current search result in the result in different formats; XML, RDF, TSV & JSON.

Single entry

Data for a single entry can be accessed in XML, RDF (trig), TSV or JSON format by adding the corresponding format extension to the Ensembl id as in the below URLs:
https://www.proteinatlas.org/ENSG00000134057.xml
https://www.proteinatlas.org/ENSG00000134057.trig
https://www.proteinatlas.org/ENSG00000134057.tsv
https://www.proteinatlas.org/ENSG00000134057.json

Archived data

As of version 16 of the Human Protein Atlas, the site can be reached using the url structure "vXX.proteinatlas.org" where XX is the version number. For example, version 16 of the Human Protein Atlas has the url https://v16.proteinatlas.org.

Tissue

Data type	Count	Data	Coverage (nr genes)
Protein expression (IHC)	45	Protein expression levels based on IHC staining for 76 cell types in 45 normal tissues	15302
RNA expression (consensus)	50	Gene level RNA seq data based on 50 consensus tissues used for expression profiling and classification	20162
RNA expression (HPA)	40	Gene level RNA seq data based on the 40 tissues in the HPA dataset	20162
RNA expression (GTEx)	35	Gene level RNA seq data for 35 tissues based on 46 tissue subtypes in the GTEx dataset	19266
RNA expression (FANTOM)	46	Gene level RNA seq data for 46 tissues based on 66 tissue subtypes in the FANTOM dataset	18292
RNA gene clustering	50	Gene expression cluster analysis based on 50 tissues	18492
RNA expression (HPA)	186	Transcript level RNA seq data based on 186 tissue samples from 40 HPA tissues	20162
Protein expression (mIHC/IF)		Multiplex profiling using fluorescent multiplex IHC (mIHC/IF) in a selection of tissues and ciliated cells	1021

Brain

Data type	Count	Data	Coverage (nr genes)
RNA expression (HPA)	13	Gene level RNA seq data for 13 brain regions in the HPA dataset used for expression profiling and classification	20162
RNA expression (HPA)	193	Gene level RNA seq data for 193 brain subregions in the HPA dataset used for expression profiling	20162
RNA expression (HPA)	966	Transcript level RNA seq data for 966 brain samples in the HPA dataset used for expression profiling	20162
RNA expression (GTEx)	10	Gene level RNA seq data for 10 brain regions from the GTEx RNA dataset used for expression profiling	19266
RNA expression (GTEx)	105	Transcript level RNA seq data for 105 GTEx retina samples used for expression profiling	20162
RNA expression (FANTOM)	14	Gene level RNA seq data for 14 brain regions from the FANTOM dataset used for expression profiling	18292
RNA expression (pfc)	20	Gene level RNA seq data for 20 prefrontal cortex (pfc) subregions used for expression profiling	20162
RNA expression (HPA pig)	15	Gene level RNA seq data for 15 pig brain regions used for expression profiling	16614
RNA expression (HPA pig)	144	Transcript level RNA seq data for 144 pig brain samples	16614
RNA expression (HPA mouse)	13	Gene level RNA seq data for 13 mouse brain regions from HPA used for expression profiling	16679
RNA expression (HPA mouse)	75	Transcript level RNA seq data for 75 mouse brain samples from HPA	16679
RNA expression (Allen mouse)	10	Gene level RNA seq data for 10 mouse brain regions from Allen brain atlas used for expression profiling	15156
RNA gene clustering	193	Gene expression cluster analysis based on 193 brain subregions	17832

Single cell type

Data type	Count	Description	Cover (nr genes)
RNA expression	31	RNA read count for genes per cell across 31 tissues	20082
RNA expression	557	RNA expression for genes across 557 clusters	20082
RNA expression	81	RNA expression levels per gene and cell type	20082

Single nuclei brain

Data type	Count	Description	Cover (nr genes)
RNA expression	11	RNA read count for genes per cell across 11 brain regions	19580
RNA expression	260	RNA expression for genes across 260 clusters	19580
RNA expression	34	RNA expression for genes across 34 cluster types	19580

Immune cell

Data type	Count	Description	Coverage (nr genes)
RNA expression (HPA)	19	RNA seq data for 19 immune cells in the HPA dataset used for expression profiling	20162
RNA expression (HPA)	18	RNA seq data for 18 immune cells in the HPA dataset used for RNA classification	20162
RNA expression (HPA)	109	RNA seq data for 109 immune cell samples in the HPA dataset used for expression profiling	20162
RNA expression (HPA)	109	Transcript level RNA seq data for 109 immune cell samples in the HPA dataset	20162
RNA expression (Monaco)	30	Monaco immune cell info	20162
RNA expression (Schmiedel)	15	RNAseq data for the 15 immune cells in the Schmiedel dataset used for expression profiling and classification	20162
RNA gene clustering	103	Gene expression cluster analysis based on 103 immune cell samples in the HPA data set	12863

Subcellular

Data type	Count	Data	Coverage (nr genes)
Protein location	49	Protein location data across 13534 genes	13534

Cancer

Data type	Count	Data	Coverage (nr genes)
Prognostic data	21	Analysis of association between TCGA RNA expression and cancer survival in 21 cancers	13698
Prognostic data	10	Validation of association between RNA expression and cancer survival in 10 cancers	13698
Protein expression (IHC)	20	IHC estimated protein expression in 20 cancer types	15302
RNA expression (TCGA)	31	Classification of RNA expression based on 8384 samples from 31 prognostic and validation cancers corresponding to 21 cancer types	19973
RNA expression (TCGA)	21	RNA expression for 8384 samples from 21 cancer types	19973
Protein expression (CPTAC MS)	11	Differential expression between cancerous and matched normal tissues across 11 cancer types	13814

Blood disease

Data type	Count	Data	Coverage (nr genes)
Protein expression	59	Differential expression analysis across 59 diseases	1162

Blood protein

Data type	Count	Data	Coverage (nr genes)
Protein concentration		Protein concentrations across 453 genes measured in Immunoassays	453
Protein concentration		Protein concentrations across 4294 genes measued with mass spectrometry	4294

Cell line

Data type	Count	Data	Coverage (nr genes)
RNA expression	1206	RNA expression in 1206 cell line	20162
RNA expression	28	RNA expression and classification based on 28 cancer cell line groups	20162
RNA expression	1132	Comparison between 1132 cancer cell lines and TCGA cancers using ranking and correlation	19973
RNA cell line analysis	1206	PROGENy and CytoSig analysis on 1206 cell lines
RNA gene clustering	1206	Gene expression cluster analysis based on 1206 cell lines	19508

Interaction

Data type	Count	Data	Coverage (nr genes)
Protein-protein interaction		Interacting protein pairs from the consensus dataset	7712

Protein atlas data

Data from the Human Protein Atlas in tab-separated format
This file contains a subset of the data in the Human Protein Atlas version 24.0 corresponding to the data seen in the search result. This data can also be downloaded for a resulting gene set when using the search function (via the TSV link on the result page).

proteinatlas.tsv.zip

Data from the Human Protein Atlas in json format
This file contains the same subset of the data as the above proteinatlas.tsv but in a different format and potentially more useful for 3rd party web APIs. This data can also be downloaded for a resulting gene set using the search function (via the Download: Custom TSV/JSON link on the result page).

proteinatlas.json.gz

Data from the Human Protein Atlas in XML format
The XML file contains most of the data in the Human Protein Atlas version 24.0, including protein expression data (in normal and tumor tissues and in cell lines), antigen sequences, Western blot data for antibodies, protein array data for antibodies, RNA-seq data, external references such as UniProt identifiers, and more. The data is based on Ensembl version 109. The file structure is presented in the XSD-schema. This data can also be downloaded for a resulting gene set when using the search function (via the xml link on the result page). The XML file presented here is compressed with gzip due to its size. It can be uncompressed with an archive program like 7‑zip.

proteinatlas.xml.gz

Data from the Human Protein Atlas in RDF format
This file contains a subset of the data in the Human Protein Atlas version 24.0 corresponding to the tissue annotations on gene level. This data can also be downloaded for a resulting gene set when using the search function (via the RDF link on the result page). This RDF release is BETA and will be extended and developed in coming releases. We thank Mark Thompson, Rajaram Kaliyaperumal and Eelke van der Horst (LUMC, The Netherlands), and Christine Chichester (SIB, Switzerland) for providing templates for generating the first beta-release of HPA nanopublications. Their contribution was made possible by IMI project Open PHACTS and EU FP7 project RD-Connect. This beta was developed within an ELIXIR collaboration.

proteinatlas.trig.gz

Cell graphic
Schematic cell containing all structures annotated within the Human Protein Atlas.

cell.svg