The Human Protein Atlas as a proteomic resource for biomarker discovery


Fredrik Pontén, Department of Immunology, Genetics and Pathology, Uppsala University/Uppsala Akademiska Hospital, Rudbecklaboratoriet C5:3, Dag Hammarskölds väg 20, S-752 37 Uppsala, Sweden.
(fax: +46-18-553354; e-mail:


Pontén F, Schwenk JM, Asplund A, Edqvist P-HD (Uppsala University, Uppsala; and KTH – Royal Institute of Technology, Stockholm; Sweden). The Human Protein Atlas as a proteomic resource for biomarker discovery (Review). J Intern Med 2011; 270: 428–446.

The analysis of tissue-specific expression at both the gene and protein levels is vital for understanding human biology and disease. Antibody-based proteomics provides a strategy for the systematic generation of antibodies against all human proteins to combine with protein profiling in tissues and cells using tissue microarrays, immunohistochemistry and immunofluorescence. The Human Protein Atlas project was launched in 2003 with the aim of creating a map of protein expression patterns in normal cells, tissues and cancer. At present, 11 200 unique proteins corresponding to over 50% of all human protein-encoding genes have been analysed. All protein expression data, including underlying high-resolution images, are published on the free and publically available Human Protein Atlas portal ( This database provides an important source of information for numerous biomedical research projects, including biomarker discovery efforts. Moreover, the global analysis of how our genome is expressed at the protein level has provided basic knowledge on the ubiquitous expression of a large proportion of our proteins and revealed the paucity of cell- and tissue-type-specific proteins.