Towards a knowledge-based Human Protein Atlas

Journal name:
Nature Biotechnology
Year published:
Published online

To the Editor:

We report on the launch of version 7 of the Human Protein Atlas with subcellular localization data and expression data for all major human tissues and organs. A milestone has been achieved with the inclusion of expression data for >50% of the human protein-coding genes. The main new feature of the release is an attempt towards a knowledge-based portal, including an annotated protein expression feature for protein targets analyzed with two or more antibodies, and the establishment of the main subcellular localization of protein targets.

In 2005, the first version of the Human Protein Atlas ( was released with protein profile data based on immunohistochemistry on tissue microarrays covering 48 different human tissues and organs, including kidney, liver, heart, brain and pancreas1. The first version included data from 718 antibodies corresponding to 650 human protein-coding genes. High-resolution images were published along with annotation of the presence or absence of a particular protein target in all represented tissues. The 2005 Human Protein Atlas also contained information regarding protein profiles from 20 different types of human cancer, including breast, colorectal, lung and prostate cancer. The data in the portal were made available freely both for academia and industry without restrictions or password protection. In 2007, the portal was extended to also include subcellular profiling data2 using immunofluorescence-based confocal microscopy in three human cancer cell lines of different (glial, mesenchymal and epithelial) origin. More data have been added to the portal every year since the first release3 and version 6, launched in March 2010, contained 11,274 antibodies corresponding to 8,489 protein-coding genes. This entire effort depends heavily on the availability of good quality antibodies, and recently a community-based portal, Antibodypedia (, has been launched to allow antibodies from different providers to be listed and compared4, 5, although the main source of information so far comes from the providers' own validation data, not by independent third-party users. At present, the Antibodypedia contains close to 100,000 antibodies, corresponding to >70% of the protein-coding genes in humans.

An important objective has now been reached with the inclusion of 10,118 protein-coding genes corresponding to >50% of the 19,559 human entries as defined by UniProt, including only entries with evidence at protein or transcript level and proteins inferred from homology6 (Fig. 1). The chromosomal coverage of protein-coding genes is shown in Figure 1a and the status for a selection of important protein classes is reported in Figure 1b. Almost 80% of the human kinases and Src-homology 2 domain–containing proteins and >50% of the transcription factors have protein profiling data in the atlas.


  1. Uhlen, M. et al. Mol. Cell Proteomics 4, 19201932 (2005).
  2. Barbe, L. et al. Mol. Cell Proteomics 7, 499508 (2008).
  3. Berglund, L. et al. Mol. Cell Proteomics 7, 20192027 (2008).
  4. Bjorling, E. & Uhlen, M. Mol. Cell Proteomics 7, 20282037 (2008).
  5. Kiermer, V. Nat. Methods 5, 860 (2008).
  6. The UniProt Consortium. Nucleic Acids Res. 38, D142148 (2010).
  7. Flicek, P. et al. Nucleic Acids Res. 38, D557D562 (2010).
  8. The International HapMap Project. Nature 426, 789796 (2003).
  9. Lukk, M. et al. Nat. Biotechnol. 28, 322324 (2010).
  10. Mathivanan, S. et al. Nat. Biotechnol. 26, 164167 (2008).
  11. Wishart, D.S. et al. Nucleic Acids Res. 35, D521526 (2007).
  12. Ong, S.E. et al. Mol. Cell Proteomics 1, 376386 (2002).
  13. Sultan, M. et al. Science 321, 956960 (2008).
  14. Ponten, F. et al. Mol. Syst. Biol. 5, 337 (2009).
  15. Anonymous. Nat. Methods 7, 661 (2010).
  16. Anonymous. Mol. Cell Proteomics 9, 427429 (2010).

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  1. School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), Stockholm, Sweden.

    • Mathias Uhlen,
    • Per Oksvold,
    • Linn Fagerberg,
    • Kalle Jonasson,
    • Mattias Forsberg,
    • Martin Zwahlen,
    • Sophia Hober,
    • Henrik Wernerus &
    • Lisa Björling
  2. Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, Sweden.

    • Mathias Uhlen &
    • Emma Lundberg
  3. Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.

    • Caroline Kampf,
    • Kenneth Wester &
    • Fredrik Ponten

Competing financial interests

The authors declare no competing financial interests.

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