Human Protein Atlas
Content
DescriptionThe Human Protein Atlas portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in normal human tissues and different cancer types, as well the sub cellular localisation in single cells.
OrganismsHuman
Contact
Research centerKTH, UU, SciLifeLab, Sweden
Primary citationUhlén M, et al. (January 2015). "Proteomics. Tissue-based map of the human proteome". Science. 347 (6220): 1260419. doi:10.1126/science.1260419. PMID 25613900. S2CID 802377.
Access
Websitewww.proteinatlas.org
Download URLwww.proteinatlas.org/about/download
Tools
WebAdvanced search, bulk retrieval/download
Miscellaneous
VersioningYes
Data release
frequency
12 months
Version21
Curation policyYes – manual
Bookmarkable
entities
Yes – both individual protein entries and searches

The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. In November 2021, version 21 was launched A lot of new data and content have been added and the resource now includes ten separate sections with complementary information about all human proteins. All data has been updated on the approximately 15 million individual web pages. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and was selected by the organization ELIXIR as a European core resource due to its fundamental importance for a wider life science community. The HPA consortium is funded by the Knut and Alice Wallenberg Foundation.

Ten sections

The Human Protein Atlas consists of ten sections:

Additional features

In addition to the ten sections of HPA, exploring gene and protein expression, there are various features available at the HPA website to assist the research community, including integrated external resources, such as Metabolic Atlas, educational material and free downloadable data.

History

The Human Protein Atlas program was started in 2003 and funded by the non-profit organization Knut and Alice Wallenberg Foundation (KAW). The main site of the project is the Royal Institute of Technology (KTH), School of Engineering Sciences in Chemistry, Biotechnology and Health (Stockholm, Sweden). Additionally, the project involves research groups at Uppsala University, Karolinska Institutet, Chalmers University of Technology and Lund University, as well as several present and past international collaborations initiated with research groups in Europe, the United States, South Korea, China, and India. Professor Mathias Uhlén is the director of the program.

The research underpinning the start of the exploration of the whole human proteome in the Human Protein Atlas program was carried out in the late 1990s and early 2000s. A pilot study employing an affinity proteomics strategy using affinity-purified antibodies raised against recombinant human protein fragments was carried out for a chromosome-wide protein profiling of chromosome 21.[10] Other projects were also carried out to establish processes for parallel and automated affinity purification of mono-specific antibodies and their validation.[11][12]

Research

Antibodies and antigens, produced in the Human Protein Atlas workflow, are used in research projects to study potential biomarkers in various diseases, such as breast cancer, prostate cancer, colon cancer, diabetes, autoimmune diseases, ovarian cancer and renal failure.[13][14][15][16][17][18]

Researchers involved with Human Protein Atlas projects, are sharing protocols and method details in an open-access group on protocols.io.[19] A large effort is put into validating the antibody reagents used for profiling of tissues and cells, and the HPA has implemented stringent antibody validation criteria as suggested by the International Working Group for Antibody Validation (IWGAV).[20][21][22]

Collaborations

The Human Protein Atlas program has participated in 9 EU research projects ENGAGE, PROSPECTS, BIO_NMD, AFFINOMICS, CAGEKID, EURATRANS, ITFoM, DIRECT and PRIMES.

See also

References

  1. ^ Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, et al. (January 2015). "Proteomics. Tissue-based map of the human proteome". Science. 347 (6220): 1260419. doi:10.1126/science.1260419. PMID 25613900. S2CID 802377.
  2. ^ Sjöstedt, E; Zhong, W; Fagerberg, L; Karlsson, M; Mitsios, N; Adori, C; Oksvold, P; Edfors, F; Limiszewska, A; Hikmet, F; Huang, J; Du, Y; Lin, L; Dong, Z; Yang, L; Liu, X; Jiang, H; Xu, X; Wang, J; Yang, H; Bolund, L; Mardinoglu, A; Zhang, C; von Feilitzen, K; Lindskog, C; Pontén, F; Luo, Y; Hökfelt, T; Uhlén, M; Mulder, J (2020). "An atlas of the protein-coding genes in the human, pig, and mouse brain". Science. 367 (6482). doi:10.1126/science.aay5947. PMID 32139519. S2CID 212560645.
  3. ^ Karlsson, M; Zhang, C; Méar, L; Zhong, W; Digre, A; Katona, B; Sjöstedt, E; Butler, L; Odeberg, J; Dusart, P; Edfors, F; Oksvold, P; von Feilitzen, K; Zwahlen, M; Arif, M; Altay, O; Li, X; Ozcan, M; Mardinoglu, A; Fagerberg, L; Mulder, J; Luo, Y; Ponten, F; Uhlén, M; Lindskog, C (July 2021). "A single-cell type transcriptomics map of human tissues". Science Advances. 7 (31). Bibcode:2021SciA....7.2169K. doi:10.1126/sciadv.abh2169. PMC 8318366. PMID 34321199.
  4. ^ Uhlen, M; Zhang, C; Lee, S; Sjöstedt, E; Fagerberg, L; Bidkhori, G; Benfeitas, R; Arif, M; Liu, Z; Edfors, F; Sanli, K; von Feilitzen, K; Oksvold, P; Lundberg, E; Hober, S; Nilsson, P; Mattsson, J; Schwenk, JM; Brunnström, H; Glimelius, B; Sjöblom, T; Edqvist, PH; Djureinovic, D; Micke, P; Lindskog, C; Mardinoglu, A; Ponten, F (18 August 2017). "A pathology atlas of the human cancer transcriptome". Science. 357 (6352). doi:10.1126/science.aan2507. PMID 28818916. S2CID 206659235.
  5. ^ Uhlen, M; Karlsson, MJ; Zhong, W; Tebani, A; Pou, C; Mikes, J; Lakshmikanth, T; Forsström, B; Edfors, F; Odeberg, J; Mardinoglu, A; Zhang, C; von Feilitzen, K; Mulder, J; Sjöstedt, E; Hober, A; Oksvold, P; Zwahlen, M; Ponten, F; Lindskog, C; Sivertsson, Å; Fagerberg, L; Brodin, P (20 December 2019). "A genome-wide transcriptomic analysis of protein-coding genes in human blood cells". Science. 366 (6472). doi:10.1126/science.aax9198. PMID 31857451. S2CID 209424418.
  6. ^ Uhlén, M; Karlsson, MJ; Hober, A; Svensson, AS; Scheffel, J; Kotol, D; Zhong, W; Tebani, A; Strandberg, L; Edfors, F; Sjöstedt, E; Mulder, J; Mardinoglu, A; Berling, A; Ekblad, S; Dannemeyer, M; Kanje, S; Rockberg, J; Lundqvist, M; Malm, M; Volk, AL; Nilsson, P; Månberg, A; Dodig-Crnkovic, T; Pin, E; Zwahlen, M; Oksvold, P; von Feilitzen, K; Häussler, RS; Hong, MG; Lindskog, C; Ponten, F; Katona, B; Vuu, J; Lindström, E; Nielsen, J; Robinson, J; Ayoglu, B; Mahdessian, D; Sullivan, D; Thul, P; Danielsson, F; Stadler, C; Lundberg, E; Bergström, G; Gummesson, A; Voldborg, BG; Tegel, H; Hober, S; Forsström, B; Schwenk, JM; Fagerberg, L; Sivertsson, Å (26 November 2019). "The human secretome". Science Signaling. 12 (609). doi:10.1126/scisignal.aaz0274. PMID 31772123. S2CID 208321549.
  7. ^ Thul, PJ; Åkesson, L; Wiking, M; Mahdessian, D; Geladaki, A; Ait Blal, H; Alm, T; Asplund, A; Björk, L; Breckels, LM; Bäckström, A; Danielsson, F; Fagerberg, L; Fall, J; Gatto, L; Gnann, C; Hober, S; Hjelmare, M; Johansson, F; Lee, S; Lindskog, C; Mulder, J; Mulvey, CM; Nilsson, P; Oksvold, P; Rockberg, J; Schutten, R; Schwenk, JM; Sivertsson, Å; Sjöstedt, E; Skogs, M; Stadler, C; Sullivan, DP; Tegel, H; Winsnes, C; Zhang, C; Zwahlen, M; Mardinoglu, A; Pontén, F; von Feilitzen, K; Lilley, KS; Uhlén, M; Lundberg, E (26 May 2017). "A subcellular map of the human proteome". Science. 356 (6340). doi:10.1126/science.aal3321. PMID 28495876. S2CID 10744558.
  8. ^ Robinson, JL; Kocabaş, P; Wang, H; Cholley, PE; Cook, D; Nilsson, A; Anton, M; Ferreira, R; Domenzain, I; Billa, V; Limeta, A; Hedin, A; Gustafsson, J; Kerkhoven, EJ; Svensson, LT; Palsson, BO; Mardinoglu, A; Hansson, L; Uhlén, M; Nielsen, J (24 March 2020). "An atlas of human metabolism". Science Signaling. 13 (624). doi:10.1126/scisignal.aaz1482. PMC 7331181. PMID 32209698.
  9. ^ "Metabolic Atlas". Retrieved 2021-01-31.
  10. ^ Agaton C, Galli J, Höidén Guthenberg I, Janzon L, Hansson M, Asplund A, Brundell E, Lindberg S, Ruthberg I, Wester K, Wurtz D, Höög C, Lundeberg J, Ståhl S, Pontén F, Uhlén M (Jun 2003). "Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues". Molecular & Cellular Proteomics. 2 (6): 405–14. doi:10.1074/mcp.M300022-MCP200. PMID 12796447.
  11. ^ Falk R, Agaton C, Kiesler E, Jin S, Wieslander L, Visa N, Hober S, Ståhl S (Dec 2003). "An improved dual-expression concept, generating high-quality antibodies for proteomics research". Biotechnology and Applied Biochemistry. 38 (Pt 3): 231–9. doi:10.1042/BA20030091. PMID 12875650. S2CID 43820440.
  12. ^ Uhlén M, Björling E, Agaton C, Szigyarto CA, Amini B, Andersen E, et al. (Dec 2005). "A human protein atlas for normal and cancer tissues based on antibody proteomics". Molecular & Cellular Proteomics. 4 (12): 1920–32. doi:10.1074/mcp.M500279-MCP200. PMID 16127175.
  13. ^ Jonsson L, Gaber A, Ulmert D, Uhlén M, Bjartell A, Jirström K (2011). "High RBM3 expression in prostate cancer independently predicts a reduced risk of biochemical recurrence and disease progression". Diagnostic Pathology. 6: 91. doi:10.1186/1746-1596-6-91. PMC 3195697. PMID 21955582.
  14. ^ Larsson A, Fridberg M, Gaber A, Nodin B, Levéen P, Jönsson G, Uhlén M, Birgisson H, Jirström K (2012). "Validation of podocalyxin-like protein as a biomarker of poor prognosis in colorectal cancer". BMC Cancer. 12: 282. doi:10.1186/1471-2407-12-282. PMC 3492217. PMID 22769594.
  15. ^ Lindskog C, Asplund A, Engkvist M, Uhlen M, Korsgren O, Ponten F (Jun 2010). "Antibody-based proteomics for discovery and exploration of proteins expressed in pancreatic islets". Discovery Medicine. 9 (49): 565–78. PMID 20587347.
  16. ^ Neiman M, Hedberg JJ, Dönnes PR, Schuppe-Koistinen I, Hanschke S, Schindler R, Uhlén M, Schwenk JM, Nilsson P (Nov 2011). "Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment". Journal of Proteome Research. 10 (11): 4925–34. doi:10.1021/pr200286c. PMID 21888404.
  17. ^ Nodin B, Fridberg M, Jonsson L, Bergman J, Uhlén M, Jirström K (2012). "High MCM3 expression is an independent biomarker of poor prognosis and correlates with reduced RBM3 expression in a prospective cohort of malignant melanoma". Diagnostic Pathology. 7: 82. doi:10.1186/1746-1596-7-82. PMC 3433373. PMID 22805320.
  18. ^ Schwenk JM, Igel U, Neiman M, Langen H, Becker C, Bjartell A, Ponten F, Wiklund F, Grönberg H, Nilsson P, Uhlen M (Nov 2010). "Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays". Molecular & Cellular Proteomics. 9 (11): 2497–507. doi:10.1074/mcp.M110.001560. PMC 2984230. PMID 20682762.
  19. ^ "Human Protein Atlas - research group on protocols.io". protocols.io. Retrieved 2019-12-12.
  20. ^ Uhlen, M; Bandrowski, A; Carr, S; Edwards, A; Ellenberg, J; Lundberg, E; Rimm, DL; Rodriguez, H; Hiltke, T; Snyder, M; Yamamoto, T (October 2016). "A proposal for validation of antibodies". Nature Methods. 13 (10): 823–7. doi:10.1038/nmeth.3995. PMID 27595404. S2CID 34259132.
  21. ^ Edfors, F; Hober, A; Linderbäck, K; Maddalo, G; Azimi, A; Sivertsson, Å; Tegel, H; Hober, S; Szigyarto, CA; Fagerberg, L; von Feilitzen, K; Oksvold, P; Lindskog, C; Forsström, B; Uhlen, M (8 October 2018). "Enhanced validation of antibodies for research applications". Nature Communications. 9 (1): 4130. Bibcode:2018NatCo...9.4130E. doi:10.1038/s41467-018-06642-y. PMC 6175901. PMID 30297845.
  22. ^ Sivertsson, Å; Lindström, E; Oksvold, P; Katona, B; Hikmet, F; Vuu, J; Gustavsson, J; Sjöstedt, E; von Feilitzen, K; Kampf, C; Schwenk, JM; Uhlén, M; Lindskog, C (10 November 2020). "Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins". Journal of Proteome Research. 19 (12): 4766–4781. doi:10.1021/acs.jproteome.0c00486. PMC 7723238. PMID 33170010.