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A human protein atlas for normal and cancer tissues based on antibody proteomics
KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).ORCID iD: 0000-0001-8993-048X
KTH, School of Biotechnology (BIO).
KTH, School of Biotechnology (BIO).
KTH, School of Biotechnology (BIO).ORCID iD: 0000-0001-6990-1905
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2005 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 4, no 12, 1920-1932 p.Article in journal (Refereed) Published
Abstract [en]

Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, similar to 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.

Place, publisher, year, edition, pages
2005. Vol. 4, no 12, 1920-1932 p.
Keyword [en]
MESSENGER-RNA, FACTOR TFIIH, IN-VITRO, EXPRESSION, FAMILY, MICROARRAYS, SUBUNIT, DISPLAY, GENES, CRIM1
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-14023DOI: 10.1074/mcp.M500279-MCP200ISI: 000233774200008Scopus ID: 2-s2.0-29244477844OAI: oai:DiVA.org:kth-14023DiVA: diva2:329168
Note

QC 20100708

Available from: 2010-07-08 Created: 2010-07-08 Last updated: 2017-12-12Bibliographically approved
In thesis
1. Databases for antibody-based proteomics
Open this publication in new window or tab >>Databases for antibody-based proteomics
2008 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Humans are believed to have ~20,500 protein-coding genes andmuch effort has over the last years been put into the characterizationand localization of the encoded proteins in order to understand theirfunctions. One such effort is the Human Proteome Resource (HPR)project, started in Sweden 2003 with the aim to generate specificantibodies to each human protein and to use those antibodies toanalyze the human proteome by screening human tissues and cells.The work reported in this thesis deals with structuring of data fromantibody-based proteomics assays, with focus on the importance ofaggregating and presenting data in a way that is easy to apprehend.The goals were to model and build databases for collecting, searchingand analyzing data coming out of the large-scale HPR project and tomake all collected data publicly available. A public website, theHuman Protein Atlas, was developed giving all end-users in thescientific community access to the HPR database with proteinexpression data. In 2008, the Human Protein Atlas was released in its4th version containing more than 6000 antibodies, covering more than25% of the human proteins. All the collected protein expression datais searchable on the public website. End-users can query for proteinsthat show high expression in one tissue and no expression in anotherand possibly find tissue specific biomarkers. Queries can also beconstructed to find proteins with different expression levels in normalvs. cancer tissues. The proteins found by such a query could identifypotential biomarkers for cancer that could be used as diagnosticmarkers and maybe even be involved in cancer therapy in the future.Validation of antibodies is important in order to get reliable resultsfrom different assays. It has been noted that some antibodies arereliable in certain assays but not in others and therefore anotherpublicly available database, the Antibodypedia, has been createdwhere any antibody producer can submit their binders together withthe validation data in order for end users to purchase the bestantibody for their protein target and their intended assay.

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. 68 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2008:24
Keyword
proteomics, antibodies, database, biomarker, website
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-9658 (URN)978-91-7415-161-9 (ISBN)
Public defence
2008-12-19, FD5, AlbaNova, Roslagstullsbacken 21, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC 20100708Available from: 2008-12-05 Created: 2008-11-24 Last updated: 2010-07-08Bibliographically approved

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Uhlén, MathiasAl-Khalili Szigyarto, CristinaFagerberg, LinnHedhammar, MyOksvold, PerSterky, FredrikTegel, HannaHober, Sophia

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Uhlén, MathiasBjörling, ErikAgaton, CharlottaAl-Khalili Szigyarto, CristinaAmini, BahramAngelidou, PiaAsplund, CarolineBerglund, LisaBergström, KristinaBrumer, HarryEkström, MaricaEriksson, CeciliaFagerberg, LinnFalk, RonnyFall, JennyForsberg, MattiasGry Björklund, MarcusHalimi, AsifHamsten, CarlHedhammar, MyLarsson, KarinLindskog, MatsLodewyckx, WaldLund, JanLundeberg, JoakimMalm, ErikNilsson, PeterÖdling, JennyOksvold, PerÖster, EmmaOttosson, JennyPersson, AnjaRimini, RebeccaRockberg, JohanSivertsson, ÅsaSköllermo, AnnaSteen, JohannaStenvall, MariaSterky, FredrikSundberg, MårtenTegel, HannaTourle, SamuelWaldén, AnnelieWan, JinghongWernérus, HenrikWestberg, JoakimWrethagen, UllaXu, Lan LanHober, Sophia
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Proteomics (closed 20130101)School of Biotechnology (BIO)Molecular Biotechnology (closed 20130101)
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