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Molecular & Cellular Proteomics 7:2019-2027, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

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Review

A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies^*

Lisa Berglund^,, Erik Björling^,, Per Oksvold, Linn Fagerberg, Anna Asplund^¶, Cristina Al-Khalili Szigyarto, Anja Persson, Jenny Ottosson, Henrik Wernérus, Peter Nilsson, Emma Lundberg, Åsa Sivertsson, Sanjay Navani^||, Kenneth Wester^¶, Caroline Kampf^¶, Sophia Hober, Fredrik Pontén^¶ and Mathias Uhlén^,**

From the Department of Proteomics, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden, ^¶ Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden, and ^|| Lab Surgpath, 204 Bombay Market, 400 034 Mumbai, India

An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of proteins in normal and disease tissues. A new version (4.0) of the Human Protein Atlas has been developed in a genecentric manner with the inclusion of all human genes and splice variants predicted from genome efforts together with a visualization of each protein with characteristics such as predicted membrane regions, signal peptide, and protein domains and new plots showing the uniqueness (sequence similarity) of every fraction of each protein toward all other human proteins. The new version is based on tissue profiles generated from 6120 antibodies with more than five million immunohistochemistry-based images covering 5067 human genes, corresponding to 25% of the human genome. Version 4.0 includes a putative list of members in various protein classes, both functional classes, such as kinases, transcription factors, G-protein-coupled receptors, etc., and project-related classes, such as candidate genes for cancer or cardiovascular diseases. The exact antigen sequence for the internally generated antibodies has also been released together with a visualization of the application-specific validation performed for each antibody, including a protein array assay, Western blot analysis, immunohistochemistry, and, for a large fraction, immunofluorescence-based confocal microscopy. New search functionalities have been added to allow complex queries regarding protein expression profiles, protein classes, and chromosome location. The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery.

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