Contribution of Antibody-based Protein Profiling to the Human Chromosome-centric Proteome Project (C-HPP)

被引：46

作者：

Fagerberg, Linn ^{[1
]}

Oksvold, Per ^{[1
]}

Skogs, Marie ^{[1
]}

Algenas, Cajsa ^{[2
]}

Lundberg, Emma ^{[1
]}

Ponten, Fredrik ^{[3
]}

Sivertsson, Asa ^{[1
]}

Odeberg, Jacob ^{[1
]}

Klevebring, Daniel ^{[1
]}

Kampf, Caroline ^{[3
]}

Asplund, Anna ^{[3
]}

Sjostedt, Evelina ^{[3
]}

Szigyarto, Cristina Al-Khalili ^{[2
]}

Edqvist, Per-Henrik ^{[3
]}

Olsson, IngMarie ^{[3
]}

Rydberg, Urban ^{[3
]}

Hudson, Paul ^{[2
]}

Takanen, Jenny Ottosson ^{[2
]}

Berling, Holger ^{[2
]}

Bjorling, Lisa ^{[1
]}

Tegel, Hanna ^{[2
]}

Rockberg, Johan ^{[2
]}

Nilsson, Peter ^{[1
]}

Navani, Sanjay ^{[4
]}

Jirstrom, Karin ^{[5
]}

Mulder, Jan ^{[6
]}

Schwenk, Jochen M. ^{[1
]}

Zwahlen, Martin ^{[1
]}

Hober, Sophia ^{[1
]}

Forsberg, Mattias ^{[1
]}

von Feilitzen, Kalle ^{[1
]}

Uhlen, Mathias ^{[1
,2
]}

机构：

[1] KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden

[2] KTH Royal Inst Technol, Sch Biotechnol, AlbaNova Univ Ctr, Stockholm, Sweden

[3] Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden

[4] Lab Surgpath, Mumbai, Maharashtra, India

[5] Lund Univ, Dept Clin Sci Pathol, Lund, Sweden

[6] Karolinska Inst, Sci Life Lab, Stockholm, Sweden

来源：

JOURNAL OF PROTEOME RESEARCH | 2013年 / 12卷 / 06期

关键词：

Antibody-based protein profiling; C-HPP; ATLAS; EXPRESSION; TISSUES; ARRAYEXPRESS;

D O I：

10.1021/pr300924j

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas (www.proteinatlas.org).

引用

页码：2439 / 2448

页数：10

共 35 条

[1] Organellar proteomics: turning inventories into insights [J].

Andersen, Jens S. ;

Mann, Matthias .

EMBO REPORTS, 2006, 7 (09) :874-879

[2] The call of the human proteome [J].

不详 .

NATURE METHODS, 2010, 7 (09) :661-661

[3] A Gene-centric Human Proteome Project HUPO-THE HUMAN PROTEOME ORGANIZATION [J].

不详 .

MOLECULAR & CELLULAR PROTEOMICS, 2010, 9 (02) :427-429

[4] Ongoing and future developments at the Universal Protein Resource [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Antunes, Ricardo ;

Barrell, Daniel ;

Bely, Benoit ;

Bingley, Mark ;

Binns, David ;

Bower, Lawrence ;

Browne, Paul ;

Chan, Wei Mun ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Fazzini, Francesco ;

Fedotov, Alexander ;

Foulger, Rebecca ;

Garavelli, John ;

Castro, Leyla Garcia ;

Huntley, Rachael ;

Jacobsen, Julius ;

Kleen, Michael ;

Laiho, Kati ;

Legge, Duncan ;

Lin, Quan ;

Liu, Wudong ;

Luo, Jie ;

Orchard, Sandra ;

Patient, Samuel ;

Pichler, Klemens ;

Poggioli, Diego ;

Pontikos, Nikolas ;

Pruess, Manuela ;

Rosanoff, Steven ;

Sawford, Tony ;

Sehra, Harminder ;

Turner, Edward ;

Corbett, Matt ;

Donnelly, Mike ;

van Rensburg, Pieter ;

Xenarios, Ioannis ;

Bougueleret, Lydie ;

Auchincloss, Andrea ;

Argoud-Puy, Ghislaine ;

Axelsen, Kristian ;

Bairoch, Amos ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D214-D219

[5] The Universal Protein Resource (UniProt) in 2010 [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Antunes, Ricardo ;

Barrell, Daniel ;

Bely, Benoit ;

Bingley, Mark ;

Binns, David ;

Bower, Lawrence ;

Browne, Paul ;

Chan, Wei Mun ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Fedotov, Alexander ;

Foulger, Rebecca ;

Garavelli, John ;

Huntley, Rachael ;

Jacobsen, Julius ;

Kleen, Michael ;

Laiho, Kati ;

Leinonen, Rasko ;

Legge, Duncan ;

Lin, Quan ;

Liu, Wudong ;

Luo, Jie ;

Orchard, Sandra ;

Patient, Samuel ;

Poggioli, Diego ;

Pruess, Manuela ;

Corbett, Matt ;

di Martino, Giuseppe ;

Donnelly, Mike ;

van Rensburg, Pieter ;

Bairoch, Amos ;

Bougueleret, Lydie ;

Xenarios, Ioannis ;

Altairac, Severine ;

Auchincloss, Andrea ;

Argoud-Puy, Ghislaine ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bolleman, Jerven ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D142-D148

[6] Toward a confocal subcellular atlas of the human proteome [J].

Barbe, Laurent ;

Lundberg, Emma ;

Oksvold, Per ;

Stenius, Anna ;

Lewin, Erland ;

Bjorling, Erik ;

Asplund, Anna ;

Ponten, Fredrik ;

Brismar, Hjalmar ;

Uhlen, Mathias ;

Andersson-Svahn, Helene .

MOLECULAR & CELLULAR PROTEOMICS, 2008, 7 (03) :499-508

[7] NCBI GEO: archive for functional genomics data sets-10 years on [J].

Barrett, Tanya ;

Troup, Dennis B. ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Evangelista, Carlos ;

Kim, Irene F. ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Muertter, Rolf N. ;

Holko, Michelle ;

Ayanbule, Oluwabukunmi ;

Yefanov, Andrey ;

Soboleva, Alexandra .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D1005-D1010

[8] ArrayExpress - a public repository for microarray gene expression data at the EBI [J].

Brazma, A ;

Parkinson, H ;

Sarkans, U ;

Shojatalab, M ;

Vilo, J ;

Abeygunawardena, N ;

Holloway, E ;

Kapushesky, M ;

Kemmeren, P ;

Lara, GG ;

Oezcimen, A ;

Rocca-Serra, P ;

Sansone, SA .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :68-71

[9]

Desiere F, 2006, NUCLEIC ACIDS RES, V34, pD655, DOI [10.1093/nar/gkj040, 10.1007/978-1-60761-444-9_19]

[10] Mapping the Subcellular Protein Distribution in Three Human Cell Lines [J].

Fagerberg, Linn ;

Stadler, Charlotte ;

Skogs, Marie ;

Hjelmare, Martin ;

Jonasson, Kalle ;

Wiking, Mikaela ;

Abergh, Annica ;

Uhlen, Mathias ;

Lundberg, Emma .

JOURNAL OF PROTEOME RESEARCH, 2011, 10 (08) :3766-3777

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