The UniProtKB guide to the human proteome

被引:108
作者
Breuza, Lionel [1 ]
Poux, Sylvain [1 ]
Estreicher, Anne [1 ]
Famiglietti, Maria Livia [1 ]
Magrane, Michele [2 ]
Tognolli, Michael [1 ]
Bridge, Alan [1 ]
Baratin, Delphine [1 ]
Redaschi, Nicole [1 ]
Xenarios, Ioannis [4 ]
Bougueleret, Lydie [4 ]
Bairoch, Amos [4 ]
Aimo, Lucila [4 ]
Auchincloss, Andrea [4 ]
Axelsen, Kristian [4 ]
Argoud-Puy, Ghislaine [4 ]
Bansal, Parit [4 ]
Binz, Pierre-Alain [4 ]
Blatter, Marie-Claude [4 ]
Boeckmann, Brigitte [4 ]
Bolleman, Jerven [4 ]
Boutet, Emmanuel [4 ]
Braconi-Quintaje, Silvia [4 ]
Casal-Casas, Cristina [4 ]
de Castro, Edouard [4 ]
Cerutti, Lorenzo [4 ]
Coudert, Elisabeth [4 ]
Cuche, Beatrice [4 ]
Cusin, Isabelle [4 ]
Doche, Mikael [4 ]
Dornevil, Dolnide [4 ]
Duvaud, Severine [4 ]
Ferro-Rojas, Serenella [4 ]
Feuermann, Marc [4 ]
Gasteiger, Elisabeth [4 ]
Gehant, Sebastien [4 ]
Gerritsen, Vivienne [4 ]
Gos, Arnaud [4 ]
Gruaz-Gumowski, Nadine [4 ]
Hinz, Ursula [4 ]
Hulo, Chantal [4 ]
James, Janet [4 ]
Jimenez, Silvia [4 ]
Jungo, Florence [4 ]
Keller, Guillaume [4 ]
Kerhornou, Arnaud [4 ]
Kappler, Thomas [4 ]
Lane, Lydie [4 ]
Lara, Vicente [4 ]
Lemercier, Philippe [4 ]
机构
[1] Ctr Med Univ Geneva, SIB Swiss Inst Bioinformat, 1 Rue Michel Servet, CH-1211 Geneva 4, Switzerland
[2] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England
[3] Georgetown Univ, Med Ctr, Prot Informat Resource, 3300 Whitehaven St North West,Suite 1200, Washington, DC 20007 USA
[4] SIB, Lausanne, Switzerland
[5] European Bioinformat Inst, Cambridge, England
[6] Prot Informat Resource, Newark, DE USA
来源
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | 2016年
基金
美国国家卫生研究院;
关键词
DRAFT; MAP;
D O I
10.1093/database/bav120
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. Using the example of the human proteome, we will describe the content of a complete proteome in the UniProt Knowledgebase (UniProtKB). We will show how manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation to build a comprehensive, high-quality and traceable resource. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB.
引用
收藏
页数:10
相关论文
共 38 条
[1]   OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders [J].
Amberger, Joanna S. ;
Bocchini, Carol A. ;
Schiettecatte, Francois ;
Scott, Alan F. ;
Hamosh, Ada .
NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D789-D798
[2]   A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance [J].
Anderson, Douglas M. ;
Anderson, Kelly M. ;
Chang, Chi-Lun ;
Makarewich, Catherine A. ;
Nelson, Benjamin R. ;
McAnally, John R. ;
Kasaragod, Prasad ;
Shelton, John M. ;
Liou, Jen ;
Bassel-Duby, Rhonda ;
Olson, Eric N. .
CELL, 2015, 160 (04) :595-606
[3]   Emerging evidence for functional peptides encoded by short open reading frames [J].
Andrews, Shea J. ;
Rothnagel, Joseph A. .
NATURE REVIEWS GENETICS, 2014, 15 (03) :193-204
[4]   UniProt: a hub for protein information [J].
Bateman, Alex ;
Martin, Maria Jesus ;
O'Donovan, Claire ;
Magrane, Michele ;
Apweiler, Rolf ;
Alpi, Emanuele ;
Antunes, Ricardo ;
Arganiska, Joanna ;
Bely, Benoit ;
Bingley, Mark ;
Bonilla, Carlos ;
Britto, Ramona ;
Bursteinas, Borisas ;
Chavali, Gayatri ;
Cibrian-Uhalte, Elena ;
Da Silva, Alan ;
De Giorgi, Maurizio ;
Dogan, Tunca ;
Fazzini, Francesco ;
Gane, Paul ;
Cas-tro, Leyla Garcia ;
Garmiri, Penelope ;
Hatton-Ellis, Emma ;
Hieta, Reija ;
Huntley, Rachael ;
Legge, Duncan ;
Liu, Wudong ;
Luo, Jie ;
MacDougall, Alistair ;
Mutowo, Prudence ;
Nightin-gale, Andrew ;
Orchard, Sandra ;
Pichler, Klemens ;
Poggioli, Diego ;
Pundir, Sangya ;
Pureza, Luis ;
Qi, Guoying ;
Rosanoff, Steven ;
Saidi, Rabie ;
Sawford, Tony ;
Shypitsyna, Aleksandra ;
Turner, Edward ;
Volynkin, Vladimir ;
Wardell, Tony ;
Watkins, Xavier ;
Zellner, Hermann ;
Cowley, Andrew ;
Figueira, Luis ;
Li, Weizhong ;
McWilliam, Hamish .
NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D204-D212
[5]   A probability-based approach for high-throughput protein phosphorylation analysis and site localization [J].
Beausoleil, Sean A. ;
Villen, Judit ;
Gerber, Scott A. ;
Rush, John ;
Gygi, Steven P. .
NATURE BIOTECHNOLOGY, 2006, 24 (10) :1285-1292
[6]   An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome [J].
Bian, Yangyang ;
Song, Chunxia ;
Cheng, Kai ;
Dong, Mingming ;
Wang, Fangjun ;
Huang, Junfeng ;
Sun, Deguang ;
Wang, Liming ;
Ye, Mingliang ;
Zou, Hanfa .
JOURNAL OF PROTEOMICS, 2014, 96 :253-262
[7]   Devising a Consensus Framework for Validation of Novel Human Coding Loci [J].
Bruford, Elspeth A. ;
Lane, Lydie ;
Harrow, Jennifer .
JOURNAL OF PROTEOME RESEARCH, 2015, 14 (12) :4945-4948
[8]   DIVALENT ION PERMEABILITY OF AMPA RECEPTOR CHANNELS IS DOMINATED BY THE EDITED FORM OF A SINGLE SUBUNIT [J].
BURNASHEV, N ;
MONYER, H ;
SEEBURG, PH ;
SAKMANN, B .
NEURON, 1992, 8 (01) :189-198
[9]   Standardized description of scientific evidence using the Evidence Ontology (ECO) [J].
Chibucos, Marcus C. ;
Mungall, Christopher J. ;
Balakrishnan, Rama ;
Christie, Karen R. ;
Huntley, Rachael P. ;
White, Owen ;
Blake, Judith A. ;
Lewis, Suzanna E. ;
Giglio, Michelle .
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2014,
[10]   Modernizing Reference Genome Assemblies [J].
Church, Deanna M. ;
Schneider, Valerie A. ;
Graves, Tina ;
Auger, Katherine ;
Cunningham, Fiona ;
Bouk, Nathan ;
Chen, Hsiu-Chuan ;
Agarwala, Richa ;
McLaren, William M. ;
Ritchie, Graham R. S. ;
Albracht, Derek ;
Kremitzki, Milinn ;
Rock, Susan ;
Kotkiewicz, Holland ;
Kremitzki, Colin ;
Wollam, Aye ;
Trani, Lee ;
Fulton, Lucinda ;
Fulton, Robert ;
Matthews, Lucy ;
Whitehead, Siobhan ;
Chow, Will ;
Torrance, James ;
Dunn, Matthew ;
Harden, Glenn ;
Threadgold, Glen ;
Wood, Jonathan ;
Collins, Joanna ;
Heath, Paul ;
Griffiths, Guy ;
Pelan, Sarah ;
Grafham, Darren ;
Eichler, Evan E. ;
Weinstock, George ;
Mardis, Elaine R. ;
Wilson, Richard K. ;
Howe, Kerstin ;
Flicek, Paul ;
Hubbard, Tim .
PLOS BIOLOGY, 2011, 9 (07)