PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

被引：1231

作者：

Hornbeck, Peter V. ^{[1
]}

Kornhauser, Jon M. ^{[1
]}

Tkachev, Sasha ^{[1
]}

Zhang, Bin ^{[1
]}

Skrzypek, Elzbieta ^{[1
]}

Murray, Beth ^{[1
]}

Latham, Vaughan ^{[1
]}

Sullivan, Michael ^{[1
]}

机构：

[1] Cell Signaling Technol, Danvers, MA 01923 USA

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

基金：

美国国家卫生研究院;

关键词：

PROTEIN-PHOSPHORYLATION; LYSINE ACETYLATION; TYROSINE; SITE; CROSSTALK;

D O I：

10.1093/nar/gkr1122

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

PhosphoSitePlus (http://www.phosphosite.org) is an open, comprehensive, manually curated and interactive resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. It encompasses 1 30 000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and acetylation. The interface is designed for clarity and ease of navigation. From the home page, users can launch simple or complex searches and browse high-throughput data sets by disease, tissue or cell line. Searches can be restricted by specific treatments, protein types, domains, cellular components, disease, cell types, cell lines, tissue and sequences or motifs. A few clicks of the mouse will take users to substrate pages or protein pages with sites, sequences, domain diagrams and molecular visualization of side-chains known to be modified; to site pages with information about how the modified site relates to the functions of specific proteins and cellular processes and to curated information pages summarizing the details from one record. PyMOL and Chimera scripts that colorize reactive groups on residues that are modified can be downloaded. Features designed to facilitate proteomic analyses include downloads of modification sites, kinase-substrate data sets, sequence logo generators, a Cytoscape plugin and BioPAX download to enable pathway visualization of the kinase-substrate interactions in PhosphoSitePlus (R).

引用

页码：D261 / D270

页数：10

共 46 条

[1] 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

[2] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[3]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]

[4] Large-scale characterization of HeLa cell nuclear phosphoproteins [J].

Beausoleil, SA ;

Jedrychowski, M ;

Schwartz, D ;

Elias, JE ;

Villén, J ;

Li, JX ;

Cohn, MA ;

Cantley, LC ;

Gygi, SP .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (33) :12130-12135

[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] Protein PTMs: post-translational modifications or pesky trouble makers? [J].

Bradshaw, Ralph A. ;

Medzihradszky, Katalin F. ;

Chalkley, Robert J. .

JOURNAL OF MASS SPECTROMETRY, 2010, 45 (10) :1095-1097

[7] Phosphoproteomic analysis of the mouse brain cytosol reveals a predominance of protein phosphorylation in regions of intrinsic sequence disorder [J].

Collins, Mark O. ;

Yu, Lu ;

Campuzano, Iain ;

Grant, Seth G. N. ;

Choudhary, Jyoti S. .

MOLECULAR & CELLULAR PROTEOMICS, 2008, 7 (07) :1331-1348

[8] ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins [J].

de Castro, Edouard ;

Sigrist, Christian J. A. ;

Gattiker, Alexandre ;

Bulliard, Virginie ;

Langendijk-Genevaux, Petra S. ;

Gasteiger, Elisabeth ;

Bairoch, Amos ;

Hulo, Nicolas .

NUCLEIC ACIDS RESEARCH, 2006, 34 :W362-W365

[9] The BioPAX community standard for pathway data sharing [J].

Demir, Emek ;

Cary, Michael P. ;

Paley, Suzanne ;

Fukuda, Ken ;

Lemer, Christian ;

Vastrik, Imre ;

Wu, Guanming ;

D'Eustachio, Peter ;

Schaefer, Carl ;

Luciano, Joanne ;

Schacherer, Frank ;

Martinez-Flores, Irma ;

Hu, Zhenjun ;

Jimenez-Jacinto, Veronica ;

Joshi-Tope, Geeta ;

Kandasamy, Kumaran ;

Lopez-Fuentes, Alejandra C. ;

Mi, Huaiyu ;

Pichler, Elgar ;

Rodchenkov, Igor ;

Splendiani, Andrea ;

Tkachev, Sasha ;

Zucker, Jeremy ;

Gopinath, Gopal ;

Rajasimha, Harsha ;

Ramakrishnan, Ranjani ;

Shah, Imran ;

Syed, Mustafa ;

Anwar, Nadia ;

Babur, Oezguen ;

Blinov, Michael ;

Brauner, Erik ;

Corwin, Dan ;

Donaldson, Sylva ;

Gibbons, Frank ;

Goldberg, Robert ;

Hornbeck, Peter ;

Luna, Augustin ;

Murray-Rust, Peter ;

Neumann, Eric ;

Reubenacker, Oliver ;

Samwald, Matthias ;

van Iersel, Martijn ;

Wimalaratne, Sarala ;

Allen, Keith ;

Braun, Burk ;

Whirl-Carrillo, Michelle ;

Cheung, Kei-Hoi ;

Dahlquist, Kam ;

Finney, Andrew .

NATURE BIOTECHNOLOGY, 2010, 28 (09) :935-942

[10] Phospho.ELM: a database of phosphorylation sites-update 2011 [J].

Dinkel, Holger ;

Chica, Claudia ;

Via, Allegra ;

Gould, Cathryn M. ;

Jensen, Lars J. ;

Gibson, Toby J. ;

Diella, Francesca .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D261-D267

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