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

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Hornbeck, Peter V ^a   Kornhauser, Jon M ^a   Tkachev, Sasha ^a   Zhang, Bin ^a   Skrzypek, Elzbieta ^a   Murray, Beth ^a   Latham, Vaughan ^a   Sullivan, Michael ^a  

^a CELL SIGNALING TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLATION; ARTICLE; COMPUTER GRAPHICS; COMPUTER INTERFACE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INFORMATION SERVICE; INTERNET; NATURAL LANGUAGE PROCESSING; PHOSPHOSITEPLUS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEOMICS; UBIQUITINATION;

ACETYLATION; AMINO ACID SEQUENCE; ANIMALS; CATTLE; DATABASES, PROTEIN; HUMANS; MICE; PHOSPHORYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; RATS; UBIQUITINATION;

EID: 84857047339     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1122     Document Type: Article

References (46)

1. Walsh,C.T., Garneau-Tsodikova,S. and Gatto,G.J. Jr (2005) Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem. Int. Ed. Engl., 44, 7342-7372.
2. Mayer,S.E. and Krebs,E.G. (1970) Studies on the phosphorylation and activation of skeletal muscle phosphorylase and phosphorylase kinase in vivo. J. Biol. Chem., 245, 3153-3160.
3. Varmus,H., Hirai,H., Morgan,D., Kaplan,J. and Bishop,J.M. (1989) Function, location, and regulation of the src protein-tyrosine kinase. Princess Takamatsu Symp., 20, 63-70.
4. Sefton,B.M., Hunter,T., Beemon,K. and Eckhart,W. (1980) Evidence that the phosphorylation of tyrosine is essential for cellular transformation by Rous sarcoma virus. Cell, 20, 807-816.
5. Pearson,R.B. and Kemp,B.E. (1991) Protein kinase phosphorylation site sequences and consensus specificity motifs: tabulations. Methods Enzymol., 200, 62-81.
6. Hornbeck,P.V., Chabra,I., Kornhauser,J.M., Skrzypek,E. and Zhang,B. (2004) PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics, 4, 1551-1561.
7. MacCoss,M.J., Wu,C.C. and Yates,J.R. III (2002) Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem., 74, 5593-5599.
8. Beausoleil,S.A., Jedrychowski,M., Schwartz,D., Elias,J.E., Villen,J., Li,J., Cohn,M.A., Cantley,L.C. and Gygi,S.P. (2004) Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl Acad. Sci. USA, 101, 12130-12135.
9. Rush,J., Moritz,A., Lee,K.A., Guo,A., Goss,V.L., Spek,E.J., Zhang,H., Zha,X.M., Polakiewicz,R.D. and Comb,M.J. (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol., 23, 94-101.
10. Olsen,J.V., Blagoev,B., Gnad,F., Macek,B., Kumar,C., Mortensen,P. and Mann,M. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell, 127, 635-648.
11. Shi,Y., Chan,D.W., Jung,S.Y., Malovannaya,A., Wang,Y. and Qin,J. (2011) A data set of human endogenous protein ubiquitination sites. Mol. Cell Proteomics, 10, M110 002089.
12. Kim,W., Bennett,E.J., Huttlin,E.L., Guo,A., Li,J., Possemato,A., Sowa,M.E., Rad,R., Rush,J., Comb,M.J. et al. (2011) Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol. Cell, 44, 325-340.
13. Xu,G., Paige,J.S. and Jaffrey,S.R. (2010) Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat. Biotechnol., 28, 868-873.
14. Kim,S.C., Sprung,R., Chen,Y., Xu,Y., Ball,H., Pei,J., Cheng,T., Kho,Y., Xiao,H., Xiao,L. et al. (2006) Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol. Cell., 23, 607-618.
15. Zhao,S., Xu,W., Jiang,W., Yu,W., Lin,Y., Zhang,T., Yao,J., Zhou,L., Zeng,Y., Li,H. et al. (2010) Regulation of cellular metabolism by protein lysine acetylation. Science., 327, 1000-1004.
16. Wang,Z., Udeshi,N.D., Slawson,C., Compton,P.D., Sakabe,K., Cheung,W.D., Shabanowitz,J., Hunt,D.F. and Hart,G.W. (2010) Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis. Sci. Signal., 3, ra2.
17. Yang,X.J. and Seto,E. (2008) Lysine acetylation: codified crosstalk with other posttranslational modifications. Mol. Cell, 31, 449-461.
18. Pettersen,E.F., Goddard,T.D., Huang,C.C., Couch,G.S., Greenblatt,D.M., Meng,E.C. and Ferrin,T.E. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605-1612.
19. Keshava Prasad,T.S., Goel,R., Kandasamy,K., Keerthikumar,S., Kumar,S., Mathivanan,S., Telikicherla,D., Raju,R., Shafreen,B., Venugopal,A. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res., 37, D767-D772.
20. Dinkel,H., Chica,C., Via,A., Gould,C.M., Jensen,L.J., Gibson,T.J. and Diella,F. (2011) Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res., 39, D261-D267.
21. Gnad,F., Gunawardena,J. and Mann,M. (2011) PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res., 39, D253-D260.
22. Li,H., Xing,X., Ding,G., Li,Q., Wang,C., Xie,L., Zeng,R. and Li,Y. (2009) SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol. Cell Proteomics, 8, 1839-1849.
23. Liu,Z., Cao,J., Gao,X., Zhou,Y., Wen,L., Yang,X., Yao,X., Ren,J. and Xue,Y. (2011) CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Res., 39, D1029-D1034.
24. Consortium,U. (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res., 39, D214-D219.
25. Sayers,E.W., Barrett,T., Benson,D.A., Bolton,E., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Federhen,S. et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38-D51.
26. Flicek,P., Amode,M.R., Barrell,D., Beal,K., Brent,S., Chen,Y., Clapham,P., Coates,G., Fairley,S., Fitzgerald,S. et al. (2011) Ensembl 2011. Nucleic Acids Res., 39, D800-D806.
27. Seal,R.L., Gordon,S.M., Lush,M.J., Wright,M.W. and Bruford,E.A. (2011) genenames.org: the HGNC resources in 2011. Nucleic Acids Res., 39, D514-D519.
28. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
29. Rose,P.W., Beran,B., Bi,C., Bluhm,W.F., Dimitropoulos,D., Goodsell,D.S., Prlic,A., Quesada,M., Quinn,G.B., Westbrook,J.D. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
30. Thomas,C.C., Deak,M., Alessi,D.R. and van Aalten,D.M. (2002) High-resolution structure of the pleckstrin homology domain of protein kinase b/akt bound to phosphatidylinositol (3,4,5)-trisphosphate. Curr. Biol., 12, 1256-1262.
31. Mirny,L.A. and Gelfand,M.S. (2002) Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biol., 3, PREPRINT0002.
32. Rikova,K., Guo,A., Zeng,Q., Possemato,A., Yu,J., Haack,H., Nardone,J., Lee,K., Reeves,C., Li,Y. et al. (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell, 131, 1190-1203.
33. Gu,T.L., Deng,X., Huang,F., Tucker,M., Crosby,K., Rimkunas,V., Wang,Y., Deng,G., Zhu,L., Tan,Z. et al. (2011) Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma. PLoS One, 6, e15640.
34. Beausoleil,S.A., Villen,J., Gerber,S.A., Rush,J. and Gygi,S.P. (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol., 24, 1285-1292.
35. Bradshaw,R.A., Medzihradszky,K.F. and Chalkley,R.J. Protein PTMs: post-translational modifications or pesky trouble makers? J. Mass. Spectrom., 45, 1095-1097.
36. Smoot,M.E., Ono,K., Ruscheinski,J., Wang,P.L. and Ideker,T. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics, 27, 431-432.
37. Demir,E., Cary,M.P., Paley,S., Fukuda,K., Lemer,C., Vastrik,I., Wu,G., D'Eustachio,P., Schaefer,C., Luciano,J. et al. (2010) The BioPAX community standard for pathway data sharing. Nat. Biotechnol., 28, 935-942.
38. Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
39. Vacic,V., Iakoucheva,L.M. and Radivojac,P. (2006) Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics, 22, 1536-1537.
40. de Castro,E., Sigrist,C.J., Gattiker,A., Bulliard,V., Langendijk-Genevaux,P.S., Gasteiger,E., Bairoch,A. and Hulo,N. (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res., 34, W362-W365.
41. Hartshorn,M.J. (2002) AstexViewer: a visualisation aid for structure-based drug design. J. Comput. Aided Mol. Des., 16, 871-881.
42. Iakoucheva,L.M., Radivojac,P., Brown,C.J., O'Connor,T.R., Sikes,J.G., Obradovic,Z. and Dunker,A.K. (2004) The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res., 32, 1037-1049.
43. Collins,M.O., Yu,L., Campuzano,I., Grant,S.G. and Choudhary,J.S. (2008) Phosphoproteomic analysis of the mouse brain cytosol reveals a predominance of protein phosphorylation in regions of intrinsic sequence disorder. Mol. Cell Proteomics., 7, 1331-1348.
44. Finn,R.D., Mistry,J., Tate,J., Coggill,P., Heger,A., Pollington,J.E., Gavin,O.L., Gunasekaran,P., Ceric,G., Forslund,K. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
45. Tan,C.S., Pasculescu,A., Lim,W.A., Pawson,T., Bader,G.D. and Linding,R. (2009) Positive selection of tyrosine loss in metazoan evolution. Science, 325, 1686-1688.
46. Li,Z., Zhao,B., Wang,P., Chen,F., Dong,Z., Yang,H., Guan,K.L. and Xu,Y. (2010) Structural insights into the YAP and TEAD complex. Genes Dev., 24, 235-240.