{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T06:56:02Z","timestamp":1773903362412,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein phosphorylation is the most common post-translational modification (PTM) regulating major cellular processes through highly dynamic and complex signaling pathways. Large-scale comparative phosphoproteomic studies have frequently been done on whole cells or organs by conventional bottom-up mass spectrometry approaches, i.e at the phosphopeptide level. Using this approach, there is no way to know from where the phosphopeptide signal originated. Also, as a consequence of the scale of these studies, important information on the localization of phosphorylation sites in subcellular compartments (SCs) is not surveyed.<\/jats:p>\n               <jats:p>Results: Here, we present a first account of the emerging field of subcellular phosphoproteomics where a support vector machine (SVM) approach was combined with a novel algorithm of discrete wavelet transform (DWT) to facilitate the identification of compartment-specific phosphorylation sites and to unravel the intricate regulation of protein phosphorylation. Our data reveal that the subcellular phosphorylation distribution is compartment type dependent and that the phosphorylation displays site-specific sequence motifs that diverge between SCs.<\/jats:p>\n               <jats:p>Availability and implementation: The method and database both are available as a web server at: http:\/\/bioinfo.ncu.edu.cn\/SubPhos.aspx .<\/jats:p>\n               <jats:p>Contact: \u00a0jdqiu@ncu.edu.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu598","type":"journal-article","created":{"date-parts":[[2014,9,19]],"date-time":"2014-09-19T04:50:41Z","timestamp":1411102241000},"page":"194-200","source":"Crossref","is-referenced-by-count":17,"title":["Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity"],"prefix":"10.1093","volume":"31","author":[{"given":"Xiang","family":"Chen","sequence":"first","affiliation":[{"name":"1 Department of Chemistry, Nanchang University, Nanchang 330031, 2 Department of Mathematics, Nanchang University, Nanchang 330031 and 3 Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China"}]},{"given":"Shao-Ping","family":"Shi","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, Nanchang University, Nanchang 330031, 2 Department of Mathematics, Nanchang University, Nanchang 330031 and 3 Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China"},{"name":"1 Department of Chemistry, Nanchang University, Nanchang 330031, 2 Department of Mathematics, Nanchang University, Nanchang 330031 and 3 Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China"}]},{"given":"Sheng-Bao","family":"Suo","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, Nanchang University, Nanchang 330031, 2 Department of Mathematics, Nanchang University, Nanchang 330031 and 3 Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China"}]},{"given":"Hao-Dong","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, Nanchang University, Nanchang 330031, 2 Department of Mathematics, Nanchang University, Nanchang 330031 and 3 Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China"}]},{"given":"Jian-Ding","family":"Qiu","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, Nanchang University, Nanchang 330031, 2 Department of Mathematics, Nanchang University, Nanchang 330031 and 3 Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China"},{"name":"1 Department of Chemistry, Nanchang University, Nanchang 330031, 2 Department of Mathematics, Nanchang University, Nanchang 330031 and 3 Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China"}]}],"member":"286","published-online":{"date-parts":[[2014,9,17]]},"reference":[{"key":"2023020116140624900_btu598-B1","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1093\/bioinformatics\/btm554","article-title":"Computing topological parameters of biological networks","volume":"24","author":"Assenov","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020116140624900_btu598-B2","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1074\/mcp.M900291-MCP200","article-title":"In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling","volume":"9","author":"Boersema","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020116140624900_btu598-B3","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/j.tcb.2003.10.006","article-title":"Organelle proteomics: looking at less to see more","volume":"13","author":"Brunet","year":"2003","journal-title":"Trends Cell Biol."},{"key":"2023020116140624900_btu598-B4","doi-asserted-by":"crossref","first-page":"4028","DOI":"10.1021\/pr100223n","article-title":"Differential phosphorylation of dynamin I isoforms in subcellular compartments demonstrates the hidden complexity of phosphoproteomes","volume":"9","author":"Chan","year":"2010","journal-title":"J. Proteome Res."},{"key":"2023020116140624900_btu598-B5","doi-asserted-by":"crossref","first-page":"e20025","DOI":"10.1371\/journal.pone.0020025","article-title":"Discovery of protein phosphorylation motifs through exploratory data analysis","volume":"6","author":"Chen","year":"2011","journal-title":"PLoS One"},{"key":"2023020116140624900_btu598-B6","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1002\/mas.10047","article-title":"Subcellular proteomics","volume":"22","author":"Dreger","year":"2003","journal-title":"Mass Spectrom Rev."},{"key":"2023020116140624900_btu598-B7","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/S1534-5807(02)00216-2","article-title":"Spatio-temporal regulation of Rac1 localization and lamellipodia dynamics during epithelial cell-cell adhesion","volume":"3","author":"Ehrlich","year":"2002","journal-title":"Dev. Cell"},{"key":"2023020116140624900_btu598-B8","doi-asserted-by":"crossref","first-page":"D808","DOI":"10.1093\/nar\/gks1094","article-title":"STRING v9.1: protein-protein interaction networks, with increased coverage and integration","volume":"41","author":"Franceschini","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020116140624900_btu598-B9","doi-asserted-by":"crossref","first-page":"2586","DOI":"10.1074\/mcp.M110.001388","article-title":"Musite, a tool for global prediction of general and kinase-specific phosphorylation sites","volume":"9","author":"Gao","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020116140624900_btu598-B10","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.devcel.2006.12.007","article-title":"Automated subcellular location determination and high-throughput microscopy","volume":"12","author":"Glory","year":"2007","journal-title":"Dev. Cell"},{"key":"2023020116140624900_btu598-B11","doi-asserted-by":"crossref","first-page":"4764","DOI":"10.1016\/j.febslet.2006.07.068","article-title":"Phosphoproteomics toolbox: computational biology, protein chemistry and mass spectrometry","volume":"580","author":"Hjerrild","year":"2006","journal-title":"FEBS Lett."},{"key":"2023020116140624900_btu598-B12","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang da","year":"2009","journal-title":"Nat. Protoc."},{"key":"2023020116140624900_btu598-B13","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1126\/science.1087361","article-title":"A Bayesian networks approach for predicting protein-protein interactions from genomic data","volume":"302","author":"Jansen","year":"2003","journal-title":"Science"},{"key":"2023020116140624900_btu598-B14","doi-asserted-by":"crossref","first-page":"429","DOI":"10.3233\/IDA-2002-6504","article-title":"The class imbalance problem: a systematic study","volume":"6","author":"Japkowicz","year":"2002","journal-title":"Intell. Data Anal."},{"key":"2023020116140624900_btu598-B15","doi-asserted-by":"crossref","first-page":"15555","DOI":"10.1016\/S0021-9258(18)98436-X","article-title":"Consensus sequences as substrate-specificity determinants for protein-kinases and protein phosphatases","volume":"266","author":"Kennelly","year":"1991","journal-title":"J. Biol. Chem."},{"key":"2023020116140624900_btu598-B16","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.cell.2006.01.044","article-title":"Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling","volume":"125","author":"Kislinger","year":"2006","journal-title":"Cell"},{"key":"2023020116140624900_btu598-B17","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1021\/ci0342977","article-title":"Maximum spectrum of continuous wavelet transform and its application in resolving an overlapped signal","volume":"44","author":"Lu","year":"2004","journal-title":"J. Chem. Inf. Comp. Sci."},{"key":"2023020116140624900_btu598-B18","doi-asserted-by":"crossref","first-page":"1912","DOI":"10.1126\/science.1075762","article-title":"The protein kinase complement of the human genome","volume":"298","author":"Manning","year":"2002","journal-title":"Science"},{"key":"2023020116140624900_btu598-B19","doi-asserted-by":"crossref","first-page":"16657","DOI":"10.1074\/jbc.272.26.16657","article-title":"A novel mechanism of JNK1 activation \u2013 nuclear translocation and activation of JNK1 during ischemia and reperfusion","volume":"272","author":"Mizukami","year":"1997","journal-title":"J. Biol. Chem."},{"key":"2023020116140624900_btu598-B20","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/0043-1648(95)06817-1","article-title":"Prediction of spalling on a ball bearing by applying the discrete wavelet transform to vibration signals","volume":"195","author":"Mori","year":"1996","journal-title":"Wear"},{"key":"2023020116140624900_btu598-B21","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.cell.2006.09.026","article-title":"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks","volume":"127","author":"Olsen","year":"2006","journal-title":"Cell"},{"key":"2023020116140624900_btu598-B22","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1002\/jcc.21115","article-title":"Using support vector machines for prediction of protein structural classes based on discrete wavelet transform","volume":"30","author":"Qiu","year":"2009","journal-title":"J. Comput. Chem."},{"key":"2023020116140624900_btu598-B23","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1038\/nbt1103","article-title":"Probabilistic model of the human protein-protein interaction network","volume":"23","author":"Rhodes","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2023020116140624900_btu598-B24","doi-asserted-by":"crossref","first-page":"5139","DOI":"10.1016\/S0021-9258(18)53512-2","article-title":"Organelle-specific phosphorylation - identification of unique membrane phosphoproteins of the endoplasmic-reticulum and endosomal apparatus","volume":"268","author":"Rindress","year":"1993","journal-title":"J. Biol. Chem."},{"key":"2023020116140624900_btu598-B25","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1038\/nbt1146","article-title":"An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets","volume":"23","author":"Schwartz","year":"2005","journal-title":"Nat. Biotech."},{"key":"2023020116140624900_btu598-B26","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023020116140624900_btu598-B27","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1016\/j.bbamcr.2011.01.011","article-title":"Identify submitochondria and subchloroplast locations with pseudo amino acid composition: approach from the strategy of discrete wavelet transform feature extraction","volume":"1813","author":"Shi","year":"2011","journal-title":"Biochim. Biophys. Acta"},{"key":"2023020116140624900_btu598-B28","doi-asserted-by":"crossref","first-page":"2927","DOI":"10.1093\/bioinformatics\/btr525","article-title":"Computational prediction of eukaryotic phosphorylation sites","volume":"27","author":"Trost","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020116140624900_btu598-B29","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1002\/mas.20297","article-title":"Subcellular phosphoproteomics","volume":"29","author":"Trost","year":"2010","journal-title":"Mass Spectrom Rev."},{"key":"2023020116140624900_btu598-B30","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1109\/72.788640","article-title":"An overview of statistical learning theory","volume":"10","author":"Vapnik","year":"1999","journal-title":"IEEE T. Neural. Networ."},{"key":"2023020116140624900_btu598-B31","doi-asserted-by":"crossref","first-page":"2421","DOI":"10.1101\/gad.922801","article-title":"Requirement of the JIP1 scaffold protein for stress-induced JNK activation","volume":"15","author":"Whitmarsh","year":"2001","journal-title":"Gene Dev."},{"key":"2023020116140624900_btu598-B32","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1038\/nrm1711","article-title":"Proteomics of organelles and large cellular structures","volume":"6","author":"Yates","year":"2005","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023020116140624900_btu598-B33","doi-asserted-by":"crossref","first-page":"e46302","DOI":"10.1371\/journal.pone.0046302","article-title":"Prediction of protein phosphorylation sites by using the composition of \n              k\n              -spaced amino acid pairs","volume":"7","author":"Zhao","year":"2012","journal-title":"PLoS One"},{"key":"2023020116140624900_btu598-B34","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1021\/pr900767j","article-title":"Analysis of the subcellular phosphoproteome using a novel phosphoproteomic reactor","volume":"9","author":"Zhou","year":"2010","journal-title":"J. Proteome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/2\/194\/49010991\/bioinformatics_31_2_194.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/2\/194\/49010991\/bioinformatics_31_2_194.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:22:04Z","timestamp":1675297324000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/2\/194\/2365295"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,9,17]]},"references-count":34,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2015,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu598","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,1,15]]},"published":{"date-parts":[[2014,9,17]]}}}