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Article: Systematic Characterization and Prediction of Post-Translational Modification Cross-Talk

TitleSystematic Characterization and Prediction of Post-Translational Modification Cross-Talk
Authors
Issue Date2015
PublisherAmerican Society for Biochemistry and Molecular Biology, Inc. The Journal's web site is located at http://www.mcponline.org/
Citation
Molecular and Cellular Proteomics, 2015, v. 14 n. 3, p. 761-770 How to Cite?
AbstractPost-translational modification (PTM)(1) plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM cross-talk. Identification of PTM cross-talks is an emerging theme in proteomics and has elicited great interest, but their properties remain to be systematically characterized. To this end, we collected 193 PTM cross-talk pairs in 77 human proteins from the literature and then tested location preference and co-evolution at the residue and modification levels. We found that cross-talk events preferentially occurred among nearby PTM sites, especially in disordered protein regions, and cross-talk pairs tended to co-evolve. Given the properties of PTM cross-talk pairs, a naïve Bayes classifier integrating different features was built to predict cross-talks for pairwise combination of PTM sites. By using a 10-fold cross-validation, the integrated prediction model showed an area under the receiver operating characteristic (ROC) curve of 0.833, superior to using any individual feature alone. The prediction performance was also demonstrated to be robust to the biases in the collected PTM cross-talk pairs. The integrated approach has the potential for large-scale prioritization of PTM cross-talk candidates for functional validation and was implemented as a web server available at http://bioinfo.bjmu.edu.cn/ptm-x/.
Persistent Identifierhttp://hdl.handle.net/10722/210798
ISSN
2017 Impact Factor: 5.236
2015 SCImago Journal Rankings: 3.213
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorHuang, Y-
dc.contributor.authorXu, B-
dc.contributor.authorZhou, X-
dc.contributor.authorLi, Y-
dc.contributor.authorLu, M-
dc.contributor.authorJiang, R-
dc.contributor.authorLi, T-
dc.date.accessioned2015-06-23T05:54:28Z-
dc.date.available2015-06-23T05:54:28Z-
dc.date.issued2015-
dc.identifier.citationMolecular and Cellular Proteomics, 2015, v. 14 n. 3, p. 761-770-
dc.identifier.issn1535-9476-
dc.identifier.urihttp://hdl.handle.net/10722/210798-
dc.description.abstractPost-translational modification (PTM)(1) plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM cross-talk. Identification of PTM cross-talks is an emerging theme in proteomics and has elicited great interest, but their properties remain to be systematically characterized. To this end, we collected 193 PTM cross-talk pairs in 77 human proteins from the literature and then tested location preference and co-evolution at the residue and modification levels. We found that cross-talk events preferentially occurred among nearby PTM sites, especially in disordered protein regions, and cross-talk pairs tended to co-evolve. Given the properties of PTM cross-talk pairs, a naïve Bayes classifier integrating different features was built to predict cross-talks for pairwise combination of PTM sites. By using a 10-fold cross-validation, the integrated prediction model showed an area under the receiver operating characteristic (ROC) curve of 0.833, superior to using any individual feature alone. The prediction performance was also demonstrated to be robust to the biases in the collected PTM cross-talk pairs. The integrated approach has the potential for large-scale prioritization of PTM cross-talk candidates for functional validation and was implemented as a web server available at http://bioinfo.bjmu.edu.cn/ptm-x/.-
dc.languageeng-
dc.publisherAmerican Society for Biochemistry and Molecular Biology, Inc. The Journal's web site is located at http://www.mcponline.org/-
dc.relation.ispartofMolecular and Cellular Proteomics-
dc.titleSystematic Characterization and Prediction of Post-Translational Modification Cross-Talk-
dc.typeArticle-
dc.identifier.emailZhou, X: zhouxy@hku.hk-
dc.identifier.authorityHuang, Y=rp02649-
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1074/mcp.M114.037994-
dc.identifier.pmid25605461-
dc.identifier.pmcidPMC4349993-
dc.identifier.scopuseid_2-s2.0-84924288933-
dc.identifier.hkuros243783-
dc.identifier.volume14-
dc.identifier.issue3-
dc.identifier.spage761-
dc.identifier.epage770-
dc.identifier.isiWOS:000350671300026-
dc.publisher.placeUnited States-

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