title: UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.
abstract: BACKGROUND
  The conjugation of ubiquitin to a substrate protein (protein ubiquitylation), which involves a sequential process--E1 activation, E2 conjugation and E3 ligation, is crucial to the regulation of protein function and activity in eukaryotes. This ubiquitin-conjugation process typically binds the last amino acid of ubiquitin (glycine 76) to a lysine residue of a target protein. The high-throughput of mass spectrometry-based proteomics has stimulated a large-scale identification of ubiquitin-conjugated peptides. Hence, a new web resource, UbiSite, was developed to identify ubiquitin-conjugation site on lysines based on large-scale proteome dataset.
  
  
  RESULTS
  Given a total of 37,647 ubiquitin-conjugated proteins, including 128,026 ubiquitylated peptides, obtained from various resources, this study carries out a large-scale investigation on ubiquitin-conjugation sites based on sequenced and structural characteristics. A TwoSampleLogo reveals that a significant depletion of histidine (H), arginine (R) and cysteine (C) residues around ubiquitylation sites may impact the conjugation of ubiquitins in closed three-dimensional environments. Based on the large-scale ubiquitylation dataset, a motif discovery tool, MDDLogo, has been adopted to characterize the potential substrate motifs for ubiquitin conjugation. Not only are single features such as amino acid composition (AAC), positional weighted matrix (PWM), position-specific scoring matrix (PSSM) and solvent-accessible surface area (SASA) considered, but also the effectiveness of incorporating MDDLogo-identified substrate motifs into a two-layered prediction model is taken into account. Evaluation by five-fold cross-validation showed that PSSM is the best feature in discriminating between ubiquitylation and non-ubiquitylation sites, based on support vector machine (SVM). Additionally, the two-layered SVM model integrating MDDLogo-identified substrate motifs could obtain a promising accuracy and the Matthews Correlation Coefficient (MCC) at 81.06% and 0.586, respectively. Furthermore, the independent testing showed that the two-layered SVM model could outperform other prediction tools, reaching at 85.10% sensitivity, 69.69% specificity, 73.69% accuracy and the 0.483 of MCC value.
  
  
  CONCLUSIONS
  The independent testing result indicated the effectiveness of incorporating MDDLogo-identified motifs into the prediction of ubiquitylation sites. In order to provide meaningful assistance to researchers interested in large-scale ubiquitinome data, the two-layered SVM model has been implemented onto a web-based system (UbiSite), which is freely available at http://csb.cse.yzu.edu.tw/UbiSite/ . Two cases given in the UbiSite provide a demonstration of effective identification of ubiquitylation sites with reference to substrate motifs.
authors.affiliation: Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan. lithsunh@gmail.com.|Ministry of Health & Welfare, Tao-Yuan Hospital, Taoyuan, 320, Taiwan. lithsunh@gmail.com.
authors.forename: Chien-Hsun
authors.initials: CH
authors.lastname: Huang
authors.affiliation: Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan. migon229@gmail.com.
authors.forename: Min-Gang
authors.initials: MG
authors.lastname: Su
authors.affiliation: Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan. rururachel311@gmail.com.
authors.forename: Hui-Ju
authors.initials: HJ
authors.lastname: Kao
authors.affiliation: Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan. euphoria5270@gmail.com.
authors.forename: Jhih-Hua
authors.initials: JH
authors.lastname: Jhong
authors.affiliation: Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsin-Chu, 300, Taiwan. 4467@mmh.org.tw.|Mackay Junior College of Medicine, Nursing and Management , Taipei, 112, Taiwan. 4467@mmh.org.tw.|Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan. 4467@mmh.org.tw.
authors.forename: Shun-Long
authors.initials: SL
authors.lastname: Weng
authors.affiliation: Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan. francis@saturn.yzu.edu.tw.|Innovation Center for Big Data and Digital Convergence, Yuan Ze University, Taoyuan, 320, Taiwan. francis@saturn.yzu.edu.tw.
authors.forename: Tzong-Yi
authors.initials: TY
authors.lastname: Lee
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D066264:Datasets as Topic; D008239:Lysine / Q000737:chemistry*; D000069550:Machine Learning; D013058:Mass Spectrometry; D008958:Models, Molecular; D000072417:Protein Domains; D020543:Proteome; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein; D012984:Software; D025801:Ubiquitin / Q000737:chemistry*; D054875:Ubiquitination
chemical_list: D020543:Proteome; D025801:Ubiquitin; D008239:Lysine
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W588-94
references.pmid: 17517770
references.citation: Brief Bioinform. 2015 Jul;16(4):640-57
references.pmid: 25212598
references.citation: BMC Bioinformatics. 2013;14 Suppl 16:S10
references.pmid: 24564381
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15280-2
references.pmid: 16230621
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D445-51
references.pmid: 23172288
references.citation: Nat Rev Mol Cell Biol. 2005 Aug;6(8):599-609
references.pmid: 16064136
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references.pmid: 10592235
references.citation: Science. 1999 Nov 12;286(5443):1321-6
references.pmid: 10558980
references.citation: Annu Rev Biochem. 1998;67:425-79
references.pmid: 9759494
references.citation: J Proteome Res. 2007 May;6(5):1833-45
references.pmid: 17428077
references.citation: Bioinformatics. 2012 Sep 1;28(17):2293-5
references.pmid: 22782549
references.citation: Protein Pept Lett. 2013 Mar;20(3):318-23
references.pmid: 22591471
references.citation: PLoS One. 2011;6(7):e22930
references.pmid: 21829559
references.citation: PLoS One. 2012;7(7):e40694
references.pmid: 22844408
references.citation: Bioinformatics. 2003 Sep 22;19(14):1849-51
references.pmid: 14512359
references.citation: Proc Natl Acad Sci U S A. 1975 Jan;72(1):11-5
references.pmid: 1078892
references.citation: J Mol Biol. 1999 Sep 17;292(2):195-202
references.pmid: 10493868
references.citation: PLoS One. 2014 Jan 17;9(1):e85744
references.pmid: 24465676
references.citation: Biochim Biophys Acta. 2004 Nov 29;1695(1-3):55-72
references.pmid: 15571809
references.citation: Biochem J. 2006 Nov 1;399(3):361-72
references.pmid: 17034365
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W226-9
references.pmid: 15980458
references.citation: BMC Bioinformatics. 2008 Jul 15;9:310
references.pmid: 18625080
references.citation: Amino Acids. 2012 Apr;42(4):1387-95
references.pmid: 21267749
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D295-305
references.pmid: 23193290
references.citation: BMC Bioinformatics. 2014;15 Suppl 16:S1
references.pmid: 25521204
references.citation: PLoS One. 2011;6(7):e21849
references.pmid: 21789187
references.citation: Biochim Biophys Acta. 2013 Aug;1834(8):1461-7
references.pmid: 23603789
references.citation: Bioinformatics. 2006 Jun 15;22(12):1536-7
references.pmid: 16632492
references.citation: Genome Res. 2004 Jun;14(6):1188-90
references.pmid: 15173120
references.citation: Bioinformatics. 2011 Jul 1;27(13):1780-7
references.pmid: 21551145
references.citation: Biomed Res Int. 2014;2014:528650
references.pmid: 25147802
references.citation: PLoS One. 2011;6(11):e27567
references.pmid: 22110674
references.citation: J Comput Chem. 2009 Nov 30;30(15):2526-37
references.pmid: 19373826
references.citation: Int J Mol Sci. 2011;12(12):8347-61
references.pmid: 22272076
references.citation: Biochim Biophys Acta. 1975 Oct 20;405(2):442-51
references.pmid: 1180967
references.citation: J Comput Aided Mol Des. 2011 Oct;25(10):987-95
references.pmid: 22038416
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W36-8
references.pmid: 15980489
references.citation: PLoS One. 2015 Apr 07;10(4):e0118752
references.pmid: 25849935
references.citation: Mol Cell. 2011 Oct 21;44(2):325-40
references.pmid: 21906983
references.citation: J Cell Sci. 2012 Feb 1;125(Pt 3):531-7
references.pmid: 22389392
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D622-7
references.pmid: 16381945
references.citation: Bioinformatics. 2004 Dec 12;20(18):3302-7
references.pmid: 15256413
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W105-10
references.pmid: 15980436
references.citation: Proteins. 2010 Feb 1;78(2):365-80
references.pmid: 19722269
references.citation: Nat Rev Mol Cell Biol. 2009 Jun;10 (6):398-409
references.pmid: 19436320
references.citation: Mol Cell Proteomics. 2011 Oct;10 (10 ):M111.013284
references.pmid: 21890473
references.citation: J Comput Chem. 2005 Jul 30;26(10):1032-41
references.pmid: 15889432
references.citation: Bioinformatics. 2010 Mar 1;26(5):680-2
references.pmid: 20053844
references.citation: Proc Natl Acad Sci U S A. 2012 Feb 7;109 (6):1925-30
references.pmid: 22308380
references.citation: PLoS One. 2011 Mar 09;6(3):e17331
references.pmid: 21408064
references.citation: Nat Rev Mol Cell Biol. 2005 Aug;6(8):610-21
references.pmid: 16064137
references.citation: Nucleic Acids Res. 2015 Jan;43(Database issue):D503-11
references.pmid: 25399423
references.citation: Nat Biotechnol. 2003 Aug;21(8):921-6
references.pmid: 12872131
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D531-6
references.pmid: 24214993
references.citation: J Proteome Res. 2012 Feb 3;11(2):796-807
references.pmid: 22053931
references.citation: BMC Bioinformatics. 2015 ;16 Suppl 1:S1
references.pmid: 25707307
references.citation: BMC Bioinformatics. 2011 Jun 26;12:261
references.pmid: 21703007
references.citation: Cell Cycle. 2008 Jan 1;7(1):96-105
references.pmid: 18202552
references.citation: Bioinformatics. 2013 Jul 1;29(13):1614-22
references.pmid: 23626001
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Proteins. 2003 Mar 1;50(4):629-35
references.pmid: 12577269