Computational Systems Biology Methods and Protocols.7z

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a combination of chemical/enzymatic tagging,
photochemical cleavage, and electron transfer
dissociation mass spectrometry. Mol Cell Pro-
teomics 9(1):153–160


  1. Wang J, Torii M, Liu H et al (2011) dbOGAP -
    an integrated bioinformatics resource for pro-
    tein O-GlcNAcylation. BMC Bioinformatics
    12(1):91

  2. Gupta R, Brunak S (2002) Prediction of glyco-
    sylation across the human proteome and the
    correlation to protein function. Pac Symp Bio-
    comput 2002:310–322

  3. Jia CZ, Liu T, Wang ZP (2013)
    O-GlcNAcPRED: a sensitive predictor to cap-
    ture protein O-GlcNAcylation sites. Mol Bio-
    syst 9(11):2909–2913

  4. Wu HY et al (2014) Characterization and iden-
    tification of protein O-GlcNAcylation sites
    with substrate specificity. BMC Bioinformatics
    15(16):S1

  5. Zhao XW et al (2015) PGlcS: prediction of
    protein O-GlcNAcylation sites with multiple
    features and analysis. J Theor Biol 380(3):524

  6. Kao HJ et al (2015) A two-layered machine
    learning method to identify protein
    O-GlcNAcylation sites with O-GlcNAc trans-
    ferase substrate motifs. BMC Bioinformatics
    16(18):S10

  7. Apweiler R, Bairoch A, Wu CH et al (2004)
    UniProt: the Universal Protein knowledge-
    base. Nucleic Acids Res 32(Database
    issue):115–119

  8. Lee TY, Huang HD, Hung JH et al (2006)
    dbPTM: an information repository of protein
    post-translational modification. Nucleic Acids
    Res 34(Database issue):622–627

  9. Hansen JE, Lund O, Nielsen JO et al (1999)
    O-GLYCBASE: a revised database of
    O-glycosylated proteins. Nucleic Acids Res 27
    (1):370–372

  10. Hornbeck PV, Kornhauser JM, Tkachev S et al
    (2012) PhosphoSitePlus: a comprehensive
    resource for investigating the structure and
    function of experimentally determined post-
    translational modifications in man and mouse.
    Nucleic Acids Res 40(Database issue):D261

  11. Shi SP et al (2015) Progress and challenges in
    predicting protein methylation sites. Mol Bio-
    syst 11:2610–2619

  12. Chen SA, Lee TY, YY O (2010) Incorporating
    significant amino acid pairs to identify O-linked
    glycosylation sites on transmembrane proteins
    and non-transmembrane proteins. BMC Bioin-
    formatics 11(1):1–13

  13. Caragea C, Sinapov J, Silvescu A et al (2007)
    Glycosylation site prediction using ensembles


of Support Vector Machine classifiers. BMC
Bioinformatics 8(1):438


  1. Trinidad JC et al (2012) Global identification
    and characterization of both O-GlcNAcylation
    and phosphorylation at the murine synapse.
    Mol Cell Proteomics 11(8):215–229

  2. Jochmann R et al (2013) O-GlcNAc transfer-
    ase inhibits KSHV propagation and modifies
    replication relevant viral proteins as detected
    by systematic O-GlcNAcylation analysis. Gly-
    cobiology 23(10):1114–1130

  3. Hahne H, Gholami A, Kuster B (2012) Dis-
    covery of O-GlcNAc-modified proteins in pub-
    lished large-scale proteome data. Mol Cell
    Proteom 11(10):843

  4. Hahne H et al (2013) Proteome wide purifica-
    tion and identification of O-GlcNAc-modified
    proteins using click chemistry and mass spec-
    trometry. J Proteome Res 12(2):927–936

  5. Allison DF et al (2012) Modification of RelA
    by O-linked N-acetylglucosamine links glucose
    metabolism to NF-κB acetylation and tran-
    scription. Proc Natl Acad Sci U S A 109
    (42):16888–16893

  6. Gawlowski T et al (2012) Modulation of
    dynamin-related protein 1 (DRP1) function
    by increased O-linked-β-N-acetylglucosamine
    modification (O-GlcNAc) in cardiac myocytes.
    J Biol Chem 287(35):30024–30034

  7. Wang S et al (2012) Extensive crosstalk
    between O-GlcNAcylation and phosphoryla-
    tion regulates Akt signaling. PLoS One 7(5):
    e37427

  8. Floyd ZE, Stephens JM (2012) Controlling a
    master switch of adipocyte development and
    insulin sensitivity: covalent modifications of
    PPARγ. Biochim Biophys Acta 1822
    (7):1090–1095

  9. Ji S et al (2012) O-GlcNAc modification of
    PPARgamma reduces its transcriptional activ-
    ity. Biochem Biophys Res Commun 417
    (4):1158–1163

  10. Alfaro JF et al (2012) Tandem mass spectrom-
    etry identifies many mouse brain
    O-GlcNAcylated proteins including EGF
    domain-specific O-GlcNAc transferase targets.
    Proc Natl Acad Sci U S A 109(19):7280–7285

  11. Pathak S et al (2012) O-GlcNAcylation of
    TAB1 modulates TAK1-mediated cytokine
    release. EMBO J 31(6):1394–1404

  12. Overath T et al (2012) Mapping of O-GlcNAc
    sites of 20 S proteasome subunits and Hsp90
    by a novel biotin-cystamine tag. Mol Cell Pro-
    teom 11(8):467

  13. Shao J et al (2009) Computational identifica-
    tion of protein methylation sites through


Computational Prediction of Protein O-GlcNAc Modification 245
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