메뉴 건너뛰기




Volumn 1834, Issue 11, 2013, Pages 2442-2453

Bioinformatics tools for secretome analysis

Author keywords

Bioinformatics; Biological database; Proteomics; Secretome data analysis; System biology

Indexed keywords

CELL PROTEIN; SECRETOME; UNCLASSIFIED DRUG;

EID: 84884669582     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.01.039     Document Type: Review
Times cited : (86)

References (125)
  • 1
    • 77957755656 scopus 로고    scopus 로고
    • Secretome proteomics for discovery of cancer biomarkers
    • M. Makridakis, and A. Vlahou Secretome proteomics for discovery of cancer biomarkers J. Proteome 73 2010 2291
    • (2010) J. Proteome , vol.73 , pp. 2291
    • Makridakis, M.1    Vlahou, A.2
  • 3
    • 0345490814 scopus 로고    scopus 로고
    • Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT
    • Y. Chen, P. Yu, J. Luo, and Y. Jiang Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT Mamm. Genome 14 2003 859
    • (2003) Mamm. Genome , vol.14 , pp. 859
    • Chen, Y.1    Yu, P.2    Luo, J.3    Jiang, Y.4
  • 5
    • 79551476407 scopus 로고    scopus 로고
    • Mapping of the secretome of primary isolates of mammalian cells, stem cells and derived cell lines
    • H. Skalnikova, J. Motlik, S.J. Gadher, and H. Kovarova Mapping of the secretome of primary isolates of mammalian cells, stem cells and derived cell lines Proteomics 11 2011 691
    • (2011) Proteomics , vol.11 , pp. 691
    • Skalnikova, H.1    Motlik, J.2    Gadher, S.J.3    Kovarova, H.4
  • 6
    • 77956419405 scopus 로고    scopus 로고
    • The cancer cell secretome: A good source for discovering biomarkers?
    • M.P. Pavlou, and E.P. Diamandis The cancer cell secretome: a good source for discovering biomarkers? J. Proteome 73 2010 1896
    • (2010) J. Proteome , vol.73 , pp. 1896
    • Pavlou, M.P.1    Diamandis, E.P.2
  • 8
    • 79958286762 scopus 로고    scopus 로고
    • Secretome of the coprophilous fungus Doratomyces stemonitis C8, isolated from koala feces
    • R. Peterson, J. Grinyer, and H. Nevalainen Secretome of the coprophilous fungus Doratomyces stemonitis C8, isolated from koala feces Appl. Environ. Microbiol. 77 2011 3793
    • (2011) Appl. Environ. Microbiol. , vol.77 , pp. 3793
    • Peterson, R.1    Grinyer, J.2    Nevalainen, H.3
  • 9
    • 84867362036 scopus 로고    scopus 로고
    • Selective enrichment of newly synthesized proteins for quantitative secretome analysis
    • K. Eichelbaum, M. Winter, M.B. Diaz, S. Herzig, and J. Krijgsveld Selective enrichment of newly synthesized proteins for quantitative secretome analysis Nat. Biotechnol. 30 2012 984
    • (2012) Nat. Biotechnol. , vol.30 , pp. 984
    • Eichelbaum, K.1    Winter, M.2    Diaz, M.B.3    Herzig, S.4    Krijgsveld, J.5
  • 10
    • 0034874277 scopus 로고    scopus 로고
    • Differential expression of CXCR3 targeting chemokines CXCL10, CXCL9, and CXCL11 in different types of skin inflammation
    • J. Flier, D.M. Boorsma, P.J. van Beek, C. Nieboer, T.J. Stoof, R. Willemze, and C.P. Tensen Differential expression of CXCR3 targeting chemokines CXCL10, CXCL9, and CXCL11 in different types of skin inflammation J. Pathol. 194 2001 398
    • (2001) J. Pathol. , vol.194 , pp. 398
    • Flier, J.1    Boorsma, D.M.2    Van Beek, P.J.3    Nieboer, C.4    Stoof, T.J.5    Willemze, R.6    Tensen, C.P.7
  • 11
    • 67649801094 scopus 로고    scopus 로고
    • CD25 shedding by human natural occurring CD4 + CD25 + regulatory T cells does not inhibit the action of IL-2
    • A.E. Pedersen, and J.P. Lauritsen CD25 shedding by human natural occurring CD4 + CD25 + regulatory T cells does not inhibit the action of IL-2 Scand. J. Immunol. 70 2009 40
    • (2009) Scand. J. Immunol. , vol.70 , pp. 40
    • Pedersen, A.E.1    Lauritsen, J.P.2
  • 12
    • 58549110244 scopus 로고    scopus 로고
    • Adipokines, myokines and cardiovascular disease
    • K. Walsh Adipokines, myokines and cardiovascular disease Circ. J. 73 2009 13
    • (2009) Circ. J. , vol.73 , pp. 13
    • Walsh, K.1
  • 16
    • 0021856417 scopus 로고
    • Signal sequences. The limits of variation
    • G. von Heijne Signal sequences. The limits of variation J. Mol. Biol. 184 1985 99
    • (1985) J. Mol. Biol. , vol.184 , pp. 99
    • Von Heijne, G.1
  • 18
    • 79551475841 scopus 로고    scopus 로고
    • Advances in membranous vesicle and exosome proteomics improving biological understanding and biomarker discovery
    • F. Raimondo, L. Morosi, C. Chinello, F. Magni, and M. Pitto Advances in membranous vesicle and exosome proteomics improving biological understanding and biomarker discovery Proteomics 11 2011 709
    • (2011) Proteomics , vol.11 , pp. 709
    • Raimondo, F.1    Morosi, L.2    Chinello, C.3    Magni, F.4    Pitto, M.5
  • 19
    • 0023046815 scopus 로고
    • A new method for predicting signal sequence cleavage sites
    • G. von Heijne A new method for predicting signal sequence cleavage sites Nucleic Acids Res. 14 1986 4683
    • (1986) Nucleic Acids Res. , vol.14 , pp. 4683
    • Von Heijne, G.1
  • 20
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • P. Rice, I. Longden, and A. Bleasby EMBOSS: the European Molecular Biology Open Software Suite Trends Genet. 16 2000 276
    • (2000) Trends Genet. , vol.16 , pp. 276
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 21
    • 3242878999 scopus 로고    scopus 로고
    • PrediSi: Prediction of signal peptides and their cleavage positions
    • K. Hiller, A. Grote, M. Scheer, R. Munch, and D. Jahn PrediSi: prediction of signal peptides and their cleavage positions Nucleic Acids Res. 32 2004 W375 W379
    • (2004) Nucleic Acids Res. , vol.32
    • Hiller, K.1    Grote, A.2    Scheer, M.3    Munch, R.4    Jahn, D.5
  • 24
    • 52949132304 scopus 로고    scopus 로고
    • High-performance signal peptide prediction based on sequence alignment techniques
    • K. Frank, and M.J. Sippl High-performance signal peptide prediction based on sequence alignment techniques Bioinformatics 24 2008 2172
    • (2008) Bioinformatics , vol.24 , pp. 2172
    • Frank, K.1    Sippl, M.J.2
  • 25
    • 84859501651 scopus 로고    scopus 로고
    • Computational comparative study of tuberculosis proteomes using a model learned from signal peptide structures
    • J.S. Lai, C.W. Cheng, T.Y. Sung, and W.L. Hsu Computational comparative study of tuberculosis proteomes using a model learned from signal peptide structures PLoS One 7 2012 e35018
    • (2012) PLoS One , vol.7 , pp. 35018
    • Lai, J.S.1    Cheng, C.W.2    Sung, T.Y.3    Hsu, W.L.4
  • 26
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • H. Nielsen, J. Engelbrecht, S. Brunak, and G. von Heijne Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Protein Eng. 10 1997 1
    • (1997) Protein Eng. , vol.10 , pp. 1
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    Von Heijne, G.4
  • 27
    • 0031603460 scopus 로고    scopus 로고
    • Prediction of signal peptides and signal anchors by a hidden Markov model
    • H. Nielsen, and A. Krogh Prediction of signal peptides and signal anchors by a hidden Markov model Proc. Int. Conf. Intell. Syst. Mol. Biol. 6 1998 122
    • (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.6 , pp. 122
    • Nielsen, H.1    Krogh, A.2
  • 29
    • 71549149451 scopus 로고    scopus 로고
    • A comprehensive assessment of N-terminal signal peptides prediction methods
    • K.H. Choo, T.W. Tan, and S. Ranganathan A comprehensive assessment of N-terminal signal peptides prediction methods BMC Bioinforma. 10 Suppl. 15 2009 S2
    • (2009) BMC Bioinforma. , vol.10 , Issue.SUPPL. 15 , pp. 2
    • Choo, K.H.1    Tan, T.W.2    Ranganathan, S.3
  • 30
    • 57249083976 scopus 로고    scopus 로고
    • SPOCTOPUS: A combined predictor of signal peptides and membrane protein topology
    • H. Viklund, A. Bernsel, M. Skwark, and A. Elofsson SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology Bioinformatics 24 2008 2928
    • (2008) Bioinformatics , vol.24 , pp. 2928
    • Viklund, H.1    Bernsel, A.2    Skwark, M.3    Elofsson, A.4
  • 31
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • L. Kall, A. Krogh, and E.L. Sonnhammer A combined transmembrane topology and signal peptide prediction method J. Mol. Biol. 338 2004 1027
    • (2004) J. Mol. Biol. , vol.338 , pp. 1027
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.L.3
  • 32
    • 57149112523 scopus 로고    scopus 로고
    • Transmembrane topology and signal peptide prediction using dynamic Bayesian networks
    • S.M. Reynolds, L. Kall, M.E. Riffle, J.A. Bilmes, and W.S. Noble Transmembrane topology and signal peptide prediction using dynamic Bayesian networks PLoS Comput. Biol. 4 2008 e1000213
    • (2008) PLoS Comput. Biol. , vol.4 , pp. 1000213
    • Reynolds, S.M.1    Kall, L.2    Riffle, M.E.3    Bilmes, J.A.4    Noble, W.S.5
  • 33
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • D.T. Jones Improving the accuracy of transmembrane protein topology prediction using evolutionary information Bioinformatics 23 2007 538
    • (2007) Bioinformatics , vol.23 , pp. 538
    • Jones, D.T.1
  • 34
    • 67649472570 scopus 로고    scopus 로고
    • Transmembrane protein topology prediction using support vector machines
    • T. Nugent, and D.T. Jones Transmembrane protein topology prediction using support vector machines BMC Bioinforma. 10 2009 159
    • (2009) BMC Bioinforma. , vol.10 , pp. 159
    • Nugent, T.1    Jones, D.T.2
  • 35
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: Discriminating signal peptides from transmembrane regions
    • T.N. Petersen, S. Brunak, G. von Heijne, and H. Nielsen SignalP 4.0: discriminating signal peptides from transmembrane regions Nat. Methods 8 2011 785
    • (2011) Nat. Methods , vol.8 , pp. 785
    • Petersen, T.N.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 36
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • A. Krogh, B. Larsson, G. von Heijne, and E.L. Sonnhammer Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J. Mol. Biol. 305 2001 567
    • (2001) J. Mol. Biol. , vol.305 , pp. 567
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.4
  • 38
    • 0036038940 scopus 로고    scopus 로고
    • Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway
    • R.W. Rose, T. Bruser, J.C. Kissinger, and M. Pohlschroder Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway Mol. Microbiol. 45 2002 943
    • (2002) Mol. Microbiol. , vol.45 , pp. 943
    • Rose, R.W.1    Bruser, T.2    Kissinger, J.C.3    Pohlschroder, M.4
  • 40
    • 78149257874 scopus 로고    scopus 로고
    • Combined prediction of Tat and Sec signal peptides with hidden Markov models
    • P.G. Bagos, E.P. Nikolaou, T.D. Liakopoulos, and K.D. Tsirigos Combined prediction of Tat and Sec signal peptides with hidden Markov models Bioinformatics 26 2010 2811
    • (2010) Bioinformatics , vol.26 , pp. 2811
    • Bagos, P.G.1    Nikolaou, E.P.2    Liakopoulos, T.D.3    Tsirigos, K.D.4
  • 42
    • 61549096272 scopus 로고    scopus 로고
    • Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model
    • P.G. Bagos, K.D. Tsirigos, T.D. Liakopoulos, and S.J. Hamodrakas Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model J. Proteome Res. 7 2008 5082
    • (2008) J. Proteome Res. , vol.7 , pp. 5082
    • Bagos, P.G.1    Tsirigos, K.D.2    Liakopoulos, T.D.3    Hamodrakas, S.J.4
  • 46
    • 59449110078 scopus 로고    scopus 로고
    • SOSUI-GramN: High performance prediction for sub-cellular localization of proteins in Gram-negative bacteria
    • K. Imai, N. Asakawa, T. Tsuji, F. Akazawa, A. Ino, M. Sonoyama, and S. Mitaku SOSUI-GramN: high performance prediction for sub-cellular localization of proteins in Gram-negative bacteria Bioinformation 2 2008 417
    • (2008) Bioinformation , vol.2 , pp. 417
    • Imai, K.1    Asakawa, N.2    Tsuji, T.3    Akazawa, F.4    Ino, A.5    Sonoyama, M.6    Mitaku, S.7
  • 47
    • 34248531753 scopus 로고    scopus 로고
    • Locating proteins in the cell using TargetP, SignalP and related tools
    • O. Emanuelsson, S. Brunak, G. von Heijne, and H. Nielsen Locating proteins in the cell using TargetP, SignalP and related tools Nat. Protoc. 2 2007 953
    • (2007) Nat. Protoc. , vol.2 , pp. 953
    • Emanuelsson, O.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 49
    • 77954199597 scopus 로고    scopus 로고
    • PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
    • N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, S.C. Sahinalp, M. Ester, L.J. Foster, and F.S. Brinkman PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes Bioinformatics 26 2010 1608
    • (2010) Bioinformatics , vol.26 , pp. 1608
    • Yu, N.Y.1    Wagner, J.R.2    Laird, M.R.3    Melli, G.4    Rey, S.5    Lo, R.6    Dao, P.7    Sahinalp, S.C.8    Ester, M.9    Foster, L.J.10    Brinkman, F.S.11
  • 51
    • 84859512402 scopus 로고    scopus 로고
    • The predicted secretome of the plant pathogenic fungus Fusarium graminearum: A refined comparative analysis
    • N.A. Brown, J. Antoniw, and K.E. Hammond-Kosack The predicted secretome of the plant pathogenic fungus Fusarium graminearum: a refined comparative analysis PLoS One 7 2012 e33731
    • (2012) PLoS One , vol.7 , pp. 33731
    • Brown, N.A.1    Antoniw, J.2    Hammond-Kosack, K.E.3
  • 52
    • 84864361963 scopus 로고    scopus 로고
    • Proteomics of protein secretion by Aggregatibacter actinomycetemcomitans
    • V. Zijnge, T. Kieselbach, and J. Oscarsson Proteomics of protein secretion by Aggregatibacter actinomycetemcomitans PLoS One 7 2012 e41662
    • (2012) PLoS One , vol.7 , pp. 41662
    • Zijnge, V.1    Kieselbach, T.2    Oscarsson, J.3
  • 53
    • 79959943460 scopus 로고    scopus 로고
    • Fungal secretome database: Integrated platform for annotation of fungal secretomes
    • J. Choi, J. Park, D. Kim, K. Jung, S. Kang, and Y.H. Lee Fungal secretome database: integrated platform for annotation of fungal secretomes BMC Genomics 11 2010 105
    • (2010) BMC Genomics , vol.11 , pp. 105
    • Choi, J.1    Park, J.2    Kim, D.3    Jung, K.4    Kang, S.5    Lee, Y.H.6
  • 54
    • 79955678515 scopus 로고    scopus 로고
    • FunSecKB: The Fungal Secretome KnowledgeBase
    • G. Lum, and X.J. Min FunSecKB: the Fungal Secretome KnowledgeBase Database. (Oxford) 2011 2011 bar001
    • (2011) Database. (Oxford) , vol.2011 , pp. 001
    • Lum, G.1    Min, X.J.2
  • 55
    • 78549296762 scopus 로고    scopus 로고
    • LAB-Secretome: A genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria
    • M. Zhou, D. Theunissen, M. Wels, and R.J. Siezen LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria BMC Genomics 11 2010 651
    • (2010) BMC Genomics , vol.11 , pp. 651
    • Zhou, M.1    Theunissen, D.2    Wels, M.3    Siezen, R.J.4
  • 58
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • R. Aebersold, and M. Mann Mass spectrometry-based proteomics Nature 422 2003 198
    • (2003) Nature , vol.422 , pp. 198
    • Aebersold, R.1    Mann, M.2
  • 59
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • S.E. Ong, B. Blagoev, I. Kratchmarova, D.B. Kristensen, H. Steen, A. Pandey, and M. Mann Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell Proteomics 1 2002 376
    • (2002) Mol. Cell Proteomics , vol.1 , pp. 376
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 62
    • 0343376097 scopus 로고    scopus 로고
    • Difference gel electrophoresis: A single gel method for detecting changes in protein extracts
    • M. Unlu, M.E. Morgan, and J.S. Minden Difference gel electrophoresis: a single gel method for detecting changes in protein extracts Electrophoresis 18 1997 2071
    • (1997) Electrophoresis , vol.18 , pp. 2071
    • Unlu, M.1    Morgan, M.E.2    Minden, J.S.3
  • 63
    • 0042861611 scopus 로고    scopus 로고
    • The role of bioinformatics in two-dimensional gel electrophoresis
    • A.W. Dowsey, M.J. Dunn, and G.Z. Yang The role of bioinformatics in two-dimensional gel electrophoresis Proteomics 3 2003 1567
    • (2003) Proteomics , vol.3 , pp. 1567
    • Dowsey, A.W.1    Dunn, M.J.2    Yang, G.Z.3
  • 64
    • 0037390115 scopus 로고    scopus 로고
    • A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection
    • P. Cutler, G. Heald, I.R. White, and J. Ruan A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection Proteomics 3 2003 392
    • (2003) Proteomics , vol.3 , pp. 392
    • Cutler, P.1    Heald, G.2    White, I.R.3    Ruan, J.4
  • 65
    • 0038047143 scopus 로고    scopus 로고
    • Using statistical image models for objective evaluation of spot detection in two-dimensional gels
    • M. Rogers, J. Graham, and R.P. Tonge Using statistical image models for objective evaluation of spot detection in two-dimensional gels Proteomics 3 2003 879
    • (2003) Proteomics , vol.3 , pp. 879
    • Rogers, M.1    Graham, J.2    Tonge, R.P.3
  • 67
    • 63649124649 scopus 로고    scopus 로고
    • Influence of image-analysis software on quantitation of two-dimensional gel electrophoresis data
    • M. Stessl, C.R. Noe, and B. Lachmann Influence of image-analysis software on quantitation of two-dimensional gel electrophoresis data Electrophoresis 30 2009 325
    • (2009) Electrophoresis , vol.30 , pp. 325
    • Stessl, M.1    Noe, C.R.2    Lachmann, B.3
  • 68
    • 34648834050 scopus 로고    scopus 로고
    • The state of the art in the analysis of two-dimensional gel electrophoresis images
    • M. Berth, F.M. Moser, M. Kolbe, and J. Bernhardt The state of the art in the analysis of two-dimensional gel electrophoresis images Appl. Microbiol. Biotechnol. 76 2007 1223
    • (2007) Appl. Microbiol. Biotechnol. , vol.76 , pp. 1223
    • Berth, M.1    Moser, F.M.2    Kolbe, M.3    Bernhardt, J.4
  • 69
  • 72
    • 0036315870 scopus 로고    scopus 로고
    • 'Top down' protein characterization via tandem mass spectrometry
    • G.E. Reid, and S.A. McLuckey 'Top down' protein characterization via tandem mass spectrometry J. Mass Spectrom. 37 2002 663
    • (2002) J. Mass Spectrom. , vol.37 , pp. 663
    • Reid, G.E.1    McLuckey, S.A.2
  • 73
    • 77957894168 scopus 로고    scopus 로고
    • Dasatinib reduces FAK phosphorylation increasing the effects of RPI-1 inhibition in a RET/PTC1-expressing cell line
    • D. Caccia, F. Micciche, G. Cassinelli, P. Mondellini, P. Casalini, and I. Bongarzone Dasatinib reduces FAK phosphorylation increasing the effects of RPI-1 inhibition in a RET/PTC1-expressing cell line Mol. Cancer 9 2010
    • (2010) Mol. Cancer , vol.9
    • Caccia, D.1    Micciche, F.2    Cassinelli, G.3    Mondellini, P.4    Casalini, P.5    Bongarzone, I.6
  • 74
    • 84866175781 scopus 로고    scopus 로고
    • Profiling of the human monocytic cell secretome by quantitative label-free mass spectrometry identifies stimulus-specific cytokines and proinflammatory proteins
    • M. Groessl, H. Luksch, A. Rosen-Wolff, A. Shevchenko, and M. Gentzel Profiling of the human monocytic cell secretome by quantitative label-free mass spectrometry identifies stimulus-specific cytokines and proinflammatory proteins Proteomics 12 2012 2833
    • (2012) Proteomics , vol.12 , pp. 2833
    • Groessl, M.1    Luksch, H.2    Rosen-Wolff, A.3    Shevchenko, A.4    Gentzel, M.5
  • 75
    • 42049123691 scopus 로고    scopus 로고
    • Algorithms and tools for analysis and management of mass spectrometry data
    • P. Veltri Algorithms and tools for analysis and management of mass spectrometry data Brief. Bioinform. 9 2008 144
    • (2008) Brief. Bioinform. , vol.9 , pp. 144
    • Veltri, P.1
  • 76
    • 12944269065 scopus 로고
    • Rapid identification of proteins by peptide-mass fingerprinting
    • D.J. Pappin, P. Hojrup, and A.J. Bleasby Rapid identification of proteins by peptide-mass fingerprinting Curr. Biol. 3 1993 327
    • (1993) Curr. Biol. , vol.3 , pp. 327
    • Pappin, D.J.1    Hojrup, P.2    Bleasby, A.J.3
  • 77
    • 0034213595 scopus 로고    scopus 로고
    • ProFound: An expert system for protein identification using mass spectrometric peptide mapping information
    • W. Zhang, and B.T. Chait ProFound: an expert system for protein identification using mass spectrometric peptide mapping information Anal. Chem. 72 2000 2482
    • (2000) Anal. Chem. , vol.72 , pp. 2482
    • Zhang, W.1    Chait, B.T.2
  • 79
    • 0037953090 scopus 로고    scopus 로고
    • Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility
    • D.L. Tabb, M.J. MacCoss, C.C. Wu, S.D. Anderson, and J.R. Yates III Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility Anal. Chem. 75 2003 2470
    • (2003) Anal. Chem. , vol.75 , pp. 2470
    • Tabb, D.L.1    Maccoss, M.J.2    Wu, C.C.3    Anderson, S.D.4    Yates III, J.R.5
  • 80
    • 0345600791 scopus 로고    scopus 로고
    • GutenTag: High-throughput sequence tagging via an empirically derived fragmentation model
    • D.L. Tabb, A. Saraf, and J.R. Yates III GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model Anal. Chem. 75 2003 6415
    • (2003) Anal. Chem. , vol.75 , pp. 6415
    • Tabb, D.L.1    Saraf, A.2    Yates III, J.R.3
  • 82
    • 0036211823 scopus 로고    scopus 로고
    • RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
    • H.I. Field, D. Fenyo, and R.C. Beavis RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database Proteomics 2 2002 36
    • (2002) Proteomics , vol.2 , pp. 36
    • Field, H.I.1    Fenyo, D.2    Beavis, R.C.3
  • 83
    • 49749115277 scopus 로고    scopus 로고
    • Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method
    • S. Ryu, B. Gallis, Y.A. Goo, S.A. Shaffer, D. Radulovic, and D.R. Goodlett Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method Cancer Informat. 6 2008 243
    • (2008) Cancer Informat. , vol.6 , pp. 243
    • Ryu, S.1    Gallis, B.2    Goo, Y.A.3    Shaffer, S.A.4    Radulovic, D.5    Goodlett, D.R.6
  • 84
    • 0344737959 scopus 로고    scopus 로고
    • Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry
    • X.J. Li, H. Zhang, J.A. Ranish, and R. Aebersold Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry Anal. Chem. 75 2003 6648
    • (2003) Anal. Chem. , vol.75 , pp. 6648
    • Li, X.J.1    Zhang, H.2    Ranish, J.A.3    Aebersold, R.4
  • 85
    • 0034789979 scopus 로고    scopus 로고
    • Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
    • D.K. Han, J. Eng, H. Zhou, and R. Aebersold Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry Nat. Biotechnol. 19 2001 946
    • (2001) Nat. Biotechnol. , vol.19 , pp. 946
    • Han, D.K.1    Eng, J.2    Zhou, H.3    Aebersold, R.4
  • 86
    • 0346122950 scopus 로고    scopus 로고
    • A correlation algorithm for the automated quantitative analysis of shotgun proteomics data
    • M.J. MacCoss, C.C. Wu, H. Liu, R. Sadygov, and J.R. Yates III A correlation algorithm for the automated quantitative analysis of shotgun proteomics data Anal. Chem. 75 2003 6912
    • (2003) Anal. Chem. , vol.75 , pp. 6912
    • Maccoss, M.J.1    Wu, C.C.2    Liu, H.3    Sadygov, R.4    Yates III, J.R.5
  • 90
    • 84861168275 scopus 로고    scopus 로고
    • OCAP: An open comprehensive analysis pipeline for iTRAQ
    • P. Wang, P. Yang, and J.Y. Yang OCAP: an open comprehensive analysis pipeline for iTRAQ Bioinformatics 28 2012 1404
    • (2012) Bioinformatics , vol.28 , pp. 1404
    • Wang, P.1    Yang, P.2    Yang, J.Y.3
  • 94
    • 78149289532 scopus 로고    scopus 로고
    • In situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: Annotation by protein set enrichment analysis and gene ontology
    • S. Cha, M.B. Imielinski, T. Rejtar, E.A. Richardson, D. Thakur, D.C. Sgroi, and B.L. Karger In situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: annotation by protein set enrichment analysis and gene ontology Mol. Cell Proteomics 9 2010 2529
    • (2010) Mol. Cell Proteomics , vol.9 , pp. 2529
    • Cha, S.1    Imielinski, M.B.2    Rejtar, T.3    Richardson, E.A.4    Thakur, D.5    Sgroi, D.C.6    Karger, B.L.7
  • 95
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: Current tools, limitations, and open problems
    • P. Khatri, and S. Draghici Ontological analysis of gene expression data: current tools, limitations, and open problems Bioinformatics 21 2005 3587
    • (2005) Bioinformatics , vol.21 , pp. 3587
    • Khatri, P.1    Draghici, S.2
  • 100
    • 80053553395 scopus 로고    scopus 로고
    • Comparative analysis of the human hepatic and adipose tissue transcriptomes during LPS-induced inflammation leads to the identification of differential biological pathways and candidate biomarkers
    • E. Szalowska, M. Dijkstra, M.G. Elferink, D. Weening, M. de Vries, M. Bruinenberg, A. Hoek, H. Roelofsen, G.M. Groothuis, and R.J. Vonk Comparative analysis of the human hepatic and adipose tissue transcriptomes during LPS-induced inflammation leads to the identification of differential biological pathways and candidate biomarkers BMC Med. Genom. 4 2011 71
    • (2011) BMC Med. Genom. , vol.4 , pp. 71
    • Szalowska, E.1    Dijkstra, M.2    Elferink, M.G.3    Weening, D.4    De Vries, M.5    Bruinenberg, M.6    Hoek, A.7    Roelofsen, H.8    Groothuis, G.M.9    Vonk, R.J.10
  • 101
    • 84861580275 scopus 로고    scopus 로고
    • Using gene expression to predict differences in the secretome of human omental vs. Subcutaneous adipose tissue
    • N. Hoggard, M. Cruickshank, K.M. Moar, S. Bashir, and C.D. Mayer Using gene expression to predict differences in the secretome of human omental vs. subcutaneous adipose tissue Obesity (Silver Spring) 20 2012 1158
    • (2012) Obesity (Silver Spring) , vol.20 , pp. 1158
    • Hoggard, N.1    Cruickshank, M.2    Moar, K.M.3    Bashir, S.4    Mayer, C.D.5
  • 102
    • 82555200805 scopus 로고    scopus 로고
    • The salivary secretome of the tsetse fly Glossina pallidipes (Diptera: Glossinidae) infected by salivary gland hypertrophy virus
    • H.M. Kariithi, I.A. Ince, S. Boeren, A.M. Abd-Alla, A.G. Parker, S. Aksoy, J.M. Vlak, and M.M. Oers The salivary secretome of the tsetse fly Glossina pallidipes (Diptera: Glossinidae) infected by salivary gland hypertrophy virus PLoS Negl. Trop. Dis. 5 2011 e1371
    • (2011) PLoS Negl. Trop. Dis. , vol.5 , pp. 1371
    • Kariithi, H.M.1    Ince, I.A.2    Boeren, S.3    Abd-Alla, A.M.4    Parker, A.G.5    Aksoy, S.6    Vlak, J.M.7    Oers, M.M.8
  • 103
    • 84869047032 scopus 로고    scopus 로고
    • Novel traits of Trichoderma predicted through the analysis of its secretome
    • I.S. Druzhinina, E. Shelest, and C.P. Kubicek Novel traits of Trichoderma predicted through the analysis of its secretome FEMS Microbiol. Lett. 337 2012 1
    • (2012) FEMS Microbiol. Lett. , vol.337 , pp. 1
    • Druzhinina, I.S.1    Shelest, E.2    Kubicek, C.P.3
  • 106
    • 42049114671 scopus 로고    scopus 로고
    • The HUPO proteomics standards initiative - Easing communication and minimizing data loss in a changing world
    • S. Orchard, and H. Hermjakob The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world Brief. Bioinform. 9 2008 166
    • (2008) Brief. Bioinform. , vol.9 , pp. 166
    • Orchard, S.1    Hermjakob, H.2
  • 110
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
    • E.W. Deutsch, H. Lam, and R. Aebersold PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows EMBO Rep. 9 2008 429
    • (2008) EMBO Rep. , vol.9 , pp. 429
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 111
    • 77449100000 scopus 로고    scopus 로고
    • Using the PRIDE proteomics identifications database for knowledge discovery and data analysis
    • P. Jones, and L. Martens Using the PRIDE proteomics identifications database for knowledge discovery and data analysis Methods Mol. Biol. 604 2010 297
    • (2010) Methods Mol. Biol. , vol.604 , pp. 297
    • Jones, P.1    Martens, L.2
  • 113
  • 114
    • 45549103524 scopus 로고    scopus 로고
    • Breast tumor microenvironment: Proteomics highlights the treatments targeting secretome
    • S.T. Chen, T.L. Pan, H.F. Juan, T.Y. Chen, Y.S. Lin, and C.M. Huang Breast tumor microenvironment: proteomics highlights the treatments targeting secretome J. Proteome Res. 7 2008 1379
    • (2008) J. Proteome Res. , vol.7 , pp. 1379
    • Chen, S.T.1    Pan, T.L.2    Juan, H.F.3    Chen, T.Y.4    Lin, Y.S.5    Huang, C.M.6
  • 117
    • 34548182124 scopus 로고    scopus 로고
    • Identification of differentially secreted biomarkers using LC-MS/MS in isogenic cell lines representing a progression of breast cancer
    • F. Mbeunkui, B.J. Metge, L.A. Shevde, and L.K. Pannell Identification of differentially secreted biomarkers using LC-MS/MS in isogenic cell lines representing a progression of breast cancer J. Proteome Res. 6 2007 2993
    • (2007) J. Proteome Res. , vol.6 , pp. 2993
    • Mbeunkui, F.1    Metge, B.J.2    Shevde, L.A.3    Pannell, L.K.4
  • 119
    • 84858964200 scopus 로고    scopus 로고
    • Adipokines: A treasure trove for the discovery of biomarkers for metabolic disorders
    • S. Lehr, S. Hartwig, and H. Sell Adipokines: a treasure trove for the discovery of biomarkers for metabolic disorders Proteomics Clin. Appl. 6 2012 91
    • (2012) Proteomics Clin. Appl. , vol.6 , pp. 91
    • Lehr, S.1    Hartwig, S.2    Sell, H.3
  • 120
    • 84857838864 scopus 로고    scopus 로고
    • Harnessing the mesenchymal stem cell secretome for the treatment of cardiovascular disease
    • S.H. Ranganath, O. Levy, M.S. Inamdar, and J.M. Karp Harnessing the mesenchymal stem cell secretome for the treatment of cardiovascular disease Cell Stem Cell 10 2012 244
    • (2012) Cell Stem Cell , vol.10 , pp. 244
    • Ranganath, S.H.1    Levy, O.2    Inamdar, M.S.3    Karp, J.M.4
  • 121
    • 80052496433 scopus 로고    scopus 로고
    • Mesenchymal stem cells rescue the Alzheimer's disease cell model from cell death induced by misfolded truncated tau
    • N. Zilka, M. Zilkova, Z. Kazmerova, M. Sarissky, V. Cigankova, and M. Novak Mesenchymal stem cells rescue the Alzheimer's disease cell model from cell death induced by misfolded truncated tau Neuroscience 193 2011 330
    • (2011) Neuroscience , vol.193 , pp. 330
    • Zilka, N.1    Zilkova, M.2    Kazmerova, Z.3    Sarissky, M.4    Cigankova, V.5    Novak, M.6
  • 122
    • 84862324402 scopus 로고    scopus 로고
    • Moonlighting is mainstream: Paradigm adjustment required
    • S.D. Copley Moonlighting is mainstream: paradigm adjustment required Bioessays 34 2012 578
    • (2012) Bioessays , vol.34 , pp. 578
    • Copley, S.D.1
  • 123
    • 73449125521 scopus 로고    scopus 로고
    • Proteomic identification of multitasking proteins in unexpected locations complicates drug targeting
    • G.S. Butler, and C.M. Overall Proteomic identification of multitasking proteins in unexpected locations complicates drug targeting Nat. Rev. Drug Discov. 8 2009 935
    • (2009) Nat. Rev. Drug Discov. , vol.8 , pp. 935
    • Butler, G.S.1    Overall, C.M.2
  • 125
    • 43249106267 scopus 로고    scopus 로고
    • The novel fragment of tyrosyl tRNA synthetase, mini-TyrRS, is secreted to induce an angiogenic response in endothelial cells
    • Y. Greenberg, M. King, W.B. Kiosses, K. Ewalt, X. Yang, P. Schimmel, J.S. Reader, and E. Tzima The novel fragment of tyrosyl tRNA synthetase, mini-TyrRS, is secreted to induce an angiogenic response in endothelial cells FASEB J. 22 2008 1597
    • (2008) FASEB J. , vol.22 , pp. 1597
    • Greenberg, Y.1    King, M.2    Kiosses, W.B.3    Ewalt, K.4    Yang, X.5    Schimmel, P.6    Reader, J.S.7    Tzima, E.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.