메뉴 건너뛰기




Volumn 24, Issue 20, 2008, Pages 2370-2375

Computational prediction of human proteins that can be secreted into the bloodstream

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; PLASMA PROTEIN; SECRETORY PROTEIN; SIGNAL PEPTIDE;

EID: 53749104774     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn418     Document Type: Article
Times cited : (57)

References (53)
  • 1
    • 0003206867 scopus 로고    scopus 로고
    • Toward a human blood serum proteome: Analysis by multidimensional separation coupled with mass spectrometry
    • Adkins,J.N. et al. (2002) Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell Proteomics, 1, 947-955.
    • (2002) Mol. Cell Proteomics , vol.1 , pp. 947-955
    • Adkins, J.N.1
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 3
    • 0001644020 scopus 로고    scopus 로고
    • The human plasma proteome: History, character, and diagnostic prospects
    • Anderson,N.L. and Anderson,N.G. (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell Proteomics 1, 845-867.
    • (2002) Mol. Cell Proteomics , vol.1 , pp. 845-867
    • Anderson, N.L.1    Anderson, N.G.2
  • 4
    • 0011542799 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Bateman,A. et al. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280.
    • (2002) Nucleic Acids Res , vol.30 , pp. 276-280
    • Bateman, A.1
  • 5
    • 25444441166 scopus 로고    scopus 로고
    • Prediction of twin-arginine signal peptides
    • Bendtsen,J.D. et al. (2005) Prediction of twin-arginine signal peptides. BMC Biomformatics, 6, 167.
    • (2005) BMC Biomformatics , vol.6 , pp. 167
    • Bendtsen, J.D.1
  • 6
    • 24744435534 scopus 로고    scopus 로고
    • Kernel methods for predicting protein-protein interactions
    • Ben-Hur,A. and Noble,W.S. (2005) Kernel methods for predicting protein-protein interactions. Biomformatics, 21 (Suppl. 1), i38-i46.
    • (2005) Biomformatics , vol.21 , Issue.SUPPL. 1
    • Ben-Hur, A.1    Noble, W.S.2
  • 7
    • 2542458612 scopus 로고    scopus 로고
    • Classification of nuclear receptors based on amino acid composition and dipeptide composition
    • Bhasin,M. and Raghava,G.P. (2004) Classification of nuclear receptors based on amino acid composition and dipeptide composition. J. Biol. Chem., 279, 23262-23266.
    • (2004) J. Biol. Chem , vol.279 , pp. 23262-23266
    • Bhasin, M.1    Raghava, G.P.2
  • 8
    • 33748510186 scopus 로고    scopus 로고
    • The sweet side of biomarker discovery
    • Bosques,C.J. et al. (2006) The sweet side of biomarker discovery. Nat. Biotechnol., 24, 1100-1101.
    • (2006) Nat. Biotechnol , vol.24 , pp. 1100-1101
    • Bosques, C.J.1
  • 9
    • 33751326131 scopus 로고    scopus 로고
    • Molecular markers of prostate cancer
    • Bradford,T.J. et al. (2006) Molecular markers of prostate cancer. Urol. Oncol., 24, 538-551.
    • (2006) Urol. Oncol , vol.24 , pp. 538-551
    • Bradford, T.J.1
  • 10
    • 0032053823 scopus 로고    scopus 로고
    • The unique physiology of solid tumors: Opportunities (and problems) for cancer therapy
    • Brown,J.M. and Giaccia,A.J. (1998) The unique physiology of solid tumors: Opportunities (and problems) for cancer therapy. Cancer Res. 58, 1408-1416.
    • (1998) Cancer Res , vol.58 , pp. 1408-1416
    • Brown, J.M.1    Giaccia, A.J.2
  • 11
    • 0035477337 scopus 로고    scopus 로고
    • Secreted and cell surface genes expressed in benign and malignant colorectal tumors
    • Buckhaults,P. et al. (2001) Secreted and cell surface genes expressed in benign and malignant colorectal tumors. Cancer Res., 61, 6996-7001.
    • (2001) Cancer Res , vol.61 , pp. 6996-7001
    • Buckhaults, P.1
  • 12
    • 0034740222 scopus 로고    scopus 로고
    • Drug design by machine learning: Support vector machines for pharmaceutical data analysis
    • Burbidge,R. et al. (2001) Drug design by machine learning: Support vector machines for pharmaceutical data analysis. Comput. Chem., 26, 5-14.
    • (2001) Comput. Chem , vol.26 , pp. 5-14
    • Burbidge, R.1
  • 13
    • 0042622243 scopus 로고    scopus 로고
    • SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence
    • Cai,C.Z. et al. (2003) SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res., 31, 3692-3697.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3692-3697
    • Cai, C.Z.1
  • 14
    • 13444269483 scopus 로고    scopus 로고
    • SPD - a web-based secreted protein database
    • Chen,Y. et al. (2005) SPD - a web-based secreted protein database. Nucleic Acids Res., 33, D169-D173.
    • (2005) Nucleic Acids Res , vol.33
    • Chen, Y.1
  • 15
    • 33748199236 scopus 로고    scopus 로고
    • Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties
    • Cui,J. et al. (2007a) Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties. Mol. Immunol., 44, 514-520.
    • (2007) Mol. Immunol , vol.44 , pp. 514-520
    • Cui, J.1
  • 16
    • 34249291647 scopus 로고    scopus 로고
    • Advances in exploration of machine learning methods for predicting functional class and interaction profiles of proteins and peptides irrespective of sequence homology
    • Cui,J. et al. (2007b) Advances in exploration of machine learning methods for predicting functional class and interaction profiles of proteins and peptides irrespective of sequence homology. Curr. Bioinformatics, 2, 95-112.
    • (2007) Curr. Bioinformatics , vol.2 , pp. 95-112
    • Cui, J.1
  • 17
    • 3943099373 scopus 로고    scopus 로고
    • Structural insights into the signal recognition particle
    • Doudna,J.A. and Batey,R.T. (2004) Structural insights into the signal recognition particle. Annu. Rev. Biochem., 73, 539-557.
    • (2004) Annu. Rev. Biochem , vol.73 , pp. 539-557
    • Doudna, J.A.1    Batey, R.T.2
  • 18
    • 0029047319 scopus 로고
    • Prediction of protein folding class using global description of amino acid sequence
    • Dubchak,I. et al. (1995) Prediction of protein folding class using global description of amino acid sequence. Proc. Natl Acad. Sci. USA 92, 8700-8704.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 8700-8704
    • Dubchak, I.1
  • 19
    • 0029946575 scopus 로고    scopus 로고
    • Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods
    • Eisenhaber,F. et al. (1996) Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods. Proteins, 25, 157-168.
    • (1996) Proteins , vol.25 , pp. 157-168
    • Eisenhaber, F.1
  • 20
    • 0033781978 scopus 로고    scopus 로고
    • Prediction of membrane protein types based on the hydrophobic index of amino acids
    • Feng,Z.P. and Zhang,C.T. (2000) Prediction of membrane protein types based on the hydrophobic index of amino acids. J. Protein Chem., 19, 269-275.
    • (2000) J. Protein Chem , vol.19 , pp. 269-275
    • Feng, Z.P.1    Zhang, C.T.2
  • 21
    • 33747375161 scopus 로고    scopus 로고
    • pTARGET: A web server for predicting protein subcellular localization
    • Guda,C. (2006) pTARGET: A web server for predicting protein subcellular localization. Nucleic Acids Res., 34, W210-W213.
    • (2006) Nucleic Acids Res , vol.34
    • Guda, C.1
  • 22
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • Hanahan,D. and Weinberg,R.A. (2000) The hallmarks of cancer. Cell, 100, 57-70.
    • (2000) Cell , vol.100 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 23
    • 34547560275 scopus 로고    scopus 로고
    • WoLF PSORT: Protein localization predictor
    • Horton,P. et al. (2007) WoLF PSORT: Protein localization predictor. Nucleic Acids Res., 35, W585-W587.
    • (2007) Nucleic Acids Res , vol.35
    • Horton, P.1
  • 24
    • 0035957531 scopus 로고    scopus 로고
    • A novel method ofprotein secondary structure prediction with high segment overlap measure: Support vector machine approach
    • Hua,S. and Sun,Z. (2001) A novel method ofprotein secondary structure prediction with high segment overlap measure: Support vector machine approach. J. Mol. Biol., 308, 397-407.
    • (2001) J. Mol. Biol , vol.308 , pp. 397-407
    • Hua, S.1    Sun, Z.2
  • 25
    • 34247170626 scopus 로고    scopus 로고
    • Proteomics-based identification of secreted protein dihydrodiol dehydrogenase as a novel serum markers of non-small cell lung cancer
    • Huang,L.J. et al. (2006) Proteomics-based identification of secreted protein dihydrodiol dehydrogenase as a novel serum markers of non-small cell lung cancer. Lung Cancer, 54, 87-94.
    • (2006) Lung Cancer , vol.54 , pp. 87-94
    • Huang, L.J.1
  • 26
    • 0000545946 scopus 로고    scopus 로고
    • Improvements to Platt's SMO algorithm for SVM classifier design
    • Keerthi,S.S. et al. (2001) Improvements to Platt's SMO algorithm for SVM classifier design. Neural Comput., 13, 637-649.
    • (2001) Neural Comput , vol.13 , pp. 637-649
    • Keerthi, S.S.1
  • 27
    • 0037012469 scopus 로고    scopus 로고
    • Osteopontin as a potential diagnostic biomarker for ovarian cancer
    • Kim,J.H. et al. (2002) Osteopontin as a potential diagnostic biomarker for ovarian cancer. J. Am. Med. Assoc., 287, 1671-1679.
    • (2002) J. Am. Med. Assoc , vol.287 , pp. 1671-1679
    • Kim, J.H.1
  • 28
    • 19944425959 scopus 로고    scopus 로고
    • Identification of gastric cancer-related genes using a cDNA microarray containing novel expressed sequence tags expressed in gastric cancer cells
    • Kim,J.M. et al. (2005) Identification of gastric cancer-related genes using a cDNA microarray containing novel expressed sequence tags expressed in gastric cancer cells. Clin. Cancer Res., 11, 473-482.
    • (2005) Clin. Cancer Res , vol.11 , pp. 473-482
    • Kim, J.M.1
  • 29
    • 0035987843 scopus 로고    scopus 로고
    • Synthesis of factor D by gastric cancer-derived cell lines
    • Kitano,E. and Kitamura,H. (2002) Synthesis of factor D by gastric cancer-derived cell lines. Int. Immunopharmacol., 2, 843-848.
    • (2002) Int. Immunopharmacol , vol.2 , pp. 843-848
    • Kitano, E.1    Kitamura, H.2
  • 30
    • 33847274230 scopus 로고    scopus 로고
    • Computational classification of classically secreted proteins
    • Klee,E.W. and Sosa,C.P. (2007) Computational classification of classically secreted proteins. Drug Discov. Today, 12, 234-240.
    • (2007) Drug Discov. Today , vol.12 , pp. 234-240
    • Klee, E.W.1    Sosa, C.P.2
  • 31
    • 40249103182 scopus 로고    scopus 로고
    • Identification of genes involved in squamous cell carcinoma of the lung using synchronized data from DNA copy number and transcript expression profiling analysis
    • Lo,K.C. et al. (2008) Identification of genes involved in squamous cell carcinoma of the lung using synchronized data from DNA copy number and transcript expression profiling analysis. Lung Cancer, 59 315-331.
    • (2008) Lung Cancer , vol.59 , pp. 315-331
    • Lo, K.C.1
  • 32
    • 0036630603 scopus 로고    scopus 로고
    • Areas beneath the relative operating characteristics (ROC) and levels (ROL) curves: Statistical significance and interpretation
    • Mason,S.J. and Graham,N.E. (2002) Areas beneath the relative operating characteristics (ROC) and levels (ROL) curves: Statistical significance and interpretation. Q. J. Roy. Meteorol. Soc., 128, 2145-2166.
    • (2002) Q. J. Roy. Meteorol. Soc , vol.128 , pp. 2145-2166
    • Mason, S.J.1    Graham, N.E.2
  • 33
    • 0033738137 scopus 로고    scopus 로고
    • A comparison of signal sequence prediction methods using a test set of signal peptides
    • Menne,K.M. et al. (2000) A comparison of signal sequence prediction methods using a test set of signal peptides. Bioinformatics, 16, 741-742.
    • (2000) Bioinformatics , vol.16 , pp. 741-742
    • Menne, K.M.1
  • 34
    • 0035802183 scopus 로고    scopus 로고
    • Prostasin, a potential serum marker for ovarian cancer: Identification through microarray technology
    • Mok,S.C. et al. (2001) Prostasin, a potential serum marker for ovarian cancer: Identification through microarray technology. J. Natl Cancer Inst., 93, 1458-1464.
    • (2001) J. Natl Cancer Inst , vol.93 , pp. 1458-1464
    • Mok, S.C.1
  • 35
    • 0036677029 scopus 로고    scopus 로고
    • Predicting protein cellular localization using a domain projection method
    • Moft,R. et al. (2002) Predicting protein cellular localization using a domain projection method. Genome Res., 12, 1168-1174.
    • (2002) Genome Res , vol.12 , pp. 1168-1174
    • Moft, R.1
  • 36
    • 16244398103 scopus 로고    scopus 로고
    • Mimicking cellular sorting improves prediction of subeellular localization
    • Nair,R. and Rost,B. (2005) Mimicking cellular sorting improves prediction of subeellular localization. J. Mol. Biol., 348, 85-100.
    • (2005) J. Mol. Biol , vol.348 , pp. 85-100
    • Nair, R.1    Rost, B.2
  • 37
    • 23944492134 scopus 로고    scopus 로고
    • Overview of the HUPO plasma proteome project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
    • Omenn,G.S. et al. (2005) Overview of the HUPO plasma proteome project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics, 5, 3226-3245.
    • (2005) Proteomics , vol.5 , pp. 3226-3245
    • Omenn, G.S.1
  • 38
    • 29144523534 scopus 로고    scopus 로고
    • A human transporter protein that mediates the final excretion step for toxic organic cations
    • Otsuka,M. et al. (2005) A human transporter protein that mediates the final excretion step for toxic organic cations. Proc. Natl Acad. Sci. USA, 102, 17923-17928.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 17923-17928
    • Otsuka, M.1
  • 39
    • 34547217974 scopus 로고    scopus 로고
    • Biomarker discovery from uveal melanoma secretomes: Identification of gp100 and cathepsin D in patient serum
    • Pardo,M. et al. (2007) Biomarker discovery from uveal melanoma secretomes: Identification of gp100 and cathepsin D in patient serum. J. Proteome Res., 6, 2802-2811.
    • (2007) J. Proteome Res , vol.6 , pp. 2802-2811
    • Pardo, M.1
  • 40
    • 12444339443 scopus 로고    scopus 로고
    • The human serum proteome: Display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins
    • Pieper,R. et al. (2003) The human serum proteome: Display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics, 3, 1345-1364.
    • (2003) Proteomics , vol.3 , pp. 1345-1364
    • Pieper, R.1
  • 41
    • 0003120218 scopus 로고    scopus 로고
    • Fast training of support vector machines using sequential minimal optimization
    • MIT Press, Cambridge, MA, USA, pp
    • Platt,J.C. (1999) Fast training of support vector machines using sequential minimal optimization. In Advances in Kernel Methods: Support Vector Learning. MIT Press, Cambridge, MA, USA, pp. 185-208.
    • (1999) Advances in Kernel Methods: Support Vector Learning , pp. 185-208
    • Platt, J.C.1
  • 42
    • 0027997161 scopus 로고
    • The DEF database of sequence based protein fold class predictions
    • Reczko,M. and Bohr,H. (1994) The DEF database of sequence based protein fold class predictions. Nucleic Acids Res., 22, 3616-3619.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3616-3619
    • Reczko, M.1    Bohr, H.2
  • 43
    • 0037387176 scopus 로고    scopus 로고
    • Use of serological proteomic methods to find biomarkers associated with breast cancer
    • Rui,Z. et al. (2003) Use of serological proteomic methods to find biomarkers associated with breast cancer. Proteomics, 3, 433-439.
    • (2003) Proteomics , vol.3 , pp. 433-439
    • Rui, Z.1
  • 44
    • 0002652573 scopus 로고    scopus 로고
    • Peptidomics technologies for human body fluids
    • Schrader,M. and Schulz-Knappe,P. (2001) Peptidomics technologies for human body fluids. Trends Biotechnol., 19, S55-S60.
    • (2001) Trends Biotechnol , vol.19
    • Schrader, M.1    Schulz-Knappe, P.2
  • 45
    • 35748966976 scopus 로고    scopus 로고
    • Protein solubility: Sequence based prediction and experimental verification
    • Smialowski,R et al. (2007) Protein solubility: Sequence based prediction and experimental verification. Bioinformatics, 23 2536-2542.
    • (2007) Bioinformatics , vol.23 , pp. 2536-2542
    • Smialowski, R.1
  • 46
    • 0021958679 scopus 로고
    • Autocrine growth factors and cancer
    • Sporn,M.B. and Roberts,A.B. (1985) Autocrine growth factors and cancer. Nature, 313, 745-747.
    • (1985) Nature , vol.313 , pp. 745-747
    • Sporn, M.B.1    Roberts, A.B.2
  • 47
    • 35448970604 scopus 로고    scopus 로고
    • Protein subcellular localization prediction based on compartment-specific features and structure conservation
    • Su,E.C. et al. (2007) Protein subcellular localization prediction based on compartment-specific features and structure conservation. BMC Bioinformatics, 8, 330.
    • (2007) BMC Bioinformatics , vol.8 , pp. 330
    • Su, E.C.1
  • 48
    • 35448932757 scopus 로고    scopus 로고
    • Derivation of stable microarray cancer-differentiating signatures using consensus scoring of multiple random sampling and gene-ranking consistency evaluation
    • Tang,Z.Q. et al. (2007) Derivation of stable microarray cancer-differentiating signatures using consensus scoring of multiple random sampling and gene-ranking consistency evaluation. Cancer Res. 67, 9996-10003.
    • (2007) Cancer Res , vol.67 , pp. 9996-10003
    • Tang, Z.Q.1
  • 49
    • 37349103372 scopus 로고    scopus 로고
    • TATPred: A Bayesian method for the identification of twin arginine translocation pathway signal sequences
    • Taylor,P.D. et al. (2006) TATPred: A Bayesian method for the identification of twin arginine translocation pathway signal sequences. Bioinformation, 1, 184-187.
    • (2006) Bioinformation , vol.1 , pp. 184-187
    • Taylor, P.D.1
  • 50
    • 0033818171 scopus 로고    scopus 로고
    • Signal peptide-dependent protein transport in Bacillus subtilis: A genome-based survey of the secretome
    • Tjalsma,H. et al. (2000) Signal peptide-dependent protein transport in Bacillus subtilis: A genome-based survey of the secretome. Microbiol. Mol. Biol. Rev., 64, 515-547.
    • (2000) Microbiol. Mol. Biol. Rev , vol.64 , pp. 515-547
    • Tjalsma, H.1
  • 51
    • 0037250739 scopus 로고    scopus 로고
    • Serological and proteomic evaluation of antibody responses in the identification of tumor antigens in renal cell carcinoma
    • Unwin,R.D. et al. (2003) Serological and proteomic evaluation of antibody responses in the identification of tumor antigens in renal cell carcinoma. Proteomics, 3, 45-55.
    • (2003) Proteomics , vol.3 , pp. 45-55
    • Unwin, R.D.1
  • 52
    • 0035970050 scopus 로고    scopus 로고
    • Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer
    • Welsh,J.B. et al. (2001) Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc. Natl Acad. Sci. USA, 98, 1176-118l.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98
    • Welsh, J.B.1
  • 53
    • 0037452997 scopus 로고    scopus 로고
    • Large-scale delineation of secreted protein biomarkers overexpressed in cancer tissue and serum
    • Welsh,J.B. et al. (2003) Large-scale delineation of secreted protein biomarkers overexpressed in cancer tissue and serum. Proc. Natl Acad. Sci. USA, 100, 3410-3415.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 3410-3415
    • Welsh, J.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.