메뉴 건너뛰기




Volumn 12, Issue 1, 2013, Pages 263-276

A critical assessment of feature selection methods for biomarker discovery in clinical proteomics

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; PEPTIDE;

EID: 84871862591     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M112.022566     Document Type: Article
Times cited : (116)

References (49)
  • 2
    • 70349664473 scopus 로고    scopus 로고
    • How-to guide on biomarkers: Biomarker definitions, validation and applications with examples from cardiovascular disease
    • Puntmann, V. O. (2009) How-to guide on biomarkers: biomarker definitions, validation and applications with examples from cardiovascular disease. Postgrad. Med. J. 85, 538-545
    • (2009) Postgrad. Med. J. , vol.85 , pp. 538-545
    • Puntmann, V.O.1
  • 3
    • 33747030845 scopus 로고    scopus 로고
    • Protein biomarker discovery and validation: The long and uncertain path to clinical utility
    • Rifai, N., Gillette, M. A., and Carr, S. A. (2006) Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 24, 971-983
    • (2006) Nat. Biotechnol. , vol.24 , pp. 971-983
    • Rifai, N.1    Gillette, M.A.2    Carr, S.A.3
  • 4
    • 84862316959 scopus 로고    scopus 로고
    • msCompare: A framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies
    • Hoekman, B., Breitling, R., Suits, F., Bischoff, R., and Horvatovich, P. (2012) msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies. Mol. Cell. Proteomics 11, M111.015974
    • (2012) Mol. Cell. Proteomics , vol.11
    • Hoekman, B.1    Breitling, R.2    Suits, F.3    Bischoff, R.4    Horvatovich, P.5
  • 5
    • 35748932917 scopus 로고    scopus 로고
    • A review of feature selection techniques in bioinformatics
    • Saeys, Y., Inza, I., and Larranaga, P. (2007) A review of feature selection techniques in bioinformatics. Bioinformatics 23, 2507-2517
    • (2007) Bioinformatics , vol.23 , pp. 2507-2517
    • Saeys, Y.1    Inza, I.2    Larranaga, P.3
  • 8
    • 0031381525 scopus 로고    scopus 로고
    • Wrappers for feature subset selection
    • Kohavi, R., and John, G. H. (1997) Wrappers for feature subset selection. Artif. Intell. 97, 273-324
    • (1997) Artif. Intell. , vol.97 , pp. 273-324
    • Kohavi, R.1    John, G.H.2
  • 9
    • 42049102625 scopus 로고    scopus 로고
    • Approaches to dimensionality reduction in proteomic biomarker studies
    • Hilario, M., and Kalousis, A. (2008) Approaches to dimensionality reduction in proteomic biomarker studies. Brief Bioinform. 9, 102-118
    • (2008) Brief Bioinform. , vol.9 , pp. 102-118
    • Hilario, M.1    Kalousis, A.2
  • 10
    • 69249159556 scopus 로고    scopus 로고
    • Development of biomarker classifiers from high-dimensional data
    • Baek, S., Tsai, C. A., and Chen, J. J. (2009) Development of biomarker classifiers from high-dimensional data. Brief Bioinform. 10, 537-546
    • (2009) Brief Bioinform. , vol.10 , pp. 537-546
    • Baek, S.1    Tsai, C.A.2    Chen, J.J.3
  • 11
    • 75649147442 scopus 로고    scopus 로고
    • Feature selection and machine learning with mass spectrometry data
    • Datta, S., and Pihur, V. (2010) Feature selection and machine learning with mass spectrometry data. Methods Mol. Biol. 593, 205-229
    • (2010) Methods Mol. Biol. , vol.593 , pp. 205-229
    • Datta, S.1    Pihur, V.2
  • 12
    • 77349109063 scopus 로고    scopus 로고
    • Data characteristics that determine classifier performance
    • Van der Walt, C., and Barnard, E. (2006) Data characteristics that determine classifier performance. SAIEE Africa Research Journal, 98, 87-93
    • (2006) SAIEE Africa Research Journal , vol.98 , pp. 87-93
    • Van Der Walt, C.1    Barnard, E.2
  • 13
    • 33746909835 scopus 로고    scopus 로고
    • Assessing the performance of statistical validation tools for megavariate metabolomics data
    • Rubingh, C., Bijlsma, S., Derks, E., Bobeldijk, I., Verheij, E., Kochhar, S., and Smilde, A. (2006) Assessing the performance of statistical validation tools for megavariate metabolomics data. Metabolomics 2, 53-61
    • (2006) Metabolomics , vol.2 , pp. 53-61
    • Rubingh, C.1    Bijlsma, S.2    Derks, E.3    Bobeldijk, I.4    Verheij, E.5    Kochhar, S.6    Smilde, A.7
  • 14
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289-300
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 15
    • 0037076272 scopus 로고    scopus 로고
    • Diagnosis of multiple cancer types by shrunken centroids of gene expression
    • Tibshirani, R., Hastie, T., Narasimhan, B., and Chu, G. (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl. Acad. Sci. U.S.A. 99, 6567-6572
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 6567-6572
    • Tibshirani, R.1    Hastie, T.2    Narasimhan, B.3    Chu, G.4
  • 16
    • 2342533421 scopus 로고    scopus 로고
    • Class prediction by nearest shrunken centroids, with applications to DNA microarrays
    • Tibshirani, R., Hastie, T., Narasimhan, B., and Chu, G. (2003) Class prediction by nearest shrunken centroids, with applications to DNA microarrays. Stat. Sci. 18, 104-117
    • (2003) Stat. Sci. , vol.18 , pp. 104-117
    • Tibshirani, R.1    Hastie, T.2    Narasimhan, B.3    Chu, G.4
  • 17
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon, I., Weston, J., Barnhill, S., and Vapnik, V. (2002) Gene selection for cancer classification using support vector machines. Mach. Learn. 46, 389-422
    • (2002) Mach. Learn. , vol.46 , pp. 389-422
    • Guyon, I.1    Weston, J.2    Barnhill, S.3    Vapnik, V.4
  • 18
    • 0037350844 scopus 로고    scopus 로고
    • Partial least squares for discrimination
    • Barker, M., and Rayens, W. (2003) Partial least squares for discrimination. J. Chemom. 17, 166-173
    • (2003) J. Chemom. , vol.17 , pp. 166-173
    • Barker, M.1    Rayens, W.2
  • 19
    • 0020824208 scopus 로고
    • Discriminant analysis by double stage principal component analysis
    • Hoogerbrugge, R., Willig, S. J., and Kistemaker, P. G. (1983) Discriminant analysis by double stage principal component analysis. Anal. Chem. 55, 1710-1712
    • (1983) Anal. Chem. , vol.55 , pp. 1710-1712
    • Hoogerbrugge, R.1    Willig, S.J.2    Kistemaker, P.G.3
  • 20
    • 4344571581 scopus 로고    scopus 로고
    • Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
    • Breitling, R., Armengaud, P., Amtmann, A., and Herzyk, P. (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett. 573, 83-92
    • (2004) FEBS Lett. , vol.573 , pp. 83-92
    • Breitling, R.1    Armengaud, P.2    Amtmann, A.3    Herzyk, P.4
  • 23
    • 0042972838 scopus 로고    scopus 로고
    • A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: Support vector machine classification of peptide MS/MS spectra and SEQUEST scores
    • Anderson, D. C., Li, W., Payan, D. G., and Noble, W. S. (2003) A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res. 2, 137-146
    • (2003) J. Proteome Res. , vol.2 , pp. 137-146
    • Anderson, D.C.1    Li, W.2    Payan, D.G.3    Noble, W.S.4
  • 24
    • 33744992230 scopus 로고    scopus 로고
    • Constructing support vector machine ensembles for cancer classification based on proteomic profiling
    • Mao, Y., Zhou, X. B., Pi, D. Y., and Sun, Y. X. (2005) Constructing support vector machine ensembles for cancer classification based on proteomic profiling. Genomics Proteomics Bioinformatics 3, 238-241
    • (2005) Genomics Proteomics Bioinformatics , vol.3 , pp. 238-241
    • Mao, Y.1    Zhou, X.B.2    Pi, D.Y.3    Sun, Y.X.4
  • 25
    • 33748763578 scopus 로고    scopus 로고
    • Support vector machine-based feature selection for classification of liver fibrosis grade in chronic hepatitis C
    • Jiang, Z., Yamauchi, K., Yoshioka, K., Aoki, K., Kuroyanagi, S., Iwata, A., Yang, J., and Wang, K. (2006) Support vector machine-based feature selection for classification of liver fibrosis grade in chronic hepatitis C. J. Med. Syst. 30, 389-394
    • (2006) J. Med. Syst. , vol.30 , pp. 389-394
    • Jiang, Z.1    Yamauchi, K.2    Yoshioka, K.3    Aoki, K.4    Kuroyanagi, S.5    Iwata, A.6    Yang, J.7    Wang, K.8
  • 26
    • 34548847449 scopus 로고    scopus 로고
    • Prediction of prostate cancer using hair trace element concentration and support vector machine method
    • Guo, J., Deng, W., Zhang, L., Li, C., Wu, P., and Mao, P. (2007) Prediction of prostate cancer using hair trace element concentration and support vector machine method. Biol. Trace Elem. Res. 116, 257-272
    • (2007) Biol. Trace Elem. Res. , vol.116 , pp. 257-272
    • Guo, J.1    Deng, W.2    Zhang, L.3    Li, C.4    Wu, P.5    Mao, P.6
  • 27
    • 34547663168 scopus 로고    scopus 로고
    • Urinary nucleosides based potential biomarker selection by support vector machine for bladder cancer recognition
    • Mao, Y., Zhao, X., Wang, S., and Cheng, Y. (2007) Urinary nucleosides based potential biomarker selection by support vector machine for bladder cancer recognition. Anal. Chim. Acta 598, 34-40
    • (2007) Anal. Chim. Acta , vol.598 , pp. 34-40
    • Mao, Y.1    Zhao, X.2    Wang, S.3    Cheng, Y.4
  • 28
    • 53749088871 scopus 로고    scopus 로고
    • A support vector machine approach to assess drug efficacy of interferon-alpha and ribavirin combination therapy
    • Lin, E., and Hwang, Y. (2008) A support vector machine approach to assess drug efficacy of interferon-alpha and ribavirin combination therapy. Mol. Diagn. Ther. 12, 219-223
    • (2008) Mol. Diagn. Ther. , vol.12 , pp. 219-223
    • Lin, E.1    Hwang, Y.2
  • 29
    • 41649102931 scopus 로고    scopus 로고
    • Support vector machine approach to separate control and breast cancer serum samples
    • Article 11
    • Pham, T. V., van de Wiel, M. A., and Jimenez, C. R. (2008) Support vector machine approach to separate control and breast cancer serum samples. Stat. Appl. Genet. Mol. Biol. 7, Article 11
    • (2008) Stat. Appl. Genet. Mol. Biol. , vol.7
    • Pham, T.V.1    Van De Wiel, M.A.2    Jimenez, C.R.3
  • 30
    • 46349085804 scopus 로고    scopus 로고
    • A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
    • Webb-Robertson, B. J., Cannon, W. R., Oehmen, C. S., Shah, A. R., Gurumoorthi, V., Lipton, M. S., and Waters, K. M. (2008) A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. Bioinformatics 24, 1503-1509
    • (2008) Bioinformatics , vol.24 , pp. 1503-1509
    • Webb-Robertson, B.J.1    Cannon, W.R.2    Oehmen, C.S.3    Shah, A.R.4    Gurumoorthi, V.5    Lipton, M.S.6    Waters, K.M.7
  • 32
    • 60849086755 scopus 로고    scopus 로고
    • Quality assessment of tandem mass spectra using support vector machine (SVM)
    • Zou, A. M., Wu, F. X., Ding, J. R., and Poirier, G. G. (2009) Quality assessment of tandem mass spectra using support vector machine (SVM). BMC Bioinformatics 10 Suppl 1, S49
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 1
    • Zou, A.M.1    Wu, F.X.2    Ding, J.R.3    Poirier, G.G.4
  • 35
  • 36
    • 0344945416 scopus 로고    scopus 로고
    • Segmentation of magnetic resonance brain images through discriminant analysis
    • Amato, U., Larobina, M., Antoniadis, A., and Alfano, B. (2003) Segmentation of magnetic resonance brain images through discriminant analysis. J. Neurosci. Meth. 131, 65-74
    • (2003) J. Neurosci. Meth. , vol.131 , pp. 65-74
    • Amato, U.1    Larobina, M.2    Antoniadis, A.3    Alfano, B.4
  • 38
    • 31344450644 scopus 로고    scopus 로고
    • Metabolic profiling using principal component analysis, discriminant partial least squares, and genetic algorithms
    • Ramadan, Z., Jacobs, D., Grigorov, M., and Kochhar, S. (2006) Metabolic profiling using principal component analysis, discriminant partial least squares, and genetic algorithms. Talanta 68, 1683-1691
    • (2006) Talanta , vol.68 , pp. 1683-1691
    • Ramadan, Z.1    Jacobs, D.2    Grigorov, M.3    Kochhar, S.4
  • 39
    • 74249085418 scopus 로고    scopus 로고
    • Metabolomic study of myocardial ischemia and intervention effects of Compound Danshen Tablets in rats using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry
    • Lv, Y., Liu, X., Yan, S., Liang, X., Yang, Y., Dai, W., and Zhang, W. (2010) Metabolomic study of myocardial ischemia and intervention effects of Compound Danshen Tablets in rats using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry. J. Pharm. Biomed. Anal. 52, 129-135
    • (2010) J. Pharm. Biomed. Anal. , vol.52 , pp. 129-135
    • Lv, Y.1    Liu, X.2    Yan, S.3    Liang, X.4    Yang, Y.5    Dai, W.6    Zhang, W.7
  • 40
    • 74449092161 scopus 로고    scopus 로고
    • Metabonomics study of urine from Sprague-Dawley rats exposed to Huang-yao-zi using (1)H NMR spectroscopy
    • Liu, Y., Huang, R., Liu, L., Peng, J., Xiao, B., Yang, J., Miao, Z., and Huang, H. (2010) Metabonomics study of urine from Sprague-Dawley rats exposed to Huang-yao-zi using (1)H NMR spectroscopy. J. Pharm. Biomed. Anal. 52, 136-141
    • (2010) J. Pharm. Biomed. Anal. , vol.52 , pp. 136-141
    • Liu, Y.1    Huang, R.2    Liu, L.3    Peng, J.4    Xiao, B.5    Yang, J.6    Miao, Z.7    Huang, H.8
  • 41
    • 74949121654 scopus 로고    scopus 로고
    • Simple quality assessment approach for herbal extracts using high performance liquid chromatography-UV based metabolomics platform
    • Lan, K., Zhang, Y., Yang, J., and Xu, L. (2010) Simple quality assessment approach for herbal extracts using high performance liquid chromatography-UV based metabolomics platform. J. Chromatogr. A 1217, 1414-1418
    • (2010) J. Chromatogr. A , vol.1217 , pp. 1414-1418
    • Lan, K.1    Zhang, Y.2    Yang, J.3    Xu, L.4
  • 43
    • 74549145500 scopus 로고    scopus 로고
    • A novel scoring system for prognostic prediction in dgalactosamine/ lipopolysaccharide-induced fulminant hepatic failure BALB/c mice
    • Feng, B., Wu, S. M., Lv, S., Liu, F., Chen, H. S., Gao, Y., Dong, F. T., and Wei, L. (2009) A novel scoring system for prognostic prediction in dgalactosamine/lipopolysaccharide-induced fulminant hepatic failure BALB/c mice. BMC Gastroenterol. 9, 99
    • (2009) BMC Gastroenterol. , vol.9 , pp. 99
    • Feng, B.1    Wu, S.M.2    Lv, S.3    Liu, F.4    Chen, H.S.5    Gao, Y.6    Dong, F.T.7    Wei, L.8
  • 45
    • 33846515112 scopus 로고    scopus 로고
    • Partial least squares: A versatile tool for the analysis of high-dimensional genomic data
    • Boulesteix, A. L., and Strimmer, K. (2007) Partial least squares: a versatile tool for the analysis of high-dimensional genomic data. Brief Bioinform. 8, 32-44
    • (2007) Brief Bioinform. , vol.8 , pp. 32-44
    • Boulesteix, A.L.1    Strimmer, K.2
  • 46
    • 34248347430 scopus 로고    scopus 로고
    • Application of PLS-DA in multivariate image analysis
    • Chevallier, S., Bertrand, D., Kohler, A., and Courcoux, P. (2006) Application of PLS-DA in multivariate image analysis. J. Chemom. 20, 221-229
    • (2006) J. Chemom. , vol.20 , pp. 221-229
    • Chevallier, S.1    Bertrand, D.2    Kohler, A.3    Courcoux, P.4
  • 48
    • 55349093570 scopus 로고    scopus 로고
    • Discriminant Q2 (DQ2) for improved discrimination in PLSDA models
    • Westerhuis, J., van Velzen, E., Hoefsloot, H., and Smilde, A. (2008) Discriminant Q2 (DQ2) for improved discrimination in PLSDA models. Metabolomics 4, 293-296
    • (2008) Metabolomics , vol.4 , pp. 293-296
    • Westerhuis, J.1    Van Velzen, E.2    Hoefsloot, H.3    Smilde, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.