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Volumn 5, Issue 2 A, 2011, Pages 894-923

Automated analysis of quantitative image data using isomorphic functional mixed models, with application to proteomics data

Author keywords

2D gel electrophoresis; Bayesian analysis; False discovery rate; Functional data analysis; Functional mixed models; Functional MRI; Image analysis; Isomorphic transformations; Proteomics; Wavelets

Indexed keywords


EID: 80054689503     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/10-AOAS407     Document Type: Article
Times cited : (59)

References (40)
  • 1
    • 0032500737 scopus 로고    scopus 로고
    • Transition from moderate to excessive drug intake: Change in hedonic set point
    • Ahmed, S. H. and Koob, G. F. (1998). Transition from moderate to excessive drug intake: Change in hedonic set point. Science 282 298-300.
    • (1998) Science , vol.282 , pp. 298-300
    • Ahmed, S.H.1    Koob, G.F.2
  • 2
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Mathematical Reviews (MathSciNet): MR1325392
    • Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57 289-300. Mathematical Reviews (MathSciNet): MR1325392
    • (1995) J. Roy. Statist. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 0034427366 scopus 로고    scopus 로고
    • Curvelets, multiresolution representation, and scaling laws
    • (A. Aldroubi, A. F. Laine and M. A. Unser, eds.). Proc. SPIE 4119. Hindawi, New York
    • Candes, E. J. and Donoho, D. L. (2000). Curvelets, multiresolution representation, and scaling laws. In SPIE Wavelet Applications in Signal and Image Processing VIII (A. Aldroubi, A. F. Laine and M. A. Unser, eds.). Proc. SPIE 4119. Hindawi, New York.
    • (2000) SPIE Wavelet Applications In Signal and Image Processing , vol.8
    • Candes, E.J.1    Donoho, D.L.2
  • 4
    • 41549140487 scopus 로고    scopus 로고
    • The myth of automated, high-throughput two-dimensional gel electrophoresis
    • Clark, B. N. and Gutstein, H. B. (2008). The myth of automated, high-throughput two-dimensional gel electrophoresis. Proteomics 8 1197-1203.
    • (2008) Proteomics , vol.8 , pp. 1197-1203
    • Clark, B.N.1    Gutstein, H.B.2
  • 5
    • 0001682758 scopus 로고    scopus 로고
    • Multiple shrinkage and subset selection in wavelets
    • Mathematical Reviews (MathSciNet): MR1649120 Zentralblatt MATH: 0938.62021 Digital Object Identifier: doi:10.1093/biomet/85.2.391
    • Clyde, M., Parmigiani, G. and Vidakovic, B. (1998). Multiple shrinkage and subset selection in wavelets. Biometrika 85 391-401. Mathematical Reviews (MathSciNet): MR1649120 Zentralblatt MATH: 0938.62021 Digital Object Identifier: doi:10.1093/biomet/85.2.391
    • (1998) Biometrika , vol.85 , pp. 391-401
    • Clyde, M.1    Parmigiani, G.2    Vidakovic, B.3
  • 6
    • 0000043041 scopus 로고
    • Some matrix-variate distribution theory: Notational considerations and a Bayesian application
    • Mathematical Reviews (MathSciNet): MR614963 Zentralblatt MATH: 0464.62039 Digital Object Identifier: doi:10.1093/biomet/68.1.265
    • Dawid, A. P. (1981). Some matrix-variate distribution theory: Notational considerations and a Bayesian application. Biometrika 68 265-274. Mathematical Reviews (MathSciNet): MR614963 Zentralblatt MATH: 0464.62039 Digital Object Identifier: doi:10.1093/biomet/68.1.265
    • (1981) Biometrika , vol.68 , pp. 265-274
    • Dawid, A.P.1
  • 7
    • 0031338873 scopus 로고    scopus 로고
    • Spectral analysis of replicated biomedical time series
    • Mathematical Reviews (MathSciNet): MR1452286 Zentralblatt MATH: 0893.62108 Digital Object Identifier: doi:10.1111/1467-9876.00047
    • Diggle, P. J. and Al Wasel, I. (1997). Spectral analysis of replicated biomedical time series. J. Roy. Statist. Soc. Ser. C 46 31-71. Mathematical Reviews (MathSciNet): MR1452286 Zentralblatt MATH: 0893.62108 Digital Object Identifier: doi:10.1111/1467-9876.00047
    • (1997) J. Roy. Statist. Soc. Ser. C , vol.46 , pp. 31-71
    • Diggle, P.J.1    Al Wasel, I.2
  • 8
    • 1242316871 scopus 로고    scopus 로고
    • (J. Stoeckler and G. V. Welland, eds.). Academic Press, New York, Mathematical Reviews (MathSciNet): MR2136835
    • Do, M. N. and Vetterli, M. (2001). Beyond Wavelets (J. Stoeckler and G. V. Welland, eds.). Academic Press, New York. Mathematical Reviews (MathSciNet): MR2136835
    • (2001) Beyond Wavelets
    • Do, M.N.1    Vetterli, M.2
  • 9
    • 28944432472 scopus 로고    scopus 로고
    • The contourlet transform: An efficient directional multiresolution image representation
    • Do, M. N. and Vetterli, M. (2005). The contourlet transform: An efficient directional multiresolution image representation. IEEE Trans. Image Process. 14 2091-2106.
    • (2005) IEEE Trans. Image Process , vol.14 , pp. 2091-2106
    • Do, M.N.1    Vetterli, M.2
  • 10
    • 41349119605 scopus 로고    scopus 로고
    • Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline
    • Dowsey, A. W., Dunn, M. J. and Yang, G. Z. (2008). Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline. Bioinformatics 24 950-957.
    • (2008) Bioinformatics , vol.24 , pp. 950-957
    • Dowsey, A.W.1    Dunn, M.J.2    Yang, G.Z.3
  • 12
    • 17444407023 scopus 로고    scopus 로고
    • An orthogonal family of quincunx wavelets with continuously adjustable order
    • Mathematical Reviews (MathSciNet): MR2128291 Digital Object Identifier: doi:10.1109/TIP.2005.843754
    • Feilner, M., Van De Ville, D. and Unser, M. (2005). An orthogonal family of quincunx wavelets with continuously adjustable order. IEEE Trans. Signal Process. 14 499-510. Mathematical Reviews (MathSciNet): MR2128291 Digital Object Identifier: doi:10.1109/TIP.2005.843754
    • (2005) IEEE Trans. Signal Process , vol.14 , pp. 499-510
    • Feilner, M.1    Van De Ville, D.2    Unser, M.3
  • 13
    • 0034662907 scopus 로고    scopus 로고
    • Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
    • Gygi, S. P., Corthals, G. L., Zhang, Y., Rochon, Y. and Aebersold, R. (2000). Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97 9390-9395.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 9390-9395
    • Gygi, S.P.1    Corthals, G.L.2    Zhang, Y.3    Rochon, Y.4    Aebersold, R.5
  • 14
    • 0036185675 scopus 로고    scopus 로고
    • Functional mixed effects models
    • Mathematical Reviews (MathSciNet): MR1891050 Digital Object Identifier: doi:10.1111/j.0006-341X.2002.00121.x
    • Guo, W. (2002). Functional mixed effects models. Biometrics 58 121-128. Mathematical Reviews (MathSciNet): MR1891050 Digital Object Identifier: doi:10.1111/j.0006-341X.2002.00121.x
    • (2002) Biometrics , vol.58 , pp. 121-128
    • Guo, W.1
  • 15
    • 0028860024 scopus 로고
    • Suppression of corticotropin-releasing factor in the amygdala attenuates aversive consequences of morphine withdrawal
    • Heinrichs, S. C., Menzaghi, F., Schulteis, G., Koob, G. F. and Stinus, L. (1995). Suppression of corticotropin-releasing factor in the amygdala attenuates aversive consequences of morphine withdrawal. Behavioral Pharmacology 6 74-80.
    • (1995) Behavioral Pharmacology , vol.6 , pp. 74-80
    • Heinrichs, S.C.1    Menzaghi, F.2    Schulteis, G.3    Koob, G.F.4    Stinus, L.5
  • 17
    • 23844491490 scopus 로고    scopus 로고
    • Maximizing sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes
    • Karp, N. A. and Lilley, K. S. (2005). Maximizing sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes. Proteomics 5 3105-3115.
    • (2005) Proteomics , vol.5 , pp. 3105-3115
    • Karp, N.A.1    Lilley, K.S.2
  • 18
    • 0018945008 scopus 로고
    • Post-amphetamine depression of self-stimulation responding from the substantia nigra: Reversal by tricyclic antidepressants
    • Kokkinidis, L., Zacharko, R. M. and Predy, P. A. (1980). Post-amphetamine depression of self-stimulation responding from the substantia nigra: Reversal by tricyclic antidepressants. Pharmacol Biochem. Behav. 12 379-383.
    • (1980) Pharmacol Biochem. Behav , vol.12 , pp. 379-383
    • Kokkinidis, L.1    Zacharko, R.M.2    Predy, P.A.3
  • 19
    • 0017229602 scopus 로고
    • Amphetamine and the reward system: Evidence for tolerance and post-drug depression
    • Leith, N. J. and Barrett, R. J. (1976). Amphetamine and the reward system: Evidence for tolerance and post-drug depression. Psychopharmacologia 46 19-25.
    • (1976) Psychopharmacologia , vol.46 , pp. 19-25
    • Leith, N.J.1    Barrett, R.J.2
  • 20
    • 84880562313 scopus 로고    scopus 로고
    • Protein profiling using two-dimensional difference gel electrophoresis (2-D DIGE)
    • Chapter 22, Unit 22.2. Wiley, New York
    • Lilley, K. S. (2003). Protein profiling using two-dimensional difference gel electrophoresis (2-D DIGE). In Current Protocols in Protein Science, Chapter 22, Unit 22.2. Wiley, New York.
    • (2003) Current Protocols In Protein Science
    • Lilley, K.S.1
  • 21
    • 0024700097 scopus 로고
    • A theory for multiresolution signal decomposition: The wavelet representation
    • Mallat, S. G. (1989). A theory for multiresolution signal decomposition: The wavelet representation. IEEE Trans. Pattern Anal. Mach. Intell. 11 674-693.
    • (1989) IEEE Trans. Pattern Anal. Mach. Intell , vol.11 , pp. 674-693
    • Mallat, S.G.1
  • 22
    • 0026730583 scopus 로고
    • Bromocriptine reverses the elevation in intracranial self-stimulation thresholds observed in a rat model of cocaine withdrawal
    • Markou, A. and Koob, G. (1992). Bromocriptine reverses the elevation in intracranial self-stimulation thresholds observed in a rat model of cocaine withdrawal. Neuropsychopharmacology 7 213-224.
    • (1992) Neuropsychopharmacology , vol.7 , pp. 213-224
    • Markou, A.1    Koob, G.2
  • 23
    • 84873376026 scopus 로고    scopus 로고
    • Supplement to "Automated analysis of quantitative image data using isomorphic functional mixed models, with application to proteomics data." DOI: 10.1214/10-AOAS407SUPPA, DOI: 10.1214/10-AOAS407SUPPB, DOI: 10.1214/10-AOAS407SUPPC, DOI: 10.1214/10-AOAS407SUPPD
    • Morris, J. S. (2010). Supplement to "Automated analysis of quantitative image data using isomorphic functional mixed models, with application to proteomics data." DOI: 10.1214/10-AOAS407SUPPA, DOI: 10.1214/10-AOAS407SUPPB, DOI: 10.1214/10-AOAS407SUPPC, DOI: 10.1214/10-AOAS407SUPPD.
    • (2010)
    • Morris, J.S.1
  • 24
    • 33846090391 scopus 로고    scopus 로고
    • Using wavelet-based functional mixed models to characterize population heterogeneity in accelerometer profiles: A case study
    • Mathematical Reviews (MathSciNet): MR2307570 Zentralblatt MATH: 1171.62357 Digital Object Identifier: doi:10.1198/016214506000000465
    • Morris, J. S., Arroyo, C., Coull, B., Ryan, L. M., Herrick, R. and Gortmaker, S. L. (2006). Using wavelet-based functional mixed models to characterize population heterogeneity in accelerometer profiles: A case study. J. Amer. Statist. Assoc. 101 1352-1364. Mathematical Reviews (MathSciNet): MR2307570 Zentralblatt MATH: 1171.62357 Digital Object Identifier: doi:10.1198/016214506000000465
    • (2006) J. Amer. Statist. Assoc , vol.101 , pp. 1352-1364
    • Morris, J.S.1    Arroyo, C.2    Coull, B.3    Ryan, L.M.4    Herrick, R.5    Gortmaker, S.L.6
  • 25
    • 43949121435 scopus 로고    scopus 로고
    • Bayesian analysis of mass spectrometry data using wavelet-based functional mixed models
    • Mathematical Reviews (MathSciNet): MR2432418 Digital Object Identifier: doi:10.1111/j.1541-0420.2007.00895.x
    • Morris, J. S., Brown, P. J., Herrick, R. C., Baggerly, K. A. and Coombes, K. R. (2008). Bayesian analysis of mass spectrometry data using wavelet-based functional mixed models. Biometrics 12 479-489. Mathematical Reviews (MathSciNet): MR2432418 Digital Object Identifier: doi:10.1111/j.1541-0420.2007.00895.x
    • (2008) Biometrics , vol.12 , pp. 479-489
    • Morris, J.S.1    Brown, P.J.2    Herrick, R.C.3    Baggerly, K.A.4    Coombes, K.R.5
  • 26
    • 33644782020 scopus 로고    scopus 로고
    • Wavelet-based functional mixed models
    • Mathematical Reviews (MathSciNet): MR2188981 Zentralblatt MATH: 1110.62053 Digital Object Identifier: doi:10.1111/j.1467-9868.2006.00539.x
    • Morris, J. S. and Carroll, R. J. (2006). Wavelet-based functional mixed models. J. Roy. Statist. Soc. Ser. B 68 179-199. Mathematical Reviews (MathSciNet): MR2188981 Zentralblatt MATH: 1110.62053 Digital Object Identifier: doi:10.1111/j.1467-9868.2006.00539.x
    • (2006) J. Roy. Statist. Soc. Ser. B , vol.68 , pp. 179-199
    • Morris, J.S.1    Carroll, R.J.2
  • 27
    • 39149101842 scopus 로고    scopus 로고
    • Pinnacle: A fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data
    • Morris, J. S., Clark, B. N. and Gutstein, H. B. (2008). Pinnacle: A fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. Bioinformatics 24 529-536.
    • (2008) Bioinformatics , vol.24 , pp. 529-536
    • Morris, J.S.1    Clark, B.N.2    Gutstein, H.B.3
  • 28
    • 0242679450 scopus 로고    scopus 로고
    • Wavelet-based nonparametric modeling of hierarchical functions in colon carcinogenesis
    • Mathematical Reviews (MathSciNet): MR2011673 Zentralblatt MATH: 1040.62104 Digital Object Identifier: doi:10.1198/016214503000000422
    • Morris, J. S., Vannucci, M., Brown, P. J. and Carroll, R. J. (2003). Wavelet-based nonparametric modeling of hierarchical functions in colon carcinogenesis. J. Amer. Statist. Assoc. 98 573-583. Mathematical Reviews (MathSciNet): MR2011673 Zentralblatt MATH: 1040.62104 Digital Object Identifier: doi:10.1198/016214503000000422
    • (2003) J. Amer. Statist. Assoc , vol.98 , pp. 573-583
    • Morris, J.S.1    Vannucci, M.2    Brown, P.J.3    Carroll, R.J.4
  • 29
    • 73649131617 scopus 로고    scopus 로고
    • Evaluting the performance of new approaches to spot quantification and differential expression in 2-dimensional gel electrophoresis studies
    • Morris, J. S., Clark, B. N., Wei, W. and Gutstein, H. B. (2010). Evaluting the performance of new approaches to spot quantification and differential expression in 2-dimensional gel electrophoresis studies. Journal of Proteome Research 9 595-604.
    • (2010) Journal of Proteome Research , vol.9 , pp. 595-604
    • Morris, J.S.1    Clark, B.N.2    Wei, W.3    Gutstein, H.B.4
  • 30
    • 10844254626 scopus 로고    scopus 로고
    • Optimal sample size for multiple testing: The case of gene expression microarrays
    • Mathematical Reviews (MathSciNet): MR2109489 Zentralblatt MATH: 1055.62127 Digital Object Identifier: doi:10.1198/016214504000001646
    • Mueller, P., Parmigiani, G., Robert, C. and Rousseau, J. (2004). Optimal sample size for multiple testing: The case of gene expression microarrays. J. Amer. Statist. Assoc. 99 990-1001. Mathematical Reviews (MathSciNet): MR2109489 Zentralblatt MATH: 1055.62127 Digital Object Identifier: doi:10.1198/016214504000001646
    • (2004) J. Amer. Statist. Assoc , vol.99 , pp. 990-1001
    • Mueller, P.1    Parmigiani, G.2    Robert, C.3    Rousseau, J.4
  • 31
    • 0029120432 scopus 로고
    • Serotonin dysfunction in the nucleus accumbens of rats during withdrawal after unlimited access to intravenous cocaine
    • Parsons, L. H., Koob, G. F. and Weiss, F. (1995). Serotonin dysfunction in the nucleus accumbens of rats during withdrawal after unlimited access to intravenous cocaine. Journal of Pharmacology and Experimental Therapeutics 274 1182-1191.
    • (1995) Journal of Pharmacology and Experimental Therapeutics , vol.274 , pp. 1182-1191
    • Parsons, L.H.1    Koob, G.F.2    Weiss, F.3
  • 32
    • 0004130505 scopus 로고    scopus 로고
    • Springer, New York, Mathematical Reviews (MathSciNet): MR2168993
    • Ramsay, J. O. and Silverman, B. W. (1997). Functional Data Analysis. Springer, New York. Mathematical Reviews (MathSciNet): MR2168993
    • (1997) Functional Data Analysis
    • Ramsay, J.O.1    Silverman, B.W.2
  • 33
    • 77949757564 scopus 로고    scopus 로고
    • Functional generalized linear models with images as predictors
    • May 8, Mathematical Reviews (MathSciNet): MR2756691 Digital Object Identifier: doi:10.1111/j.1541-0420.2009.01233.x
    • Reiss, P. T. and Ogden, R. T. (2009). Functional generalized linear models with images as predictors. Biometrics. Published online May 8, 2009. Mathematical Reviews (MathSciNet): MR2756691 Digital Object Identifier: doi:10.1111/j.1541-0420.2009.01233.x
    • (2009) Biometrics. Published Online , pp. 2009
    • Reiss, P.T.1    Ogden, R.T.2
  • 34
    • 0033563987 scopus 로고    scopus 로고
    • In vivo CRF release in rat amygdala is increased during cocaine withdrawal in self-administering rats
    • Richter, R. and Weiss, F. (1999). In vivo CRF release in rat amygdala is increased during cocaine withdrawal in self-administering rats. Synapse 32 254-261.
    • (1999) Synapse , vol.32 , pp. 254-261
    • Richter, R.1    Weiss, F.2
  • 35
    • 0000832522 scopus 로고
    • Nonparametric estimation of nonstationary spatial covariance structure
    • Sampson, P. D. and Guttorp, P. (1992). Nonparametric estimation of nonstationary spatial covariance structure. J. Amer. Statist. Assoc. 87 108-119.
    • (1992) J. Amer. Statist. Assoc , vol.87 , pp. 108-119
    • Sampson, P.D.1    Guttorp, P.2
  • 37
    • 34249029761 scopus 로고    scopus 로고
    • Spatial Bayesian variable selection with application to functional magnetic resonance imaging
    • Mathematical Reviews (MathSciNet): MR2370843 Zentralblatt MATH: 1134.62322 Digital Object Identifier: doi:10.1198/016214506000001031
    • Smith, M. and Fahrmeir, L. (2007). Spatial Bayesian variable selection with application to functional magnetic resonance imaging. J. Amer. Statist. Assoc. 102 417-431. Mathematical Reviews (MathSciNet): MR2370843 Zentralblatt MATH: 1134.62322 Digital Object Identifier: doi:10.1198/016214506000001031
    • (2007) J. Amer. Statist. Assoc , vol.102 , pp. 417-431
    • Smith, M.1    Fahrmeir, L.2
  • 38
    • 0345822598 scopus 로고    scopus 로고
    • The positive false discovery rate: A Bayesian interpretation and the q-value
    • Mathematical Reviews (MathSciNet): MR2036398 Zentralblatt MATH: 1042.62026 Digital Object Identifier: doi:10.1214/aos/1074290335 Project Euclid: euclid.aos/1074290335
    • Storey, J. D. (2003). The positive false discovery rate: A Bayesian interpretation and the q-value. Ann. Statist. 31 2013-2035. Mathematical Reviews (MathSciNet): MR2036398 Zentralblatt MATH: 1042.62026 Digital Object Identifier: doi:10.1214/aos/1074290335 Project Euclid: euclid.aos/1074290335
    • (2003) Ann. Statist , vol.31 , pp. 2013-2035
    • Storey, J.D.1
  • 39
    • 45449097447 scopus 로고    scopus 로고
    • fdrtool: A versitile R package for estimating local and tail area-based false discovery rates
    • Strimmer, K. (2008). fdrtool: A versitile R package for estimating local and tail area-based false discovery rates. Bioinformatics 24 1461-1462.
    • (2008) Bioinformatics , vol.24 , pp. 1461-1462
    • Strimmer, K.1
  • 40
    • 0026663188 scopus 로고
    • Basal extracellular dopamine levels in the nucleus accumbens are decreased during cocaine withdrawal after unlimited-access self-ad ministration
    • Weiss, F., Markou, A., Lorang, M. T. and Koob, G. F. (1992). Basal extracellular dopamine levels in the nucleus accumbens are decreased during cocaine withdrawal after unlimited-access self-ad ministration. Brain Research 593 314-318.
    • (1992) Brain Research , vol.593 , pp. 314-318
    • Weiss, F.1    Markou, A.2    Lorang, M.T.3    Koob, G.F.4


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