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Volumn 5, Issue 1, 2012, Pages 89-98

Generalized linear and mixed models for label-free shotgun proteomics

Author keywords

Count data; FDR; Generalized linear models; Label free quantitative proteomics; Mixture model; Negative binomial model; p values; Quasi Poisson model; Spectral count; Statistical models

Indexed keywords


EID: 84864395727     PISSN: 19387989     EISSN: 19387997     Source Type: Journal    
DOI: 10.4310/SII.2012.v5.n1.a8     Document Type: Article
Times cited : (5)

References (26)
  • 1
    • 1542399989 scopus 로고    scopus 로고
    • FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
    • Al-Shahrour, F., az-Uriarte, R. and Dopazo, J. (2004). FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20 578-580.
    • (2004) Bioinformatics , vol.20 , pp. 578-580
    • Al-Shahrour, F.1    Az-Uriarte, R.2    Dopazo, J.3
  • 2
    • 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. Journal of the Royal Statistical Society 57 289300.
    • (1995) Journal of the Royal Statistical Society , vol.57 , pp. 289300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 0037106398 scopus 로고    scopus 로고
    • Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatographytandem mass spectrometry
    • Bondarenko, P. V., Chelius, D. and Shaler, T. A. (2002). Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatographytandem mass spectrometry. Anal. Chem. 74 4741-4749.
    • (2002) Anal. Chem , vol.74 , pp. 4741-4749
    • Bondarenko, P.V.1    Chelius, D.2    Shaler, T.A.3
  • 5
    • 0036665581 scopus 로고    scopus 로고
    • Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry
    • Chelius, D. and Bondarenko, P. V. (2002). Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J. Proteome. Res. 1 317-323.
    • (2002) J. Proteome. Res , vol.1 , pp. 317-323
    • Chelius, D.1    Bondarenko, P.V.2
  • 6
    • 58149299336 scopus 로고    scopus 로고
    • Significance analysis of spectral count data in label-free shotgun proteomics. Mol
    • Choi, H., Fermin, D. and Nesvizhskii, A. I. (2008). Significance analysis of spectral count data in label-free shotgun proteomics. Mol. Cell Proteomics 7 2373-2385.
    • (2008) Cell Proteomics , vol.7 , pp. 2373-2385
    • Choi, H.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 7
    • 74049132731 scopus 로고    scopus 로고
    • Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
    • Griffin, N. M., Yu, J., Long, F., Oh, P., Shore, S., Li, Y., Koziol, J. A. and Schnitzer, J. E. (2010). Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat. Biotechnol. 28 83-89.
    • (2010) Nat. Biotechnol , vol.28 , pp. 83-89
    • Griffin, N.M.1    Yu, J.2    Long, F.3    Oh, P.4    Shore, S.5    Li, Y.6    Koziol, J.A.7    Schnitzer, J.E.8
  • 8
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H. and Aebersold, R. (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 994-999.
    • (1999) Nat. Biotechnol , vol.17 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 9
    • 0025066941 scopus 로고
    • More powerful procedures for multiple significance testing
    • Hochberg, Y. and Benjamini, Y. (1990). More powerful procedures for multiple significance testing. Stat. Med. 9 811-818.
    • (1990) Stat. Med , vol.9 , pp. 811-818
    • Hochberg, Y.1    Benjamini, Y.2
  • 10
    • 41649108679 scopus 로고    scopus 로고
    • Clustering analysisof SAGE transcription profiles using a Poisson approach
    • Huang, H., Cai, L. and Wong, W. H. (2008). Clustering analysisof SAGE transcription profiles using a Poisson approach. Methods Mol. Biol. 387 185-198.
    • (2008) Methods Mol. Biol. , vol.387 , pp. 185-198
    • Huang, H.1    Cai, L.2    Wong, W.H.3
  • 13
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu, H., Sadygov, R. G. and Yates, J. R., III (2004). A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76 4193-4201.
    • (2004) Anal. Chem. , vol.76 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates III, J.R.3
  • 14
    • 37649006805 scopus 로고    scopus 로고
    • Inference in regression models of heavily skewed alcohol use data: A comparison of ordinary least squares, generalized linear models, and bootstrap resampling. Psychol
    • Neal, D. J. and Simons, J. S. (2007). Inference in regression models of heavily skewed alcohol use data: A comparison of ordinary least squares, generalized linear models, and bootstrap resampling. Psychol. Addict. Behav. 21 441-452.
    • (2007) Addict. Behav , vol.21 , pp. 441-452
    • Neal, D.J.1    Simons, J.S.2
  • 16
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A. and Mann, M. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics. 1 376-386.
    • (2002) Mol. Cell Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 21
    • 65549119729 scopus 로고    scopus 로고
    • Statistical quality assessment and outlier detection for liquid chromatographymass spectrometry experiments
    • Schulz-Trieglaff, O., Machtejevas, E., Reinert, K., Schluter, H., Thiemann, J. and Unger, K. (2009). Statistical quality assessment and outlier detection for liquid chromatographymass spectrometry experiments. BioData. Min. 2 4.
    • (2009) BioData. Min. , vol.2 , pp. 4
    • Schulz-Trieglaff, O.1    Machtejevas, E.2    Reinert, K.3    Schluter, H.4    Thiemann, J.5    Unger, K.6
  • 23
    • 38449113722 scopus 로고    scopus 로고
    • Quasi-Poisson vs. negative binomial regression: How should we model overdispersed count data?
    • Ver Hoef, J. M. and Boveng, P. L. (2007). Quasi-Poisson vs. negative binomial regression: How should we model overdispersed count data? Ecology 88 2766-2772.
    • (2007) Ecology , vol.88 , pp. 2766-2772
    • Ver Hoef, J.M.1    Boveng, P.L.2
  • 24
    • 51649124498 scopus 로고    scopus 로고
    • Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data
    • Vogel, C. and Marcotte, E. M. (2008). Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat. Protoc. 3 1444-1451.
    • (2008) Nat. Protoc. , vol.3 , pp. 1444-1451
    • Vogel, C.1    Marcotte, E.M.2
  • 25
    • 33748319353 scopus 로고    scopus 로고
    • Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
    • Zybailov, B., Mosley, A. L., Sardiu, M. E., Coleman, M. K., Florens, L. and Washburn, M. P. (2006). Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J. Proteome Res. 5 2339-2347.
    • (2006) J. Proteome Res , vol.5 , pp. 2339-2347
    • Zybailov, B.1    Mosley, A.L.2    Sardiu, M.E.3    Coleman, M.K.4    Florens, L.5    Washburn, M.P.6
  • 26
    • 84864384498 scopus 로고    scopus 로고
    • Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors
    • Zybailov, B. L., Florens, L. and Washburn, M. P. (2011). Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. Mol. Biosyst.
    • (2011) Mol. Biosyst
    • Zybailov, B.L.1    Florens, L.2    Washburn, M.P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.