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Volumn 17, Issue 1, 2016, Pages

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics

Author keywords

Categorical data analysis; Differential abundance; Environmental sequencing; False discovery rate; Next generation sequencing; Receiver operating characteristic

Indexed keywords

EFFECT SIZE; METAGENOME; METAGENOMICS; MODEL; NOISE; POISSON DISTRIBUTION; RNA SEQUENCE; SAMPLE SIZE; STATISTICAL MODEL; GENETICS; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE;

EID: 84955314492     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2386-y     Document Type: Article
Times cited : (102)

References (61)
  • 1
    • 0032192790 scopus 로고    scopus 로고
    • Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products
    • Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998;5:R245-9.
    • (1998) Chem Biol , vol.5 , pp. R245-R249
    • Handelsman, J.1    Rondon, M.R.2    Brady, S.F.3    Clardy, J.4    Goodman, R.M.5
  • 2
    • 18844481269 scopus 로고    scopus 로고
    • Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms
    • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, et al. Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol. 2000;66:2541-7.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 2541-2547
    • Rondon, M.R.1    August, P.R.2    Bettermann, A.D.3    Brady, S.F.4    Grossman, T.H.5    Liles, M.R.6
  • 3
    • 23944495106 scopus 로고    scopus 로고
    • Metagenomics for studying unculturable microorganisms: cutting the Gordian knot
    • Schloss PD, Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol. 2005;6:229.
    • (2005) Genome Biol , vol.6 , pp. 229
    • Schloss, P.D.1    Handelsman, J.2
  • 4
    • 84867074831 scopus 로고    scopus 로고
    • A metagenome-wide association study of gut microbiota in type 2 diabetes
    • Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490:55-60.
    • (2012) Nature , vol.490 , pp. 55-60
    • Qin, J.1    Li, Y.2    Cai, Z.3    Li, S.4    Zhu, J.5    Zhang, F.6
  • 8
    • 84925883482 scopus 로고    scopus 로고
    • Studying the microbiology of the indoor environment
    • Kelley ST, Gilbert JA. Studying the microbiology of the indoor environment. Genome Biol. 2013;14:202.
    • (2013) Genome Biol , vol.14 , pp. 202
    • Kelley, S.T.1    Gilbert, J.A.2
  • 9
    • 84903386153 scopus 로고    scopus 로고
    • Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses
    • Ferreira AJS, Siam R, Setubal JC, Moustafa A, Sayed A, Chambergo FS, et al. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. PLoS One. 2014;9.
    • (2014) PLoS One , pp. 9
    • Ferreira, A.J.S.1    Siam, R.2    Setubal, J.C.3    Moustafa, A.4    Sayed, A.5    Chambergo, F.S.6
  • 11
    • 75749135218 scopus 로고    scopus 로고
    • Metagenomics: Facts and artifacts, and computational challenges
    • Wooley JC, Ye Y. Metagenomics: Facts and artifacts, and computational challenges. J Comput Sci Technol. 2009;25:71-81.
    • (2009) J Comput Sci Technol , vol.25 , pp. 71-81
    • Wooley, J.C.1    Ye, Y.2
  • 12
    • 84862024684 scopus 로고    scopus 로고
    • Unlocking the potential of metagenomics through replicated experimental design
    • Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, et al. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol. 2012;30:513-20.
    • (2012) Nat Biotechnol , vol.30 , pp. 513-520
    • Knight, R.1    Jansson, J.2    Field, D.3    Fierer, N.4    Desai, N.5    Fuhrman, J.A.6
  • 13
    • 84937046992 scopus 로고    scopus 로고
    • The effects of variable sample biomass on comparative metagenomics
    • Chafee M, Maignien L, Simmons SL. The effects of variable sample biomass on comparative metagenomics. Environ Microbiol. 2015;17:2239-53.
    • (2015) Environ Microbiol , vol.17 , pp. 2239-2253
    • Chafee, M.1    Maignien, L.2    Simmons, S.L.3
  • 17
    • 84862024797 scopus 로고    scopus 로고
    • IMG/M: the integrated metagenome data management and comparative analysis system
    • Markowitz VM, Chen I-M A, Chu K, Szeto E, Palaniappan K, Grechkin Y, et al. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 2012;40(Database issue):D123-9.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE , pp. D123-D129
    • Markowitz, V.M.1    Chen I-M, A.2    Chu, K.3    Szeto, E.4    Palaniappan, K.5    Grechkin, Y.6
  • 18
    • 70349993601 scopus 로고    scopus 로고
    • ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
    • Kristiansson E, Hugenholtz P, Dalevi D. ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics. 2009;25:2737-8.
    • (2009) Bioinformatics , vol.25 , pp. 2737-2738
    • Kristiansson, E.1    Hugenholtz, P.2    Dalevi, D.3
  • 19
    • 66249145772 scopus 로고    scopus 로고
    • Statistical methods for detecting differentially abundant features in clinical metagenomic samples
    • White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol. 2009;5:e1000352.
    • (2009) PLoS Comput Biol , vol.5
    • White, J.R.1    Nagarajan, N.2    Pop, M.3
  • 20
    • 84911429654 scopus 로고    scopus 로고
    • STAMP: statistical analysis of taxonomic and functional profiles
    • Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30:3123-4.
    • (2014) Bioinformatics , vol.30 , pp. 3123-3124
    • Parks, D.H.1    Tyson, G.W.2    Hugenholtz, P.3    Beiko, R.G.4
  • 21
    • 77951945504 scopus 로고    scopus 로고
    • Identifying biologically relevant differences between metagenomic communities
    • Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics. 2010;26:715-21.
    • (2010) Bioinformatics , vol.26 , pp. 715-721
    • Parks, D.H.1    Beiko, R.G.2
  • 24
    • 84888865593 scopus 로고    scopus 로고
    • Differential abundance analysis for microbial marker-gene surveys
    • Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013;10:1200-2.
    • (2013) Nat Methods , vol.10 , pp. 1200-1202
    • Paulson, J.N.1    Stine, O.C.2    Bravo, H.C.3    Pop, M.4
  • 25
    • 4544341015 scopus 로고    scopus 로고
    • Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
    • Smyth GK. Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Stat Appl Genet Mol Biol. 2004;3:1-25.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , pp. 1-25
    • Smyth, G.K.1
  • 26
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-40.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 27
    • 84882921441 scopus 로고    scopus 로고
    • Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing
    • Ross EM, Moate PJ, Marett L, Cocks BG, Hayes BJ. Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing. J Dairy Sci. 2013;96:6030-46.
    • (2013) J Dairy Sci , vol.96 , pp. 6030-6046
    • Ross, E.M.1    Moate, P.J.2    Marett, L.3    Cocks, B.G.4    Hayes, B.J.5
  • 28
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2
    • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 2014;15:550.
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 30
    • 84896735766 scopus 로고    scopus 로고
    • Voom: precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law CW, Chen Y, Shi W, Smyth GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15:R29.
    • (2014) Genome Biol , vol.15
    • Law, C.W.1    Chen, Y.2    Shi, W.3    Smyth, G.K.4
  • 32
    • 84869014474 scopus 로고    scopus 로고
    • A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
    • Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlén M, et al. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res. 2012;40:10084-97.
    • (2012) Nucleic Acids Res , vol.40 , pp. 10084-10097
    • Nookaew, I.1    Papini, M.2    Pornputtapong, N.3    Scalcinati, G.4    Fagerberg, L.5    Uhlén, M.6
  • 33
    • 84874677498 scopus 로고    scopus 로고
    • A comparison of methods for differential expression analysis of RNA-seq data
    • Soneson C, Delorenzi M. A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics. 2013;14:91.
    • (2013) BMC Bioinformatics , vol.14 , pp. 91
    • Soneson, C.1    Delorenzi, M.2
  • 35
    • 0001243836 scopus 로고
    • The Transformation of Poisson. Binomial and Negative-Binomial Data
    • Anscombe FJ. The Transformation of Poisson. Binomial and Negative-Binomial Data. Biometrika. 1948;35:246.
    • (1948) Biometrika , vol.35 , pp. 246
    • Anscombe, F.J.1
  • 38
    • 84901363655 scopus 로고    scopus 로고
    • Waste not, want not: why rarefying microbiome data is inadmissible
    • McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014;10:e1003531.
    • (2014) PLoS Comput Biol , vol.10
    • McMurdie, P.J.1    Holmes, S.2
  • 40
    • 84936076693 scopus 로고    scopus 로고
    • Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses
    • Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, et al. Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Res. 2015;43:e97.
    • (2015) Nucleic Acids Res , vol.43
    • Liu, R.1    Holik, A.Z.2    Su, S.3    Jansz, N.4    Chen, K.5    Leong, H.S.6
  • 41
    • 84961945798 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289-300.
    • (1995) J R Stat Soc Ser B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 42
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003;100:9440-5.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 43
    • 84905454882 scopus 로고    scopus 로고
    • Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
    • Karlsson FH, Nookaew I, Nielsen J. Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue. PLoS Comput Biol. 2014;10:e1003706.
    • (2014) PLoS Comput Biol , vol.10
    • Karlsson, F.H.1    Nookaew, I.2    Nielsen, J.3
  • 45
    • 79952159600 scopus 로고    scopus 로고
    • The effect of correlation in false discovery rate estimation
    • Schwartzman A, Lin X. The effect of correlation in false discovery rate estimation. Biometrika. 2011;98:199-214.
    • (2011) Biometrika , vol.98 , pp. 199-214
    • Schwartzman, A.1    Lin, X.2
  • 46
    • 77954834592 scopus 로고    scopus 로고
    • Average genome size: a potential source of bias in comparative metagenomics
    • Beszteri B, Temperton B, Frickenhaus S, Giovannoni SJ. Average genome size: a potential source of bias in comparative metagenomics. ISME J. 2010;4:1075-7.
    • (2010) ISME J , vol.4 , pp. 1075-1077
    • Beszteri, B.1    Temperton, B.2    Frickenhaus, S.3    Giovannoni, S.J.4
  • 47
    • 84941635324 scopus 로고    scopus 로고
    • A robust approach for identifying differentially abundant features in metagenomic samples
    • Sohn MB, Du R, An L. A robust approach for identifying differentially abundant features in metagenomic samples. Bioinformatics. 2015;31:2269-75.
    • (2015) Bioinformatics , vol.31 , pp. 2269-2275
    • Sohn, M.B.1    Du, R.2    An, L.3
  • 48
    • 79953276286 scopus 로고    scopus 로고
    • Quantitative Metagenomic Analyses Based on Average Genome Size Normalization
    • Frank JA, Sorensen SJ. Quantitative Metagenomic Analyses Based on Average Genome Size Normalization. Appl Environ Microbiol. 2011;77:2513-21.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 2513-2521
    • Frank, J.A.1    Sorensen, S.J.2
  • 49
    • 36448981743 scopus 로고    scopus 로고
    • Moderated statistical tests for assessing differences in tag abundance
    • Robinson MD, Smyth GK. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics. 2007;23:2881-7.
    • (2007) Bioinformatics , vol.23 , pp. 2881-2887
    • Robinson, M.D.1    Smyth, G.K.2
  • 50
    • 84858041341 scopus 로고    scopus 로고
    • Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
    • McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40:4288-97.
    • (2012) Nucleic Acids Res , vol.40 , pp. 4288-4297
    • McCarthy, D.J.1    Chen, Y.2    Smyth, G.K.3
  • 51
    • 84963641621 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • Vienna, Austria
    • R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria; 2014. http://www.R-project.org/
    • (2014)
  • 53
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.
    • (2010) Genome Biol , vol.11
    • Robinson, M.D.1    Oshlack, A.2
  • 54
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.
    • (2010) Genome Biol , vol.11
    • Anders, S.1    Huber, W.2
  • 55
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59-65.
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1    Li, R.2    Raes, J.3    Arumugam, M.4    Burgdorf, K.S.5    Manichanh, C.6
  • 56
    • 0037249633 scopus 로고    scopus 로고
    • The TIGRFAMs database of protein families
    • Haft DH. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003;31:371-3.
    • (2003) Nucleic Acids Res , vol.31 , pp. 371-373
    • Haft, D.H.1
  • 57
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated Profile HMM Searches
    • Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7:e1002195.
    • (2011) PLoS Comput Biol , vol.7
    • Eddy, S.R.1
  • 58
    • 84979530154 scopus 로고    scopus 로고
    • Tentacle: distributed quantification of genes in metagenomes
    • Boulund F, Sjögren A, Kristiansson E. Tentacle: distributed quantification of genes in metagenomes. Gigascience. 2015;4:40.
    • (2015) Gigascience , vol.4 , pp. 40
    • Boulund, F.1    Sjögren, A.2    Kristiansson, E.3
  • 59
    • 0036226603 scopus 로고    scopus 로고
    • BLAT---The BLAST-Like Alignment Tool
    • Kent WJ. BLAT---The BLAST-Like Alignment Tool. Genome Res. 2002;12:656-64.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 60
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3    Olson, R.4    Glass, E.M.5    Kubal, M.6
  • 61
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett T. An introduction to ROC analysis. Pattern Recognit Lett. 2006;27:861-74.
    • (2006) Pattern Recognit Lett , vol.27 , pp. 861-874
    • Fawcett, T.1


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