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Volumn 12, Issue , 2011, Pages

RNA-seq: Technical variability and sampling

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; EXON; FEMALE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENE MAPPING; GENE NUMBER; GENE TECHNOLOGY; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; MALE; NONHUMAN; NUCLEIC ACID ANALYSIS; RNA ANALYSIS; RNA REPLICATION; RNA SEQUENCE; SAMPLING; SPECIES DIFFERENCE; ANIMAL; DROSOPHILA; GENETICS; METHODOLOGY; SEQUENCE ANALYSIS;

EID: 79957882567     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-293     Document Type: Article
Times cited : (220)

References (43)
  • 1
    • 46249130709 scopus 로고    scopus 로고
    • The beginning of the end for microarrays?
    • 10.1038/nmeth0708-585, 18587314
    • Shendure J. The beginning of the end for microarrays?. Nat Methods 2008, 5:585-587. 10.1038/nmeth0708-585, 18587314.
    • (2008) Nat Methods , vol.5 , pp. 585-587
    • Shendure, J.1
  • 2
    • 74049148179 scopus 로고    scopus 로고
    • 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer
    • 10.1186/1471-2164-10-531, 2781828, 19917133
    • Asmann Y, Klee E, Thompson EA, Perez E, Middha S, Oberg A, Therneau T, Smith D, Poland G, Wieben E, Kocher JP. 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics 2009, 10:531. 10.1186/1471-2164-10-531, 2781828, 19917133.
    • (2009) BMC Genomics , vol.10 , pp. 531
    • Asmann, Y.1    Klee, E.2    Thompson, E.A.3    Perez, E.4    Middha, S.5    Oberg, A.6    Therneau, T.7    Smith, D.8    Poland, G.9    Wieben, E.10    Kocher, J.P.11
  • 3
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • 10.1038/nmeth.1226, 18516045
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
    • (2008) Nat Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 6
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • 10.1038/nrg2484, 2949280, 19015660
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63. 10.1038/nrg2484, 2949280, 19015660.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 7
    • 70349910898 scopus 로고    scopus 로고
    • Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
    • 10.1093/bioinformatics/btp579, 2788925, 19808877
    • Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 2009, 25:3207-3212. 10.1093/bioinformatics/btp579, 2788925, 19808877.
    • (2009) Bioinformatics , vol.25 , pp. 3207-3212
    • Degner, J.F.1    Marioni, J.C.2    Pai, A.A.3    Pickrell, J.K.4    Nkadori, E.5    Gilad, Y.6    Pritchard, J.K.7
  • 8
    • 70350088369 scopus 로고    scopus 로고
    • Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing
    • 10.1261/rna.1699809, 2764476, 19745027
    • Willenbrock H, Salomon J, Søkilde R, Barken KB, Hansen TN, Nielsen FC, Møller S, Litman T. Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing. RNA 2009, 15:2028-2034. 10.1261/rna.1699809, 2764476, 19745027.
    • (2009) RNA , vol.15 , pp. 2028-2034
    • Willenbrock, H.1    Salomon, J.2    Søkilde, R.3    Barken, K.B.4    Hansen, T.N.5    Nielsen, F.C.6    Møller, S.7    Litman, T.8
  • 9
    • 77954139210 scopus 로고    scopus 로고
    • Incorporating sequence quality data into alignment improves DNA read mapping
    • 10.1093/nar/gkq010, 2853142, 20110255
    • Frith MC, Wan R, Horton P. Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res 2010, 38:e100. 10.1093/nar/gkq010, 2853142, 20110255.
    • (2010) Nucleic Acids Res , vol.38
    • Frith, M.C.1    Wan, R.2    Horton, P.3
  • 10
    • 65649126066 scopus 로고    scopus 로고
    • Transcript length bias in RNA-seq data confounds systems biology
    • 10.1186/1745-6150-4-14, 2678084, 19371405
    • Oshlack A, Wakefield M. Transcript length bias in RNA-seq data confounds systems biology. Biol Direct 2009, 4:14. 10.1186/1745-6150-4-14, 2678084, 19371405.
    • (2009) Biol Direct , vol.4 , pp. 14
    • Oshlack, A.1    Wakefield, M.2
  • 11
    • 69849093232 scopus 로고    scopus 로고
    • Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity
    • 10.1093/nar/gkp492, 2731892, 19531739
    • Philippe N, Boureux A, Bréhélin L, Tarhio J, Commes T, Rivals E. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Res 2009, 37:e104. 10.1093/nar/gkp492, 2731892, 19531739.
    • (2009) Nucleic Acids Res , vol.37
    • Philippe, N.1    Boureux, A.2    Bréhélin, L.3    Tarhio, J.4    Commes, T.5    Rivals, E.6
  • 12
    • 77955504378 scopus 로고    scopus 로고
    • Statistical Design and Analysis of RNA Sequencing Data Genetics
    • Auer P, Doerge RW. Statistical Design and Analysis of RNA Sequencing Data Genetics. 2010, 185:405-416.
    • (2010) , vol.185 , pp. 405-416
    • Auer, P.1    Doerge, R.W.2
  • 13
    • 0004245434 scopus 로고
    • The Design of Experiments
    • Hafner, New York
    • Fisher RA. The Design of Experiments. 1960, Hafner, New York.
    • (1960)
    • Fisher, R.A.1
  • 14
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • Bullard J, Purdom E, Hansen K, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinf 2010, 11:94.
    • (2010) BMC Bioinf , vol.11 , pp. 94
    • Bullard, J.1    Purdom, E.2    Hansen, K.3    Dudoit, S.4
  • 15
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    • 10.1101/gr.079558.108, 2527709, 18550803
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
    • (2008) Genome Res , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 17
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • 10.1038/nbt.1621, 20436464
    • Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 2010, 28:511-5. 10.1038/nbt.1621, 20436464.
    • (2010) Nature Biotechnology , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.M.4    Kwan, G.5    van Baren, M.J.6    Salzberg, S.L.7    Wold, B.8    Pachter, L.9
  • 18
    • 75949093653 scopus 로고    scopus 로고
    • Identifiability of isoform deconvolution from junction arrays and RNA-Seq
    • 10.1093/bioinformatics/btp544, 19762346
    • Hiller D, Jiang H, Xu W, Wong WH. Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics 2009, 25:3056-3059. 10.1093/bioinformatics/btp544, 19762346.
    • (2009) Bioinformatics , vol.25 , pp. 3056-3059
    • Hiller, D.1    Jiang, H.2    Xu, W.3    Wong, W.H.4
  • 19
    • 49649116149 scopus 로고    scopus 로고
    • FlyBase: a database for the Drosophila research community
    • 10.1007/978-1-59745-583-1_3, 18641940, FlyBase Consortium
    • Drysdale R, . FlyBase Consortium FlyBase: a database for the Drosophila research community. Methods Mol Biol 2008, 420:45-59. 10.1007/978-1-59745-583-1_3, 18641940, FlyBase Consortium.
    • (2008) Methods Mol Biol , vol.420 , pp. 45-59
    • Drysdale, R.1
  • 20
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • 10.1093/bioinformatics/btp120, 2672628, 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 21
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • 10.1186/gb-2009-10-3-r25, 2690996, 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 23
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6    Marth, G.7    Abecasis, G.8    Durbin, R.9
  • 24
    • 0023676027 scopus 로고
    • Misleading Statistics: errors in textbooks, software and manuals
    • Bland JM, Altman DG. Misleading Statistics: errors in textbooks, software and manuals. International Journal of Epidemiology 1988, 17:201-203.
    • (1988) International Journal of Epidemiology , vol.17 , pp. 201-203
    • Bland, J.M.1    Altman, D.G.2
  • 25
    • 0003877646 scopus 로고
    • Statistical methods for rates and proportions
    • John Wiley, New York, 2
    • Fleiss JL. Statistical methods for rates and proportions. 1981, 38-46. John Wiley, New York, 2.
    • (1981) , pp. 38-46
    • Fleiss, J.L.1
  • 26
    • 84908219488 scopus 로고
    • Statistical methods for assessing agreement between two methods of clinical measurement
    • Bland JM, Altman DG. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1986, 307-310.
    • (1986) Lancet , pp. 307-310
    • Bland, J.M.1    Altman, D.G.2
  • 27
    • 0036376993 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
    • Dudoit S, Yang YH, Callow MJ, Speed TP. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 2002, 12:111-139.
    • (2002) Statistica Sinica , vol.12 , pp. 111-139
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 29
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • 10.1186/gb-2010-11-3-r25, 2864565, 20196867
    • Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 2010, 11:R25. 10.1186/gb-2010-11-3-r25, 2864565, 20196867.
    • (2010) Genome Biology , vol.11
    • Robinson, M.D.1    Oshlack, A.2
  • 30
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 10.1093/bioinformatics/19.2.185, 12538238
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 32
    • 0001223199 scopus 로고
    • On the error of counting with a haemacytometer
    • Student
    • Student On the error of counting with a haemacytometer. Biometrika 1907, 5:351-360. Student.
    • (1907) Biometrika , vol.5 , pp. 351-360
  • 33
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • 10.1186/gb-2010-11-10-r106, 20979621
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biology 2010, 11:R106. 10.1186/gb-2010-11-10-r106, 20979621.
    • (2010) Genome Biology , vol.11
    • Anders, S.1    Huber, W.2
  • 34
    • 41149085992 scopus 로고    scopus 로고
    • 9,2, pp. 321-332, and Bioinformatics (2007), vol. 23 n° 21, pages 2881-2887), Robinson and Smyth, Biostatistics
    • Robinson and Smyth, Biostatistics 2008, 9,2, pp. 321-332, and Bioinformatics (2007), vol. 23 n° 21, pages 2881-2887), Robinson and Smyth, Biostatistics.
    • (2008)
  • 35
    • 63949083912 scopus 로고    scopus 로고
    • Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
    • 10.1038/nmeth.1311, 2664327, 19287394
    • Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 2009, 6:291-295. 10.1038/nmeth.1311, 2664327, 19287394.
    • (2009) Nat Methods , vol.6 , pp. 291-295
    • Kozarewa, I.1    Ning, Z.2    Quail, M.A.3    Sanders, M.J.4    Berriman, M.5    Turner, D.J.6
  • 36
    • 0029937426 scopus 로고    scopus 로고
    • DNA condensation
    • 10.1016/S0959-440X(96)80052-2, 8804837
    • Bloomfield VA. DNA condensation. Curr Opin Struct Biol 1996, 6:334-341. 10.1016/S0959-440X(96)80052-2, 8804837.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 334-341
    • Bloomfield, V.A.1
  • 37
    • 79960639076 scopus 로고    scopus 로고
    • Assay of Random RNA Oligomerization in Buffers with High Concentrations of Divalent Metal Ions
    • [Accessed April 28, 2010]
    • Vlassov A. Assay of Random RNA Oligomerization in Buffers with High Concentrations of Divalent Metal Ions. ChemInform 2005, 36. [Accessed April 28, 2010].
    • (2005) ChemInform , vol.36
    • Vlassov, A.1
  • 38
    • 0027488624 scopus 로고
    • Isolation of new ribozymes from a large pool of random sequences
    • 10.1126/science.7690155, 7690155
    • Bartel DP, Szostak JW. Isolation of new ribozymes from a large pool of random sequences. Science 1993, 261:1411-1418. 10.1126/science.7690155, 7690155.
    • (1993) Science , vol.261 , pp. 1411-1418
    • Bartel, D.P.1    Szostak, J.W.2
  • 39
    • 0003493777 scopus 로고
    • Statistical Methods for Research Workers
    • London, Oliver and Boyd
    • Fisher RA. Statistical Methods for Research Workers. 1932, London, Oliver and Boyd.
    • (1932)
    • Fisher, R.A.1
  • 40
    • 66749171697 scopus 로고    scopus 로고
    • Statistical design of quantitative mass spectrometry-based proteomic experiments
    • 10.1021/pr8010099, 19222236
    • Oberg AL, Vitek O. Statistical design of quantitative mass spectrometry-based proteomic experiments. J Proteome Res 2009, 8(5):2144-56. 10.1021/pr8010099, 19222236.
    • (2009) J Proteome Res , vol.8 , Issue.5 , pp. 2144-2156
    • Oberg, A.L.1    Vitek, O.2
  • 41
    • 0000884487 scopus 로고    scopus 로고
    • Experimental design for gene expression microarrays
    • 10.1093/biostatistics/2.2.183, 12933549
    • Kerr MK, Churchill GA. Experimental design for gene expression microarrays. Biostatistics 2001, 2(2):183-201. 10.1093/biostatistics/2.2.183, 12933549.
    • (2001) Biostatistics , vol.2 , Issue.2 , pp. 183-201
    • Kerr, M.K.1    Churchill, G.A.2
  • 42
    • 0036855402 scopus 로고    scopus 로고
    • Comparison of microarray designs for class comparison and class discovery
    • 10.1093/bioinformatics/18.11.1438, 12424114
    • Dobbin K, Simon R. Comparison of microarray designs for class comparison and class discovery. Bioinformatics 2002, 18:1438-1445. 10.1093/bioinformatics/18.11.1438, 12424114.
    • (2002) Bioinformatics , vol.18 , pp. 1438-1445
    • Dobbin, K.1    Simon, R.2


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