메뉴 건너뛰기




Volumn , Issue , 2012, Pages 169-190

Differential expression for RNA sequencing (RNA-Seq) data: Mapping, summarization, statistical analysis, and experimental design

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; MAPPING; STATISTICS;

EID: 84887141165     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/9781461407829_10     Document Type: Chapter
Times cited : (5)

References (78)
  • 1
    • 57149085481 scopus 로고    scopus 로고
    • Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    • Hoen PA, Ariyurek Y, Thygesen HH, et al. (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 36:e141
    • (2008) Nucleic Acids Res , vol.141 , pp. 36
    • Hoen, P.A.1    Ariyurek, Y.2    Thygesen, H.H.3
  • 2
    • 77953203584 scopus 로고    scopus 로고
    • Global and unbiased detection of splice junctions from rna-seq data
    • Ameur A, Wetterbom A, Feuk L, et al. (2010) Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol 11:R34
    • (2010) Genome Biol , vol.11 , pp. 34
    • Ameur, A.1    Wetterbom, A.2    Feuk, L.3
  • 3
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S and Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106
    • (2010) Genome Biol , vol.11 , pp. 106
    • Anders, S.1    Huber, W.2
  • 5
    • 77955504378 scopus 로고    scopus 로고
    • Statistical design and analysis of rna sequencing data
    • Auer PL and Doerge RW (2010) Statistical design and analysis of RNA sequencing data. Genetics 185:405-16
    • (2010) Genetics , vol.185 , pp. 405-416
    • Auer, P.L.1    Doerge, R.W.2
  • 6
    • 77955489278 scopus 로고    scopus 로고
    • Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation
    • Babak T, Garrett-Engele P, Armour CD, et al. (2010) Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation. BMC Genomics 11:473
    • (2010) BMC Genomics , vol.11 , pp. 473
    • Babak, T.1    Garrett-Engele, P.2    Armour, C.D.3
  • 7
    • 9944226811 scopus 로고    scopus 로고
    • Sensitivity of microarray oligonucleotide probes: Variability and effect of base composition
    • Binder H, Kirsten T, Loeffler M, et al. (2004) Sensitivity of Microarray Oligonucleotide Probes: Variability and Effect of Base Composition. The Journal of Physical Chemistry B 108:18003-14
    • (2004) The Journal of Physical Chemistry B , vol.108 , pp. 18003-18014
    • Binder, H.1    Kirsten, T.2    Loeffler, M.3
  • 8
    • 75649102520 scopus 로고    scopus 로고
    • Sex-specific and lineage-specific alternative splicing in primates
    • Blekhman R, Marioni JC, Zumbo P, et al. (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Res 20:180-9
    • (2010) Genome Res , vol.20 , pp. 180-189
    • Blekhman, R.1    Marioni, J.C.2    Zumbo, P.3
  • 9
    • 77957937011 scopus 로고    scopus 로고
    • Quantitative comparison of genome-wide dna methylation mapping technologies
    • Bock C, Tomazou EM, Brinkman AB, et al. (2010) Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 28:1106-14
    • (2010) Nat Biotechnol , vol.28 , pp. 1106-1114
    • Bock, C.1    Tomazou, E.M.2    Brinkman, A.B.3
  • 10
    • 77951777930 scopus 로고    scopus 로고
    • A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
    • Bradford JR, Hey Y, Yates T, et al. (2010) A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics 11:282
    • (2010) BMC Genomics , vol.11 , pp. 282
    • Bradford, J.R.1    Hey, Y.2    Yates, T.3
  • 11
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mrna-seq experiments
    • Bullard JH, Purdom E, Hansen KD, et al. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11:94
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.H.1    Purdom, E.2    Hansen, K.D.3
  • 12
    • 47949130351 scopus 로고    scopus 로고
    • Identifying differences in protein expression levels by spectral counting and feature selection
    • Carvalho PC, Hewel J, Barbosa VC, et al. (2008) Identifying differences in protein expression levels by spectral counting and feature selection. Genet Mol Res 7:342-56
    • (2008) Genet Mol Res , vol.7 , pp. 342-356
    • Carvalho, P.C.1    Hewel, J.2    Barbosa, V.C.3
  • 13
    • 0036900895 scopus 로고    scopus 로고
    • Fundamentals of experimental design for cdna microarrays
    • Churchill GA (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32 Suppl:490-5
    • (2002) Nat Genet , vol.32 , pp. 490-495
    • Churchill, G.A.1
  • 14
    • 46249103973 scopus 로고    scopus 로고
    • Stem cell transcriptome profiling via massive-scale mrna sequencing
    • Cloonan N, Forrest AR, Kolle G, et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5:613-9
    • (2008) Nat Methods , vol.5 , pp. 613-619
    • Cloonan, N.1    Forrest, A.R.2    Kolle, G.3
  • 15
    • 49549102475 scopus 로고    scopus 로고
    • Optimal spliced alignments of short sequence reads
    • De Bona F, Ossowski S, Schneeberger K, et al. (2008) Optimal spliced alignments of short sequence reads. Bioinformatics 24:174-80
    • (2008) Bioinformatics , vol.24 , pp. 174-180
    • De Bona, F.1    Ossowski, S.2    Schneeberger, K.3
  • 16
    • 70349910898 scopus 로고    scopus 로고
    • Effect of read-mapping biases on detecting allele- specific expression from rna-sequencing data
    • Degner JF, Marioni JC, Pai AA, et al. (2009) Effect of read-mapping biases on detecting allele- specific expression from RNA-sequencing data. Bioinformatics 25:3207-12
    • (2009) Bioinformatics , vol.25 , pp. 3207-3212
    • Degner, J.F.1    Marioni, J.C.2    Pai, A.A.3
  • 17
    • 0038005018 scopus 로고    scopus 로고
    • David: Database for annotation, visualization, and integrated discovery
    • Dennis G, Jr., Sherman BT, Hosack DA, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4:P3
    • (2003) Genome Biol , vol.4 , pp. 3
    • Dennis, G.1    Sherman, B.T.2    Hosack, D.A.3
  • 19
    • 70449701942 scopus 로고    scopus 로고
    • Sense from sequence reads: Methods for alignment and assembly
    • Flicek P and Birney E (2009) Sense from sequence reads: methods for alignment and assembly. Nat Methods 6:S6-S12
    • (2009) Nat Methods , vol.6 , pp. SS6-S12
    • Flicek, P.1    Birney, E.2
  • 20
    • 65649083411 scopus 로고    scopus 로고
    • Estimating accuracy of rna-seq and microarrays with proteomics
    • Fu X, Fu N, Guo S, et al. (2009) Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 10:161
    • (2009) BMC Genomics , vol.10 , pp. 161
    • Fu, X.1    Fu, N.2    Guo, S.3
  • 21
    • 77957663917 scopus 로고    scopus 로고
    • Alternative expression analysis by rna sequencing
    • Griffith M, Griffith OL, Mwenifumbo J, et al. (2010) Alternative expression analysis by RNA sequencing. Nat Methods 7:843-7
    • (2010) Nat Methods , vol.7 , pp. 843-847
    • Griffith, M.1    Griffith, O.L.2    Mwenifumbo, J.3
  • 22
    • 77955883388 scopus 로고    scopus 로고
    • Biases in illumina transcriptome sequencing caused by random hexamer priming
    • Hansen KD, Brenner SE and Dudoit S (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38:e131
    • (2010) Nucleic Acids Res , vol.38
    • Hansen, K.D.1    Brenner, S.E.2    Dudoit, S.3
  • 23
    • 77955298482 scopus 로고    scopus 로고
    • Bayseq: Empirical bayesian methods foridentifying differential expression in sequence count data
    • Hardcastle TJ and Kelly KA (2010) baySeq: empirical Bayesian methods foridentifying differential expression in sequence count data. BMC Bioinformatics 11:422
    • (2010) BMC Bioinformatics , vol.11
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 24
    • 77951884076 scopus 로고    scopus 로고
    • Genome-wide analysis of alternative splicing evolution among mus subspecies
    • Harr B and Turner LM (2010) Genome-wide analysis of alternative splicing evolution among Mus subspecies. Mol Ecol 19 Suppl 1:228-39
    • (2010) Mol Ecol , vol.19 , Issue.1 , pp. 228-239
    • Harr, B.1    Turner, L.M.2
  • 25
    • 77957932941 scopus 로고    scopus 로고
    • Comparison of sequencing-based methods to profile dna methylation and identification of monoallelic epigenetic modifications
    • Harris RA, Wang T, Coarfa C, et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28:1097-1105
    • (2010) Nat Biotechnol , vol.28 , pp. 1097-1105
    • Harris, R.A.1    Wang, T.2    Coarfa, C.3
  • 26
    • 77953808473 scopus 로고    scopus 로고
    • Next-generation genomics: An integrative approach
    • Hawkins RD, Hon GC and Ren B (2010) Next-generation genomics: an integrative approach. Nat Rev Genet 11:476-86
    • (2010) Nat Rev Genet , vol.11 , pp. 476-486
    • Hawkins, R.D.1    Hon, G.C.2    Ren, B.3
  • 27
    • 16344384887 scopus 로고    scopus 로고
    • The importance of experimental design in proteomic mass spectrometry experiments: Some cautionary tales
    • Hu J, Coombes KR, Morris JS, et al. (2005) The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct Genomic Proteomic 3:322-31
    • (2005) Brief Funct Genomic Proteomic , vol.3 , pp. 322-331
    • Hu, J.1    Coombes, K.R.2    Morris, J.S.3
  • 28
    • 64549119707 scopus 로고    scopus 로고
    • Statistical inferences for isoform expression in rna-seq
    • Jiang H and Wong WH (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25:1026-32
    • (2009) Bioinformatics , vol.25 , pp. 1026-1032
    • Jiang, H.1    Wong, W.H.2
  • 29
    • 0033982936 scopus 로고    scopus 로고
    • Kegg: Kyoto encyclopedia of genes and genomes
    • Kanehisa M and Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27-30
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 30
    • 77955343193 scopus 로고    scopus 로고
    • Cloud-scale rna-sequencing differential expression analysis with myrna
    • Langmead B, Hansen KD and Leek JT (2010) Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol 11:R83
    • (2010) Genome Biol , vol.11 , pp. 83
    • Langmead, B.1    Hansen, K.D.2    Leek, J.T.3
  • 31
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short dna sequences to the human genome
    • Langmead B, Trapnell C, Pop M, et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
    • (2009) Genome Biol , vol.10 , pp. 25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3
  • 32
    • 77956340995 scopus 로고    scopus 로고
    • Comprehensive comparative analysis of strand-specific rna sequencing methods
    • Levin JZ, Yassour M, Adiconis X, et al. (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7:709-15
    • (2010) Nat Methods , vol.7 , pp. 709-715
    • Levin, J.Z.1    Yassour, M.2    Adiconis, X.3
  • 33
    • 77949507153 scopus 로고    scopus 로고
    • Rna-seq gene expression estimation with read mapping uncertainty
    • Li B, Ruotti V, Stewart RM, et al. (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26:493-500
    • (2010) Bioinformatics , vol.26 , pp. 493-500
    • Li, B.1    Ruotti, V.2    Stewart, R.M.3
  • 34
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with burrows-wheeler transform
    • Li H and Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-60
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 35
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short dna sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J and Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851-8
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 36
    • 67649595548 scopus 로고    scopus 로고
    • Limitations and possibilities of small rna digital gene expression profiling
    • Linsen SE, de Wit E, Janssens G, et al. (2009) Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods 6:474-6
    • (2009) Nat Methods , vol.6 , pp. 474-476
    • Linsen, S.E.1    De Wit, E.2    Janssens, G.3
  • 37
    • 70450217879 scopus 로고    scopus 로고
    • Human dna methylomes at base resolution show widespread epigenomic differences
    • Lister R, Pelizzola M, Dowen RH, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315-22
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3
  • 38
    • 79551495627 scopus 로고    scopus 로고
    • A comparison of rna-seq and high-density exon array for detecting differential gene expression between closely related species
    • Liu S, Lin L, Jiang P, et al. (2011) A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res 39:578-88
    • (2011) Nucleic Acids Res , vol.39 , pp. 578-588
    • Liu, S.1    Lin, L.2    Jiang, P.3
  • 39
    • 25444469952 scopus 로고    scopus 로고
    • Identifying differential expression in multiple sage libraries: An overdispersed log-linear model approach
    • Lu J, Tomfohr JK and Kepler TB (2005) Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach. BMC Bioinformatics 6:165
    • (2005) BMC Bioinformatics , vol.6 , pp. 165
    • Lu, J.1    Tomfohr, J.K.2    Kepler, T.B.3
  • 40
    • 62049085786 scopus 로고    scopus 로고
    • Transcriptome sequencing to detect gene fusions in cancer
    • Maher CA, Kumar-Sinha C, Cao X, et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature 458:97-101
    • (2009) Nature , vol.458 , pp. 97-101
    • Maher, C.A.1    Kumar-Sinha, C.2    Cao, X.3
  • 41
    • 50649089207 scopus 로고    scopus 로고
    • Rna-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni JC, Mason CE, Mane SM, et al. (2008) RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509-17
    • (2008) Genome Res , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3
  • 43
    • 77950458649 scopus 로고    scopus 로고
    • Transcriptome genetics using second generation sequencing in a caucasian population
    • Montgomery SB, Sammeth M, Gutierrez-Arcelus M, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464:773-7
    • (2010) Nature , vol.464 , pp. 773-777
    • Montgomery, S.B.1    Sammeth, M.2    Gutierrez-Arcelus, M.3
  • 44
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian tran- scriptomes by rna-seq
    • Mortazavi A, Williams BA, McCue K, et al. (2008) Mapping and quantifying mammalian tran- scriptomes by RNA-Seq. Nat Methods 5:621-8
    • (2008) Nat Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3
  • 45
    • 85035214096 scopus 로고    scopus 로고
    • Olving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays
    • 011906 NCBI (2011) NCBI - Entrez Genome, Accessed October 14
    • Naef F and Magnasco MO (2003) Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. Phys Rev E Stat Nonlin Soft Matter Phys 68:011906 NCBI (2011) NCBI - Entrez Genome. http://www.ncbi.nlm.nih.gov/sites/genome Accessed October 14
    • (2003) Phys Rev E Stat Nonlin Soft Matter Phys , vol.68
    • Naef, F.1    Magnasco, M.O.2
  • 46
    • 65649126066 scopus 로고    scopus 로고
    • Transcript length bias in rna-seq data confounds systems biology
    • Oshlack A and Wakefield MJ (2009) Transcript length bias in RNA-seq data confounds systems biology. Biol Direct 4:14
    • (2009) Biol Direct , vol.4 , pp. 14
    • Oshlack, A.1    Wakefield, M.J.2
  • 47
    • 76049125511 scopus 로고    scopus 로고
    • Chip-seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
    • Ouyang Z, Zhou Q and Wong WH (2009) ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci USA 106:21521-6
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 21521-21526
    • Ouyang, Z.1    Zhou, Q.2    Wong, W.H.3
  • 48
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan Q, Shai O, Lee LJ, et al. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413-5
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3
  • 49
    • 77953179050 scopus 로고    scopus 로고
    • Conserved developmental transcriptomes in evolutionarily divergent species
    • Parikh A, Miranda ER, Katoh-Kurasawa M, et al. (2010) Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol 11:R35
    • (2010) Genome Biol , vol.11 , pp. 35
    • Parikh, A.1    Miranda, E.R.2    Katoh-Kurasawa, M.3
  • 50
    • 77955812141 scopus 로고    scopus 로고
    • Large-scale detection and analysis of rna editing in grape mtdna by rna deep-sequencing
    • Picardi E, Horner DS, Chiara M, et al. (2010) Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucleic Acids Res 38:4755-67
    • (2010) Nucleic Acids Res , vol.38 , pp. 4755-4767
    • Picardi, E.1    Horner, D.S.2    Chiara, M.3
  • 51
    • 77950460661 scopus 로고    scopus 로고
    • Understanding mechanisms underlying human gene expression variation with rna sequencing
    • Pickrell JK, Marioni JC, Pai AA, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464:768-72
    • (2010) Nature , vol.464 , pp. 768-772
    • Pickrell, J.K.1    Marioni, J.C.2    Pai, A.A.3
  • 52
    • 0036898577 scopus 로고    scopus 로고
    • Microarray data normalization and transformation
    • Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32 Suppl: 496-501
    • (2002) Nat Genet 32 Suppl , pp. 496-501
    • Quackenbush, J.1
  • 53
    • 57049122389 scopus 로고    scopus 로고
    • A large genome center’s improvements to the illumina sequencing system
    • Quail MA, Kozarewa I, Smith F, et al. (2008) A large genome center&s improvements to the Illumina sequencing system. Nat Methods 5:1005-10
    • (2008) Nat Methods , vol.5 , pp. 1005-1010
    • Quail, M.A.1    Kozarewa, I.2    Smith, F.3
  • 54
    • 77649268269 scopus 로고    scopus 로고
    • Close association of rna polymerase ii and many transcription factors with pol iii genes
    • Raha D, Wang Z, Moqtaderi Z, et al. (2010) Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci USA 107:3639-44
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 3639-3644
    • Raha, D.1    Wang, Z.2    Moqtaderi, Z.3
  • 55
    • 78049346632 scopus 로고    scopus 로고
    • De novo assembly and analysis of rna-seq data
    • Robertson G, Schein J, Chiu R, et al. (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7:909-12
    • (2010) Nat Methods , vol.7 , pp. 909-912
    • Robertson, G.1    Schein, J.2    Chiu, R.3
  • 56
    • 75249087100 scopus 로고    scopus 로고
    • Mccarthy dj and smyth gk (2010) edger: A bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ and Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-40
    • Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1
  • 57
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of rna-seq data
    • Robinson MD and Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11:R25
    • (2010) Genome Biol , vol.11 , pp. 25
    • Robinson, M.D.1    Oshlack, A.2
  • 58
    • 36448981743 scopus 로고    scopus 로고
    • Moderated statistical tests for assessing differences in tag abundance
    • Robinson MD and Smyth GK (2007) Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23:2881-7
    • (2007) Bioinformatics , vol.23 , pp. 2881-2887
    • Robinson, M.D.1    Smyth, G.K.2
  • 59
    • 41149085992 scopus 로고    scopus 로고
    • Small-sample estimation of negative binomial dispersion, with applications to sage data
    • Robinson MD and Smyth GK (2008) Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 9:321-32
    • (2008) Biostatistics , vol.9 , pp. 321-332
    • Robinson, M.D.1    Smyth, G.K.2
  • 60
    • 78650058320 scopus 로고    scopus 로고
    • Evaluation of affinity-based genome-wide dna methylation data: Effects of cpg density, amplification bias, and copy number variation
    • Robinson MD, Stirzaker C, Statham AL, et al. (2010) Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res 20:1719-29
    • (2010) Genome Res , vol.20 , pp. 1719-1729
    • Robinson, M.D.1    Stirzaker, C.2    Statham, A.L.3
  • 61
    • 77955868506 scopus 로고    scopus 로고
    • Computational solutions to large-scale data management and analysis
    • Schadt EE, Linderman MD, Sorenson J, et al. (2010) Computational solutions to large-scale data management and analysis. Nat Rev Genet 11:647-57
    • (2010) Nat Rev Genet , vol.11 , pp. 647-657
    • Schadt, E.E.1    Linderman, M.D.2    Sorenson, J.3
  • 62
    • 66449136667 scopus 로고    scopus 로고
    • Abyss: A parallel assembler for short read sequence data
    • Simpson JT, Wong K, Jackman SD, et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117-23
    • (2009) Genome Res , vol.19 , pp. 1117-1123
    • Simpson, J.T.1    Wong, K.2    Jackman, S.D.3
  • 63
    • 85052549687 scopus 로고    scopus 로고
    • A two-parameter generalized poisson model to improve the analysis of rna-seq data
    • Srivastava S and Chen L (2010) A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Res 38:e170
    • (2010) Nucleic Acids Res , vol.170 , pp. 38
    • Srivastava, S.1    Chen, L.2
  • 64
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge- based approach for interpreting genome-wide expression profiles
    • Subramanian A, Tamayo P, Mootha VK, et al. (2005) Gene set enrichment analysis: a knowledge- based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545-50
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3
  • 65
    • 47649124124 scopus 로고    scopus 로고
    • A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    • Sultan M, Schulz MH, Richard H, et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321:956-60
    • (2008) Science , vol.321 , pp. 956-960
    • Sultan, M.1    Schulz, M.H.2    Richard, H.3
  • 67
    • 65449136284 scopus 로고    scopus 로고
    • Tophat: Discovering splice junctions with rna-seq
    • Trapnell C, Pachter L and Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-11
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 68
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by rna- seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G, et al. (2010) Transcript assembly and quantification by RNA- Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology 28:511-515
    • (2010) Nature Biotechnology , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3
  • 69
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcrip- tomes
    • Wang ET, Sandberg R, Luo S, et al. (2008) Alternative isoform regulation in human tissue transcrip- tomes. Nature 456:470-6
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1    Sandberg, R.2    Luo, S.3
  • 70
    • 77649135463 scopus 로고    scopus 로고
    • A statistical method for the detection of alternative splicing using rna-seq
    • Wang L, Xi Y, Yu J, et al. (2010) A statistical method for the detection of alternative splicing using RNA-seq. PLoS One 5:e8529
    • (2010) Plos One , vol.8529 , pp. 5
    • Wang, L.1    Xi, Y.2    Yu, J.3
  • 71
    • 57749195712 scopus 로고    scopus 로고
    • Rna-seq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M and Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 72
    • 66249145772 scopus 로고    scopus 로고
    • Statistical methods for detecting differentially abundant features in clinical metagenomic samples
    • White JR, Nagarajan N and Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5:e1000352
    • (2009) Plos Comput Biol , pp. 5
    • White, J.R.1    Nagarajan, N.2    Pop, M.3
  • 73
    • 77955889132 scopus 로고    scopus 로고
    • Roast: Rotation gene set tests for complex microarray experiments
    • Wu D, Lim E, Vaillant F, et al. (2010) ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics 26:2176-82
    • (2010) Bioinformatics , vol.26 , pp. 2176-2182
    • Wu, D.1    Lim, E.2    Vaillant, F.3
  • 74
    • 23844551199 scopus 로고    scopus 로고
    • Stochastic models inspired by hybridization theory for short oligonucleotide arrays
    • Wu Z and Irizarry RA (2005) Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol 12:882-93
    • (2005) J Comput Biol , vol.12 , pp. 882-893
    • Wu, Z.1    Irizarry, R.A.2
  • 75
    • 0036319960 scopus 로고    scopus 로고
    • Design issues for cdna microarray experiments
    • Yang YH and Speed T (2002) Design issues for cDNA microarray experiments. Nat Rev Genet 3:579-88
    • (2002) Nat Rev Genet , vol.3 , pp. 579-588
    • Yang, Y.H.1    Speed, T.2
  • 76
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for rna-seq: Accounting for selection bias
    • Young MD, Wakefield MJ, Smyth GK, et al. (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14
    • (2010) Genome Biol , vol.11 , pp. 14
    • Young, M.D.1    Wakefield, M.J.2    Smyth, G.K.3
  • 77
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de bruijn graphs
    • Zerbino DR and Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821-9
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 78
    • 68349089152 scopus 로고    scopus 로고
    • Digital rna allelotyping reveals tissue-specific and allele- specific gene expression in human
    • Zhang K, Li JB, Gao Y, et al. (2009) Digital RNA allelotyping reveals tissue-specific and allele- specific gene expression in human. Nat Methods 6:613-8
    • (2009) Nat Methods , vol.6 , pp. 613-618
    • Zhang, K.1    Li, J.B.2    Gao, Y.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.