메뉴 건너뛰기




Volumn 9, Issue 1, 2014, Pages

Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE RECEPTOR CCR6; RNA; TRANSCRIPTOME;

EID: 84898618335     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0078644     Document Type: Article
Times cited : (737)

References (41)
  • 3
    • 39449097889 scopus 로고    scopus 로고
    • Techniques for clustering gene expression data
    • DOI 10.1016/j.compbiomed.2007.11.001, PII S0010482507001801
    • Kerr G, Ruskin HJ, Crane M, Doolan P (2008) Techniques for clustering gene expression data. Computers in Biology and Medicine 38: 283-293. (Pubitemid 351273199)
    • (2008) Computers in Biology and Medicine , vol.38 , Issue.3 , pp. 283-293
    • Kerr, G.1    Ruskin, H.J.2    Crane, M.3    Doolan, P.4
  • 4
    • 33846641686 scopus 로고    scopus 로고
    • Quantitative trait transcripts for nicotine resistance in Drosophila melanogaster
    • DOI 10.1038/ng1944, PII NG1944
    • Passador-Gurgel G, Hsieh W, Hunt P, Deighton N, Gibson G (2007) Quantitative trait transcripts for nicotine resistance in Drosophila melanogaster. Nat Genet 39: 264-268. (Pubitemid 46184360)
    • (2007) Nature Genetics , vol.39 , Issue.2 , pp. 264-268
    • Passador-Gurgel, G.1    Hsieh, W.-P.2    Hunt, P.3    Deighton, N.4    Gibson, G.5
  • 5
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • DOI 10.1038/nmeth.1226, PII NMETH.1226
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mam-malian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
    • (2008) Nature Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 7
    • 77950458649 scopus 로고    scopus 로고
    • Transcriptome genetics using second generation sequencing in a caucasian population
    • Montgomery S, Sammeth M, Gutierrez-Arcelus M, Lach R, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a caucasian population. Nature 464: 773-777.
    • (2010) Nature , vol.464 , pp. 773-777
    • Montgomery, S.1    Sammeth, M.2    Gutierrez-Arcelus, M.3    Lach, R.4    Ingle, C.5
  • 10
    • 79957842166 scopus 로고    scopus 로고
    • Computational methods for transcriptome annotation and quantification using RNA-seq
    • Garber M, Grabherr MG, Guttman M, Trapnell C (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8: 469-477.
    • (2011) Nat Methods , vol.8 , pp. 469-477
    • Garber, M.1    Grabherr, M.G.2    Guttman, M.3    Trapnell, C.4
  • 11
    • 79953034289 scopus 로고    scopus 로고
    • Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays
    • Bottomly D, Walter NAR, Hunter JE, Darakjian P, Kawane S, et al. (2011) Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays. PLoS ONE 6: e17820.
    • (2011) PLoS ONE , vol.6
    • Bottomly, D.1    Walter, N.A.R.2    Hunter, J.E.3    Darakjian, P.4    Kawane, S.5
  • 12
    • 84862006717 scopus 로고    scopus 로고
    • Effector CD4+ T cell expression signatures and immune-mediated disease associated genes
    • Zhang W, Ferguson J, Ng SM, Hui K, Goh G, et al. (2012) Effector CD4+ T cell expression signatures and immune-mediated disease associated genes. PLoS ONE 7: e38510
    • (2012) PLoS ONE , vol.7
    • Zhang, W.1    Ferguson, J.2    Ng, S.M.3    Hui, K.4    Goh, G.5
  • 13
    • 84870876433 scopus 로고    scopus 로고
    • RNA-Seq vs dual- and singlechannel microarray data: Sensitivity analysis for differential expression and clustering
    • Sîrbu A, Kerr G, Crane M, Ruskin HJ (2012) RNA-Seq vs dual- and singlechannel microarray data: sensitivity analysis for differential expression and clustering. PLoS ONE 7: e50986.
    • (2012) PLoS ONE , vol.7
    • Sîrbu, A.1    Kerr, G.2    Crane, M.3    Ruskin, H.J.4
  • 14
    • 50649089207 scopus 로고    scopus 로고
    • RNA-Seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni J, Mason C, Mane S, Stephens M, Gilad Y (2008) RNA-Seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509.
    • (2008) Genome Res , vol.18 , pp. 1509
    • Marioni, J.1    Mason, C.2    Mane, S.3    Stephens, M.4    Gilad, Y.5
  • 15
    • 65649083411 scopus 로고    scopus 로고
    • Estimating accuracy of RNA-Seq and microarrays with proteomics
    • Fu X, Fu N, Guo S, Yan Z, Xu Y, 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    Yan, Z.4    Xu, Y.5
  • 16
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, 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
  • 17
    • 66349083834 scopus 로고    scopus 로고
    • Measuring differential gene expression by short read sequencing: Quantitative comparison to 2-channel gene expression microarrays
    • Bloom J, Khan Z, Kruglyak L, Singh M, Caudy A (2009) Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC genomics 10: 221.
    • (2009) BMC Genomics , vol.10 , pp. 221
    • Bloom, J.1    Khan, Z.2    Kruglyak, L.3    Singh, M.4    Caudy, A.5
  • 18
    • 70249146903 scopus 로고    scopus 로고
    • Advantages of next-generation sequencing versus the microarray in epigenetic research
    • Hurd PJ, Nelson CJ (2009) Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomic Proteomic 8: 174-183.
    • (2009) Brief Funct Genomic Proteomic , vol.8 , pp. 174-183
    • Hurd, P.J.1    Nelson, C.J.2
  • 19
    • 77951777930 scopus 로고    scopus 로고
    • A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
    • Bradford J, Hey Y, Yates T, Li Y, Pepper S, 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.1    Hey, Y.2    Yates, T.3    Li, Y.4    Pepper, S.5
  • 20
    • 79957665988 scopus 로고    scopus 로고
    • Microarrays, deep sequencing and the true measure of the transcriptome
    • Malone J, Oliver B (2011) Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol 9: 34.
    • (2011) BMC Biol , vol.9 , pp. 34
    • Malone, J.1    Oliver, B.2
  • 21
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • DOI 10.1093/bioinformatics/19.2.185
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias". Bioinformatics 19: 185-193. (Pubitemid 36181903)
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 22
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
    • (2003) Biostatistics , vol.4 , pp. 249-264
    • Irizarry, R.A.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.D.4    Antonellis, K.J.5
  • 23
    • 84864134986 scopus 로고    scopus 로고
    • OSA: A fast and accurate alignment tool for RNA-Seq
    • Hu J, Ge H, Newman M, Liu K (2012) OSA: a fast and accurate alignment tool for RNA-Seq. Bioinformatics 28: 1933-1934.
    • (2012) Bioinformatics , vol.28 , pp. 1933-1934
    • Hu, J.1    Ge, H.2    Newman, M.3    Liu, K.4
  • 25
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y(1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57: 289-300.
    • (1995) J R Stat Soc B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 26
    • 66849099394 scopus 로고    scopus 로고
    • Retinoid-related orphan receptors (RORs): Critical roles in development, immunity, circadian rhythm, and cellular metabolism
    • Jetten AM (2009) Retinoid-related orphan receptors (RORs): critical roles in development, immunity, circadian rhythm, and cellular metabolism. Nucl Recept Signal 7:e003
    • (2009) Nucl Recept Signal , vol.7
    • Jetten, A.M.1
  • 27
    • 33846647537 scopus 로고    scopus 로고
    • Commonly used reference genes are actively regulated in in vitro stimulated lymphocytes
    • DOI 10.1111/j.1365-3083.2006.01879.x
    • Røge R, Thorsen J, Tørring C, Ozbay A, Møller BK, Carstens J (2007) Commonly used reference genes are actively regulated in in vitro stimulated lymphocytes. Scand J Immunol 65:202-209 (Pubitemid 46174929)
    • (2007) Scandinavian Journal of Immunology , vol.65 , Issue.2 , pp. 202-209
    • Roge, R.1    Thorsen, J.2    Torring, C.3    Ozbay, A.4    Moller, B.K.5    Carstens, J.6
  • 28
    • 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, et al. (2012) 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 40: 10084-10097.
    • (2012) Nucleic Acids Res , vol.40 , pp. 10084-10097
    • Nookaew, I.1    Papini, M.2    Pornputtapong, N.3    Scalcinati, G.4    Fagerberg, L.5
  • 29
    • 33846986793 scopus 로고    scopus 로고
    • Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips
    • Stalteri MA, Harrison AP (2007) Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics 8: 13
    • (2007) BMC Bioinformatics , vol.8 , pp. 13
    • Stalteri, M.A.1    Harrison, A.P.2
  • 30
    • 59349094837 scopus 로고    scopus 로고
    • Consistency analysis of redundant probe sets on Affymetrix three-prime expression arrays and applications to differential mRNA processing
    • Cui X, Loraine AE (2009) Consistency analysis of redundant probe sets on Affymetrix three-prime expression arrays and applications to differential mRNA processing. PLoS ONE 4: e4229.
    • (2009) PLoS ONE , vol.4
    • Cui, X.1    Loraine, A.E.2
  • 33
    • 77955883388 scopus 로고    scopus 로고
    • Biases in illumina transcriptome sequencing caused by random hexamer priming
    • Hansen KD, Brenner SE, 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
  • 37
    • 79960557820 scopus 로고    scopus 로고
    • Bias detection and correction in RNASequencing data
    • Zheng W, Chung LM, Zhao H (2011) Bias detection and correction in RNASequencing data. BMC Bioinformatics 12: 290.
    • (2011) BMC Bioinformatics , vol.12 , pp. 290
    • Zheng, W.1    Chung, L.M.2    Zhao, H.3
  • 39
    • 77954975104 scopus 로고    scopus 로고
    • Next-generation sequencing adjusting to data overload
    • Baker M (2010) Next-generation sequencing: adjusting to data overload. Nat Methods 7: 495-499.
    • (2010) Nat Methods , vol.7 , pp. 495-499
    • Baker, M.1
  • 41
    • 77954526823 scopus 로고    scopus 로고
    • The case for cloud computing in genome informatics
    • Stein LD (2010) The case for cloud computing in genome informatics. Genome Biol 11: 207.
    • (2010) Genome Biol , vol.11 , pp. 207
    • Stein, L.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.