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Volumn 7, Issue 6, 2012, Pages

Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs - A comparative study

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RECOMBINANT TUMOR NECROSIS FACTOR ALPHA;

EID: 84862489277     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038946     Document Type: Article
Times cited : (45)

References (39)
  • 1
    • 84858446579 scopus 로고    scopus 로고
    • MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship
    • Pasquinelli AE, (2012) MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet 13: 271-282.
    • (2012) Nat Rev Genet , vol.13 , pp. 271-282
    • Pasquinelli, A.E.1
  • 2
    • 38549120730 scopus 로고    scopus 로고
    • Profiling microRNA expression with microarrays
    • Yin JQ, Zhao RC, Morris KV, (2008) Profiling microRNA expression with microarrays. Trends Biotechnol 26: 70-76.
    • (2008) Trends Biotechnol , vol.26 , pp. 70-76
    • Yin, J.Q.1    Zhao, R.C.2    Morris, K.V.3
  • 3
    • 70349671437 scopus 로고    scopus 로고
    • Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis
    • Chen Y, Gelfond JA, McManus LM, Shireman PK, (2009) Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics 10: 407.
    • (2009) BMC Genomics , vol.10 , pp. 407
    • Chen, Y.1    Gelfond, J.A.2    McManus, L.M.3    Shireman, P.K.4
  • 4
    • 57449119832 scopus 로고    scopus 로고
    • Strategies for profiling microRNA expression
    • Kong W, Zhao JJ, He L, Cheng JQ, (2009) Strategies for profiling microRNA expression. J Cell Physiol 218: 22-25.
    • (2009) J Cell Physiol , vol.218 , pp. 22-25
    • Kong, W.1    Zhao, J.J.2    He, L.3    Cheng, J.Q.4
  • 5
    • 77954045451 scopus 로고    scopus 로고
    • Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs
    • Pradervand S, Weber J, Lemoine F, Consales F, Paillusson A, et al. (2010) Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs. Biotechniques 48: 219-222.
    • (2010) Biotechniques , vol.48 , pp. 219-222
    • Pradervand, S.1    Weber, J.2    Lemoine, F.3    Consales, F.4    Paillusson, A.5
  • 6
    • 37349051019 scopus 로고    scopus 로고
    • Real-time PCR quantification of precursor and mature microRNA
    • Schmittgen TD, Lee EJ, Jiang J, Sarkar A, Yang L, et al. (2008) Real-time PCR quantification of precursor and mature microRNA. Methods 44: 31-38.
    • (2008) Methods , vol.44 , pp. 31-38
    • Schmittgen, T.D.1    Lee, E.J.2    Jiang, J.3    Sarkar, A.4    Yang, L.5
  • 7
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    • Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24: 1151-1161.
    • (2006) Nat Biotechnol , vol.24 , pp. 1151-1161
    • Shi, L.1    Reid, L.H.2    Jones, W.D.3    Shippy, R.4    Warrington, J.A.5
  • 9
    • 65849488472 scopus 로고    scopus 로고
    • Intra-platform repeatability and inter-platform comparability of microRNA microarray technology
    • Sato F, Tsuchiya S, Terasawa K, Tsujimoto G, (2009) Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One 4: e5540.
    • (2009) PLoS One , vol.4
    • Sato, F.1    Tsuchiya, S.2    Terasawa, K.3    Tsujimoto, G.4
  • 10
    • 79951828031 scopus 로고    scopus 로고
    • Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array
    • Wang B, Howel P, Bruheim S, Ju J, Owen LB, et al. (2011) Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array. PLoS One 6: e17167.
    • (2011) PLoS One , vol.6
    • Wang, B.1    Howel, P.2    Bruheim, S.3    Ju, J.4    Owen, L.B.5
  • 11
    • 70349258646 scopus 로고    scopus 로고
    • A modified LOESS normalization applied to microRNA arrays: a comparative evaluation
    • Risso D, Massa MS, Chiogna M, Romualdi C, (2009) A modified LOESS normalization applied to microRNA arrays: a comparative evaluation. Bioinformatics 25: 2685-2691.
    • (2009) Bioinformatics , vol.25 , pp. 2685-2691
    • Risso, D.1    Massa, M.S.2    Chiogna, M.3    Romualdi, C.4
  • 12
    • 60849111385 scopus 로고    scopus 로고
    • Impact of normalization on miRNA microarray expression profiling
    • Pradervand S, Weber J, Thomas J, Bueno M, Wirapati P, et al. (2009) Impact of normalization on miRNA microarray expression profiling. RNA 15: 493-501.
    • (2009) RNA , vol.15 , pp. 493-501
    • Pradervand, S.1    Weber, J.2    Thomas, J.3    Bueno, M.4    Wirapati, P.5
  • 13
    • 46949098160 scopus 로고    scopus 로고
    • Comparison of normalization methods with microRNA microarray
    • Hua YJ, Tu K, Tang ZY, Li YX, Xiao HS, (2008) Comparison of normalization methods with microRNA microarray. Genomics 92: 122-128.
    • (2008) Genomics , vol.92 , pp. 122-128
    • Hua, Y.J.1    Tu, K.2    Tang, Z.Y.3    Li, Y.X.4    Xiao, H.S.5
  • 14
    • 78149407836 scopus 로고    scopus 로고
    • Normalization strategies for microRNA profiling experiments: a 'normal' way to a hidden layer of complexity?
    • Meyer SU, Pfaffl MW, Ulbrich SE, (2010) Normalization strategies for microRNA profiling experiments: a 'normal' way to a hidden layer of complexity? Biotechnol Lett 32: 1777-1788.
    • (2010) Biotechnol Lett , vol.32 , pp. 1777-1788
    • Meyer, S.U.1    Pfaffl, M.W.2    Ulbrich, S.E.3
  • 15
    • 42449098100 scopus 로고    scopus 로고
    • Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues
    • Peltier HJ, Latham GJ, (2008) Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues. RNA 14: 844-852.
    • (2008) RNA , vol.14 , pp. 844-852
    • Peltier, H.J.1    Latham, G.J.2
  • 16
    • 77951587943 scopus 로고    scopus 로고
    • MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer
    • Chang KH, Mestdagh P, Vandesompele J, Kerin MJ, Miller N, (2010) MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer. BMC Cancer 10: 173.
    • (2010) BMC Cancer , vol.10 , pp. 173
    • Chang, K.H.1    Mestdagh, P.2    Vandesompele, J.3    Kerin, M.J.4    Miller, N.5
  • 17
    • 64149097786 scopus 로고    scopus 로고
    • The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments
    • Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55: 611-622.
    • (2009) Clin Chem , vol.55 , pp. 611-622
    • Bustin, S.A.1    Benes, V.2    Garson, J.A.3    Hellemans, J.4    Huggett, J.5
  • 18
    • 78649637699 scopus 로고    scopus 로고
    • Modified least-variant set normalization for miRNA microarray
    • Suo C, Salim A, Chia KS, Pawitan Y, Calza S, (2010) Modified least-variant set normalization for miRNA microarray. RNA 16: 2293-2303.
    • (2010) RNA , vol.16 , pp. 2293-2303
    • Suo, C.1    Salim, A.2    Chia, K.S.3    Pawitan, Y.4    Calza, S.5
  • 19
    • 77954670531 scopus 로고    scopus 로고
    • Evaluation of normalization methods for two-channel microRNA microarrays
    • Zhao Y, Wang E, Liu H, Rotunno M, Koshiol J, et al. (2010) Evaluation of normalization methods for two-channel microRNA microarrays. J Transl Med 8: 69.
    • (2010) J Transl Med , vol.8 , pp. 69
    • Zhao, Y.1    Wang, E.2    Liu, H.3    Rotunno, M.4    Koshiol, J.5
  • 20
    • 67649729608 scopus 로고    scopus 로고
    • A novel and universal method for microRNA RT-qPCR data normalization
    • Mestdagh P, Van VP, De WA, Muth D, Westermann F, et al. (2009) A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol 10: R64.
    • (2009) Genome Biol , vol.10
    • Mestdagh, P.1    Van, V.P.2    de, W.A.3    Muth, D.4    Westermann, F.5
  • 21
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 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.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 22
    • 41349099850 scopus 로고    scopus 로고
    • Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data
    • Xiong H, Zhang D, Martyniuk CJ, Trudeau VL, Xia X, (2008) Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data. BMC Bioinformatics 9: 25.
    • (2008) BMC Bioinformatics , vol.9 , pp. 25
    • Xiong, H.1    Zhang, D.2    Martyniuk, C.J.3    Trudeau, V.L.4    Xia, X.5
  • 23
    • 80855161003 scopus 로고    scopus 로고
    • How to choose a normalization strategy for miRNA quantitative real-time (qPCR) arrays
    • Deo A, Carlsson J, Lindlof A, (2011) How to choose a normalization strategy for miRNA quantitative real-time (qPCR) arrays. J Bioinform Comput Biol 9: 795-812.
    • (2011) J Bioinform Comput Biol , vol.9 , pp. 795-812
    • Deo, A.1    Carlsson, J.2    Lindlof, A.3
  • 24
    • 84862489810 scopus 로고    scopus 로고
    • Computer-aided identification of prostatic adenocarcinoma: Segmentation of glandular structures
    • Peng Y, Jiang Y, Eisengart L, Healy MA, Straus FH, et al. (2011) Computer-aided identification of prostatic adenocarcinoma: Segmentation of glandular structures. J Pathol Inform 2: 33.
    • (2011) J Pathol Inform , vol.2 , pp. 33
    • Peng, Y.1    Jiang, Y.2    Eisengart, L.3    Healy, M.A.4    Straus, F.H.5
  • 25
    • 0018079655 scopus 로고
    • Basic principles of ROC analysis
    • Metz CE, (1978) Basic principles of ROC analysis. Semin Nucl Med 8: 283-298.
    • (1978) Semin Nucl Med , vol.8 , pp. 283-298
    • Metz, C.E.1
  • 27
    • 0001368373 scopus 로고
    • Étude comparative de la distribution florale dans une portion des Alpes et des Jura
    • Jaccard P, (1901) Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bulletin de la Société Vaudoise des Sciences Naturelles 37: 547-579.
    • (1901) Bulletin De La Société Vaudoise Des Sciences Naturelles , vol.37 , pp. 547-579
    • Jaccard, P.1
  • 28
    • 80053903291 scopus 로고    scopus 로고
    • miR-155 inhibits expression of the MEF2A protein to repress skeletal muscle differentiation
    • Seok HY, Tatsuguchi M, Callis TE, He A, Pu WT, et al. (2011) miR-155 inhibits expression of the MEF2A protein to repress skeletal muscle differentiation. J Biol Chem 286: 35339-35346.
    • (2011) J Biol Chem , vol.286 , pp. 35339-35346
    • Seok, H.Y.1    Tatsuguchi, M.2    Callis, T.E.3    He, A.4    Pu, W.T.5
  • 29
    • 77954385461 scopus 로고    scopus 로고
    • MicroRNAs 1, 133, and 206: critical factors of skeletal and cardiac muscle development, function, and disease
    • Townley-Tilson WH, Callis TE, Wang D, (2010) MicroRNAs 1, 133, and 206: critical factors of skeletal and cardiac muscle development, function, and disease. Int J Biochem Cell Biol 42: 1252-1255.
    • (2010) Int J Biochem Cell Biol , vol.42 , pp. 1252-1255
    • Townley-Tilson, W.H.1    Callis, T.E.2    Wang, D.3
  • 30
    • 0032573398 scopus 로고    scopus 로고
    • TNF inhibits insulin induced STAT5 activation in differentiated mouse muscle cells pmi28
    • Storz P, Doppler H, Wernig A, Pfizenmaier K, Muller G, (1998) TNF inhibits insulin induced STAT5 activation in differentiated mouse muscle cells pmi28. FEBS Lett 440: 41-45.
    • (1998) FEBS Lett , vol.440 , pp. 41-45
    • Storz, P.1    Doppler, H.2    Wernig, A.3    Pfizenmaier, K.4    Muller, G.5
  • 31
    • 0037246058 scopus 로고    scopus 로고
    • ArrayExpress-a public repository for microarray gene expression data at the EBI
    • Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, et al. (2003) ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 31: 68-71.
    • (2003) Nucleic Acids Res , vol.31 , pp. 68-71
    • Brazma, A.1    Parkinson, H.2    Sarkans, U.3    Shojatalab, M.4    Vilo, J.5
  • 33
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • Vandesompele J, De PK, Pattyn F, Poppe B, Van RN, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: RESEARCH0034.
    • (2002) Genome Biol , vol.3
    • Vandesompele, J.1    de, P.K.2    Pattyn, F.3    Poppe, B.4    van, R.N.5
  • 34
    • 3442876969 scopus 로고    scopus 로고
    • Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets
    • Andersen CL, Jensen JL, Orntoft TF, (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64: 5245-5250.
    • (2004) Cancer Res , vol.64 , pp. 5245-5250
    • Andersen, C.L.1    Jensen, J.L.2    Orntoft, T.F.3
  • 35
    • 67649444944 scopus 로고    scopus 로고
    • Reference Gene Validation Software for Improved Normalization
    • In Logan J, Edwards K and and Saunders N (eds.), Caister Academic Press, Norfolk, UK
    • Vandesompele J, Kubista M, Pfaffl MW, (2009) Reference Gene Validation Software for Improved Normalization. In Logan J, Edwards K and and Saunders N (eds.), Real-time PCR Current Technology and Applications. Caister Academic Press, Norfolk, UK, 47-49.
    • (2009) Real-time PCR Current Technology and Applications , pp. 47-49
    • Vandesompele, J.1    Kubista, M.2    Pfaffl, M.W.3
  • 36
    • 70149113077 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria, R Development Core Team
    • R Development Core Team (2009) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria.
    • (2009) R: A language and environment for statistical computing
  • 37
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: open software development for computational biology and bioinformatics
    • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
    • (2004) Genome Biol , vol.5
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3    Bolstad, B.4    Dettling, M.5
  • 38
    • 0035710746 scopus 로고    scopus 로고
    • Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method
    • Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
    • (2001) Methods , vol.25 , pp. 402-408
    • Livak, K.J.1    Schmittgen, T.D.2
  • 39
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher VG, Tibshirani R, Chu G, (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3


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