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Volumn 2014, Issue , 2014, Pages

MultiRankSeq: Multiperspective approach for RNAseq differential expression analysis and quality control

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENETIC ANALYSIS; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; QUALITY CONTROL; RNA SEQUENCE; ALGORITHM; BIOLOGY; CLUSTER ANALYSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; PROCEDURES; REPRODUCIBILITY; SEQUENCE ANALYSIS;

EID: 84902203573     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/248090     Document Type: Article
Times cited : (49)

References (31)
  • 1
    • 46249130709 scopus 로고    scopus 로고
    • The beginning of the end for microarrays?
    • DOI 10.1038/nmeth0708-585, PII NMETH0708-585
    • Shendure J., The beginning of the end for microarrays? Nature Methods 2008 5 7 585 587 2-s2.0-46249130709 10.1038/nmeth0708-585 (Pubitemid 351911858)
    • (2008) Nature Methods , vol.5 , Issue.7 , pp. 585-587
    • Shendure, J.1
  • 4
    • 84882692468 scopus 로고    scopus 로고
    • Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data
    • e71462 10.1371/journal.pone.0071462
    • Guo Y., Sheng Q., Li J., Ye F., Samuels D. C., Shyr Y., Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS ONE 2013 8 8 e71462 10.1371/journal.pone.0071462
    • (2013) PLoS ONE , vol.8 , Issue.8
    • Guo, Y.1    Sheng, Q.2    Li, J.3    Ye, F.4    Samuels, D.C.5    Shyr, Y.6
  • 5
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • 2-s2.0-50649089207 10.1101/gr.079558.108
    • Marioni J. C., Mason C. E., Mane S. M., Stephens M., Gilad Y., RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 2008 18 9 1509 1517 2-s2.0-50649089207 10.1101/gr.079558.108
    • (2008) Genome Research , vol.18 , Issue.9 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 6
    • 57749195712 scopus 로고    scopus 로고
    • RNA-seq: A revolutionary tool for transcriptomics
    • 2-s2.0-57749195712 10.1038/nrg2484
    • Wang Z., Gerstein M., Snyder M., RNA-seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 2009 10 1 57 63 2-s2.0-57749195712 10.1038/nrg2484
    • (2009) Nature Reviews Genetics , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 7
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • DOI 10.1038/nmeth.1226, PII NMETH.1226
    • Mortazavi A., Williams B. A., McCue K., Schaeffer L., Wold B., Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods 2008 5 7 621 628 2-s2.0-46249106990 10.1038/nmeth.1226 (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
  • 8
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
    • 2-s2.0-77952123055 10.1038/nbt.1621
    • Trapnell C., Williams B. A., Pertea G., Mortazavi A., Kwan G., van Baren M. J., Salzberg S. L., Wold B. J., Pachter L., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 2010 28 5 511 515 2-s2.0-77952123055 10.1038/nbt.1621
    • (2010) Nature Biotechnology , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 9
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-seq data with or without a reference genome
    • 2-s2.0-79961123152 10.1186/1471-2105-12-3231 2323
    • Li B., Dewey C. N., RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics 2011 12, article 323 2-s2.0-79961123152 10.1186/1471-2105-12-323
    • (2011) BMC Bioinformatics
    • Li, B.1    Dewey, C.N.2
  • 10
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • 2-s2.0-77958471357 10.1186/gb-2010-11-10-r106
    • Anders S., Huber W., Differential expression analysis for sequence count data. Genome Biology 2010 11 10, article R106 2-s2.0-77958471357 10.1186/gb-2010-11-10-r106
    • (2010) Genome Biology , vol.11 , Issue.10 ARTICLE R106
    • Anders, S.1    Huber, W.2
  • 11
    • 75249095274 scopus 로고    scopus 로고
    • DEGseq: An R package for identifying differentially expressed genes from RNA-seq data
    • 2-s2.0-75249095274 10.1093/bioinformatics/btp612
    • Wang L., Feng Z., Wang X., Wang X., Zhang X., DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 2009 26 1 136 138 2-s2.0-75249095274 10.1093/bioinformatics/btp612
    • (2009) Bioinformatics , vol.26 , Issue.1 , pp. 136-138
    • Wang, L.1    Feng, Z.2    Wang, X.3    Wang, X.4    Zhang, X.5
  • 12
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A bioconductor package for differential expression analysis of digital gene expression data
    • 2-s2.0-77449084524
    • Robinson M. D., McCarthy D. J., Smyth G. K., edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010 26 1 139 140 2-s2.0-77449084524
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 13
    • 77955298482 scopus 로고    scopus 로고
    • BaySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
    • 2-s2.0-77955298482 10.1186/1471-2105-11-422 11422
    • Hardcastle T. J., Kelly K. A., BaySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 2010 11, article 422 2-s2.0-77955298482 10.1186/1471-2105-11-422
    • (2010) BMC Bioinformatics
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 14
    • 79958115654 scopus 로고    scopus 로고
    • A two-stage poisson model for testing RNA-seq data
    • 2-s2.0-79958115654 10.2202/1544-6115.1627
    • Auer P. L., Doerge R. W., A two-stage poisson model for testing RNA-seq data. Statistical Applications in Genetics and Molecular Biology 2011 10 1, article 26 2-s2.0-79958115654 10.2202/1544-6115.1627
    • (2011) Statistical Applications in Genetics and Molecular Biology , vol.10 , Issue.1 ARTICLE 26
    • Auer, P.L.1    Doerge, R.W.2
  • 15
    • 79958117254 scopus 로고    scopus 로고
    • The NBP negative binomial model for assessing differential gene expression from RNA-seq
    • 2-s2.0-79958117254 10.2202/1544-6115.1637
    • Di Y., Schafer D. W., Cumbie J. S., Chang J. H., The NBP negative binomial model for assessing differential gene expression from RNA-seq. Statistical Applications in Genetics and Molecular Biology 2011 10 1, article 24 2-s2.0-79958117254 10.2202/1544-6115.1637
    • (2011) Statistical Applications in Genetics and Molecular Biology , vol.10 , Issue.1 ARTICLE 24
    • Di, Y.1    Schafer, D.W.2    Cumbie, J.S.3    Chang, J.H.4
  • 16
    • 84886557480 scopus 로고    scopus 로고
    • Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-seq data
    • 10.1177/0962280211428386
    • Li J., Tibshirani R., Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-seq data. Statistical Methods in Medical Research 2011 22 5 519 536 10.1177/0962280211428386
    • (2011) Statistical Methods in Medical Research , vol.22 , Issue.5 , pp. 519-536
    • Li, J.1    Tibshirani, R.2
  • 17
    • 83055192078 scopus 로고    scopus 로고
    • Differential expression in RNA-seq: A matter of depth
    • 2-s2.0-83055192078 10.1101/gr.124321.111
    • Tarazona S., García-Alcalde F., Dopazo J., Ferrer A., Conesa A., Differential expression in RNA-seq: a matter of depth. Genome Research 2011 21 12 2213 2223 2-s2.0-83055192078 10.1101/gr.124321.111
    • (2011) Genome Research , vol.21 , Issue.12 , pp. 2213-2223
    • Tarazona, S.1    García-Alcalde, F.2    Dopazo, J.3    Ferrer, A.4    Conesa, A.5
  • 19
    • 84858606519 scopus 로고    scopus 로고
    • A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data
    • 2-s2.0-84858606519 10.3732/ajb.1100340
    • Kvam V. M., Liu P., Yaqing S., A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data. The American Journal of Botany 2012 99 2 248 256 2-s2.0-84858606519 10.3732/ajb.1100340
    • (2012) The American Journal of Botany , vol.99 , Issue.2 , pp. 248-256
    • Kvam, V.M.1    Liu, P.2    Yaqing, S.3
  • 20
    • 84866158885 scopus 로고    scopus 로고
    • Efficient experimental design and analysis strategies for the detection of differential expression using RNA-sequencing
    • 10.1186/1471-2164-13-484 13484
    • Robles J. A., Qureshi S. E., Stephen S. J., Wilson S. R., Burden C. J., Taylor J. M., Efficient experimental design and analysis strategies for the detection of differential expression using RNA-sequencing. BMC Genomics 2012 13, article 484 10.1186/1471-2164-13-484
    • (2012) BMC Genomics
    • Robles, J.A.1    Qureshi, S.E.2    Stephen, S.J.3    Wilson, S.R.4    Burden, C.J.5    Taylor, J.M.6
  • 21
    • 84874677498 scopus 로고    scopus 로고
    • A comparison of methods for differential expression analysis of RNA-seq data
    • 10.1186/1471-2105-14-91
    • Soneson C., Delorenzi M., A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics 2013 14, article 91 10.1186/1471-2105-14-91
    • (2013) BMC Bioinformatics , vol.1491
    • Soneson, C.1    Delorenzi, M.2
  • 24
    • 84865074382 scopus 로고    scopus 로고
    • RSeQC: Quality control of RNA-seq experiments
    • 10.1093/bioinformatics/bts356
    • Wang L., Wang S., Li W., RSeQC: quality control of RNA-seq experiments. Bioinformatics 2012 28 16 2184 2185 10.1093/bioinformatics/bts356
    • (2012) Bioinformatics , vol.28 , Issue.16 , pp. 2184-2185
    • Wang, L.1    Wang, S.2    Li, W.3
  • 25
    • 33750616076 scopus 로고    scopus 로고
    • Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma
    • DOI 10.1186/1471-2164-7-252
    • Diboun I., Wernisch L., Orengo C. A., Koltzenburg M., Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics 2006 7, article 252 2-s2.0-33750616076 10.1186/1471-2164-7-252 (Pubitemid 44687315)
    • (2006) BMC Genomics , vol.7 , pp. 252
    • Diboun, I.1    Wernisch, L.2    Orengo, C.A.3    Koltzenburg, M.4
  • 26
    • 84858068675 scopus 로고    scopus 로고
    • Removing technical variability in RNA-seq data using conditional quantile normalization
    • 2-s2.0-84858068675 10.1093/biostatistics/kxr054
    • Hansen K. D., Irizarry R. A., Wu Z., Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics 2012 13 2 204 216 2-s2.0-84858068675 10.1093/biostatistics/kxr054
    • (2012) Biostatistics , vol.13 , Issue.2 , pp. 204-216
    • Hansen, K.D.1    Irizarry, R.A.2    Wu, Z.3
  • 27
    • 84943709252 scopus 로고
    • Use of ranks in one-criterion variance analysis
    • 10.1080/01621459.1952.10483441
    • Kruskal W. H., Wallis W. A., Use of ranks in one-criterion variance analysis. Journal of the American Statistical Association 1952 47 260 583 621 10.1080/01621459.1952.10483441
    • (1952) Journal of the American Statistical Association , vol.47 , Issue.260 , pp. 583-621
    • Kruskal, W.H.1    Wallis, W.A.2
  • 28
    • 0019636384 scopus 로고
    • Comparative study of tests for homogeneity of variances, with applications to the outer continental shelf bidding data
    • Conover W. J., Johnson M. E., Johnson M. M., A comparative study of tests for homogeneity of variances, with applications to the outer continental shelf bidding data. Technometrics 1981 23 4 351 361 2-s2.0-0019636384 (Pubitemid 12456651)
    • (1981) Technometrics , vol.23 , Issue.4 , pp. 351-361
    • Conover, W.J.1    Johnson Mark, E.2    Johnson Myrle, M.3
  • 30
    • 84889664774 scopus 로고    scopus 로고
    • Evaluation of read count based RNAseq analysis methods
    • supplement 8, article S2 10.1186/1471-2164-14-S8-S2
    • Guo Y., Li C. I., Ye F., Shyr Y., Evaluation of read count based RNAseq analysis methods. BMC Genomics 2013 14 supplement 8, article S2 10.1186/1471-2164-14-S8-S2
    • (2013) BMC Genomics , vol.14
    • Guo, Y.1    Li, C.I.2    Ye, F.3    Shyr, Y.4


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