메뉴 건너뛰기




Volumn 14, Issue SUPP 8, 2013, Pages

Evaluation of read count based RNAseq analysis methods

Author keywords

baySeq; DEGseq; DESeq; edger; expression; NBPSeq; RNAseq; TSPM

Indexed keywords

ACCURACY; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; GENE EXPRESSION; RECEIVER OPERATING CHARACTERISTIC; RNA SEQUENCE; SENSITIVITY ANALYSIS; SIMULATION; STATISTICAL SIGNIFICANCE;

EID: 84889664774     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-S8-S2     Document Type: Article
Times cited : (46)

References (14)
  • 1
    • 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(1):57-63. 10.1038/nrg2484, 2949280, 19015660.
    • (2009) Nat Rev Genet , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 2
    • 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(7):585-587. 10.1038/nmeth0708-585, 18587314.
    • (2008) Nat Methods , vol.5 , Issue.7 , pp. 585-587
    • Shendure, J.1
  • 3
    • 84882692468 scopus 로고    scopus 로고
    • Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
    • 10.1371/journal.pone.0071462, 3748065, 23977046
    • Guo Y, Sheng Q, Li J, Ye F, Samuels DC, 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, 3748065, 23977046.
    • (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
  • 4
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • 10.1093/biostatistics/4.2.249, 12925520
    • Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264. 10.1093/biostatistics/4.2.249, 12925520.
    • (2003) Biostatistics , vol.4 , Issue.2 , pp. 249-264
    • Irizarry, R.A.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.D.4    Antonellis, K.J.5    Scherf, U.6    Speed, T.P.7
  • 5
    • 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(7):621-628. 10.1038/nmeth.1226, 18516045.
    • (2008) Nat Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 6
    • 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, 3146043, 20436464
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28(5):511-515. 10.1038/nbt.1621, 3146043, 20436464.
    • (2010) Nat Biotechnol , 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
  • 7
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • 10.1186/gb-2010-11-10-r106, 3218662, 20979621
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010, 11(10):R106. 10.1186/gb-2010-11-10-r106, 3218662, 20979621.
    • (2010) Genome Biol , vol.11 , Issue.10
    • Anders, S.1    Huber, W.2
  • 8
    • 75249095274 scopus 로고    scopus 로고
    • DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
    • 10.1093/bioinformatics/btp612, 19855105
    • Wang L, Feng Z, Wang X, Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 2010, 26(1):136-138. 10.1093/bioinformatics/btp612, 19855105.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 136-138
    • Wang, L.1    Feng, Z.2    Wang, X.3    Zhang, X.4
  • 9
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • 10.1093/bioinformatics/btp616, 2796818, 19910308
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26(1):139-140. 10.1093/bioinformatics/btp616, 2796818, 19910308.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 10
    • 77955298482 scopus 로고    scopus 로고
    • BaySeq: empirical Bayesian methods for identifying differential expression in sequence count data
    • 10.1186/1471-2105-11-422, 2928208, 20698981
    • Hardcastle TJ, Kelly KA. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 2010, 11:422. 10.1186/1471-2105-11-422, 2928208, 20698981.
    • (2010) BMC Bioinformatics , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 13
    • 79959838081 scopus 로고    scopus 로고
    • Integrated genomic analyses of ovarian carcinoma
    • 10.1038/nature10166, 3163504, 21720365
    • Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474(7353):609-615. 10.1038/nature10166, 3163504, 21720365.
    • (2011) Nature , vol.474 , Issue.7353 , pp. 609-615
  • 14
    • 84863922124 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of human colon and rectal cancer
    • 10.1038/nature11252, 3401966, 22810696
    • Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012, 487(7407):330-337. 10.1038/nature11252, 3401966, 22810696.
    • (2012) Nature , vol.487 , Issue.7407 , pp. 330-337


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.