메뉴 건너뛰기




Volumn 802, Issue , 2012, Pages 259-274

How to analyze gene expression using RNA-sequencing data

Author keywords

Genomics; RNA Seq; Tutorial

Indexed keywords

TRANSCRIPTOME;

EID: 84555191516     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-400-1_17     Document Type: Article
Times cited : (26)

References (59)
  • 1
    • 57749195712 scopus 로고    scopus 로고
    • RNASeq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, SnyderM(2009) RNASeq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Snyderm, G.M.2
  • 3
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan Q, Shai O, Lee L et al (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413-1415
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.3
  • 4
    • 62649160909 scopus 로고    scopus 로고
    • Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing
    • Yoder-Himes DR, Chain PSG, Zhu Y et al (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci USA 106:3976-3981
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 3976-3981
    • Yoder-Himes, D.R.1    Psg, C.2    Zhu, Y.3
  • 5
    • 69549112743 scopus 로고    scopus 로고
    • Digital transcriptome profiling using selective hexamer priming for cDNA synthesis
    • Armour CD, Castle JC, Chen R et al (2009) Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat Methods 6:647-649
    • (2009) Nat Methods , vol.6 , pp. 647-649
    • Armour, C.D.1    Castle, J.C.2    Chen, R.3
  • 6
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core LJ, Waterfall JJ and Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845-1848
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 7
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia NT, Ghaemmaghami S, Newman JRS et al (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-223
    • (2009) Science , vol.324 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Jrs, N.3
  • 8
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies-The next generation
    • Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11:31-46
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 9
    • 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 et al (2008) Mapping and quantifying mammalian 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
  • 10
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman M, Garber M, Levin JZ et al (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28:503-510
    • (2010) Nat Biotechnol , vol.28 , pp. 503-510
    • Guttman, M.1    Garber, M.2    Levin, J.Z.3
  • 11
    • 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. Nat Biotechnol 28:511-515
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3
  • 12
    • 84860883182 scopus 로고    scopus 로고
    • Sequence Read Archive
    • Sequence Read Archive. http://www.ncbi.nlm.nih.gov/sra.
  • 13
    • 84860888289 scopus 로고    scopus 로고
    • Gene Expression Omnibus
    • Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo.
  • 14
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing B, Hillier L, Wendl MC et al (1998) Base-calling of automated sequencer traces using phred I accuracy assessment. Genome Res 8:175-185 (Pubitemid 28177229)
    • (1998) Genome Research , vol.8 , Issue.3 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 15
    • 77951226627 scopus 로고    scopus 로고
    • The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
    • Cock PJA, Fields CJ, Goto N et al (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767-1771
    • (2010) Nucleic Acids Res , vol.38 , pp. 1767-1771
    • Pja, C.1    Fields, C.J.2    Goto, N.3
  • 18
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: Freely available Python tools for computational molecular biology and bioinformatics
    • Cock PJA, Antao T, Chang JT et al (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422-1423
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Pja, C.1    Antao, T.2    Chang, J.T.3
  • 19
    • 84860887554 scopus 로고    scopus 로고
    • NCBI, Accessed 2 Nov 2010
    • NCBI (2010) Sequence Read Archive Submission Guidelines. http://www.ncbi.nlm. nih.gov/Traces/sra/static/SRA-Submission-Guidelines.pdf. Accessed 2 Nov 2010
    • (2010) Sequence Read Archive Submission Guidelines
  • 20
    • 84860888290 scopus 로고    scopus 로고
    • SOLiD Sequence Read Format package
    • SOLiD Sequence Read Format package. http://solidsoftwaretools.com/gf/ project/srf/
  • 21
    • 84860883180 scopus 로고    scopus 로고
    • Staden IO module
    • Staden IO module. http://staden.sourceforge. net/
  • 22
    • 84860888421 scopus 로고    scopus 로고
    • Sequenceread package
    • Sequenceread package http://sourceforge.net/projects/sequenceread/
  • 23
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNA-seq studies
    • Pepke S, Wold B, Mortazavi A (2009) Computation for ChIP-seq and RNA-seq studies. Nat Methods 6:S22-S32
    • (2009) Nat Methods , vol.6
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 24
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm JC, Lottaz C, Borodina T et al (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36:e105
    • (2008) Nucleic Acids Res , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3
  • 25
    • 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
    • Langmead, B.1    Trapnell, C.2    Pop, M.3
  • 26
    • 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 25:1105-1111
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 27
    • 70349886587 scopus 로고    scopus 로고
    • PerM: Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
    • Chen Y, Souaiaia T and Chen T (2009) PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 25:2514-2521
    • (2009) Bioinformatics , vol.25 , pp. 2514-2521
    • Chen, Y.1    Souaiaia, T.2    Chen, T.3
  • 28
    • 84860882788 scopus 로고    scopus 로고
    • Galaxy
    • Galaxy. http://g2.bx.psu.edu
  • 29
    • 84860888418 scopus 로고    scopus 로고
    • Galaxy Experimental Features
    • Galaxy Experimental Features. http://test.g2.bx.psu.edu
  • 30
    • 84860883179 scopus 로고    scopus 로고
    • Novoalign
    • Novoalign. http://www.novocraft.com
  • 31
    • 70450177746 scopus 로고    scopus 로고
    • BFAST: An alignment tool for large scale genome resequencing
    • Homer N, Merriman B, Nelson SF (2009) BFAST: an alignment tool for large scale genome resequencing. PLoS ONE 4:e7767
    • (2009) PLoS ONE , vol.4
    • Homer, N.1    Merriman, B.2    Nelson, S.F.3
  • 32
    • 84860883177 scopus 로고    scopus 로고
    • Mosaik
    • Mosaik. http://bioinformatics.bc.edu/marthlab/Mosaik
  • 34
    • 84860888419 scopus 로고    scopus 로고
    • Tophat
    • Tophat. http://tophat.cbcb.umd.edu/index.html
  • 35
    • 84860882787 scopus 로고    scopus 로고
    • UCSC Genome Browser FAQ File Formats
    • UCSC Genome Browser FAQ File Formats. http://genome.ucsc.edu/FAQ/ FAQformathtml#format1
  • 36
    • 84555210896 scopus 로고    scopus 로고
    • Bowtie http://bowtie-bio.sourceforge.net
    • Bowtie. http://bowtie-bio.sourceforge.net
  • 37
    • 84860888420 scopus 로고    scopus 로고
    • RNA-Seq files at sandberg lab homepage
    • RNA-Seq files at sandberg lab homepage. http://sandberg.cmb.ki.se/rnaseq/
  • 38
    • 84860883178 scopus 로고    scopus 로고
    • PerM
    • PerM. http://code.google.com/p/perm/
  • 39
    • 84860883176 scopus 로고    scopus 로고
    • Python
    • Python. http://www.python.org
  • 40
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li H, Handsaker B, Wysoker A et al (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 41
    • 84860888416 scopus 로고    scopus 로고
    • UCSC Genome Browser Downloads
    • UCSC Genome Browser Downloads. http://hgdownload.cse.ucsc.edu/downloads. html
  • 42
    • 77952905505 scopus 로고    scopus 로고
    • Most "dark matter" transcripts are associated with known genes
    • van Bakel H, Nislow C, Blencowe BJ et al (2010) Most "dark matter" transcripts are associated with known genes. PLoS Biol 8: e1000371
    • (2010) PLoS Biol , vol.8
    • Van Bakel, H.1    Nislow, C.2    Blencowe, B.J.3
  • 43
    • 84860888417 scopus 로고    scopus 로고
    • Integrative Genome Browser
    • Integrative Genome Browser. http://www.broadinstitute.org/igv
  • 44
    • 46249092601 scopus 로고    scopus 로고
    • Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer microRNA target sites
    • DOI 10.1126/science.1155390
    • Sandberg R, Neilson JR, Sarma A et al (2008) Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer micro-RNA target sites. Science 320:1643-7 (Pubitemid 351931255)
    • (2008) Science , vol.320 , Issue.5883 , pp. 1643-1647
    • Sandberg, R.1    Neilson, J.R.2    Sarma, A.3    Sharp, P.A.4    Burge, C.B.5
  • 45
    • 77952576233 scopus 로고    scopus 로고
    • Heterogeneity in mammalian RNA 30 end formation
    • Neilson JR and Sandberg R (2010) Heterogeneity in mammalian RNA 30 end formation. Exp Cell Res 316:1357-1364
    • (2010) Exp Cell Res , vol.316 , pp. 1357-1364
    • Neilson, J.R.1    Sandberg, R.2
  • 46
    • 74549125753 scopus 로고    scopus 로고
    • An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
    • Ramsköld D,Wang ET, Burge CB et al (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5:e1000598
    • (2009) PLoS Comput Biol , vol.5
    • Ramsköld, D.1    Wang, E.T.2    Burge, C.B.3
  • 47
    • 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 464:773-777
    • (2010) Nature , vol.464 , pp. 773-777
    • Montgomery, S.B.1    Sammeth, M.2    Gutierrez-Arcelus, M.3
  • 48
    • 84860883173 scopus 로고    scopus 로고
    • NumPy
    • NumPy. http://numpy.scipy.org
  • 49
    • 77955895425 scopus 로고    scopus 로고
    • BigWig and BigBed: Enabling browsing of large distributed datasets
    • Kent WJ, Zweig AS, Barber G et al (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26:2204-2207
    • (2010) Bioinformatics , vol.26 , pp. 2204-2207
    • Kent, W.J.1    Zweig, A.S.2    Barber, G.3
  • 50
    • 84860883174 scopus 로고    scopus 로고
    • UCSC stand-alone bioinformatic programs
    • UCSC stand-alone bioinformatic programs. http://hgdownload.cse.ucsc.edu/ admin/exe/linux.x86-64/
  • 51
    • 84860883175 scopus 로고    scopus 로고
    • UCSC Mappability Data
    • UCSC Mappability Data. http://hgdownload. cse.ucsc.edu/goldenPath/hg19/ encodeDCC/wgEncodeMapability/
  • 52
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni JC,Mason CE, Mane SMet al (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509-1517
    • (2008) Genome Res , vol.18 , pp. 1509-1517
    • Marioni Jcmason, C.E.1    Smet Al, M.2
  • 53
    • 29244448340 scopus 로고    scopus 로고
    • Microarray data analysis: From disarray to consolidation and consensus
    • DOI 10.1038/nrg1749
    • Allison DB, Cui X, Page GP et al (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7:55-65 (Pubitemid 41828948)
    • (2006) Nature Reviews Genetics , vol.7 , Issue.1 , pp. 55-65
    • Allison, D.B.1    Cui, X.2    Page, G.P.3    Sabripour, M.4
  • 54
    • 75249087100 scopus 로고    scopus 로고
    • 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 26:139-140
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 55
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106
    • (2010) Genome Biol , vol.11
    • Anders, S.1    Huber, W.2
  • 56
    • 84860888415 scopus 로고    scopus 로고
    • Scripture
    • Scripture. http://www.broadinstitute.org/software/scripture
  • 57
    • 84860883170 scopus 로고    scopus 로고
    • R
    • R, http://www.r-project.org/
  • 58
    • 84860883171 scopus 로고    scopus 로고
    • Bioconductor
    • Bioconductor, http://www.bioconductor. org/
  • 59
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851-1858
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.