메뉴 건너뛰기




Volumn 8, Issue 7, 2013, Pages

TCW: Transcriptome Computational Workbench

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

EID: 84880434857     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0069401     Document Type: Article
Times cited : (17)

References (40)
  • 1
    • 84859699831 scopus 로고    scopus 로고
    • The Gene Ontology: enhancements for 2011
    • The GO Consortium
    • The GO Consortium, (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Res 40: D559-564.
    • (2012) Nucleic Acids Res , vol.40
  • 2
    • 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
  • 3
    • 43949138227 scopus 로고    scopus 로고
    • Blast2GO: A comprehensive suite for functional analysis in plant genomics
    • Conesa A, Gotz S, (2008) Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008: 619832.
    • (2008) Int J Plant Genomics , vol.2008 , pp. 619832
    • Conesa, A.1    Gotz, S.2
  • 4
    • 84858602406 scopus 로고    scopus 로고
    • InterPro in 2011: new developments in the family and domain prediction database
    • Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40: D306-312.
    • (2012) Nucleic Acids Res , vol.40
    • Hunter, S.1    Jones, P.2    Mitchell, A.3    Apweiler, R.4    Attwood, T.K.5
  • 5
    • 84864483625 scopus 로고    scopus 로고
    • RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
    • Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, et al. (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 40: W622-627.
    • (2012) Nucleic Acids Res , vol.40
    • Lohse, M.1    Bolger, A.M.2    Nagel, A.3    Fernie, A.R.4    Lunn, J.E.5
  • 6
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, 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
  • 7
    • 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
  • 9
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL, (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    Salzberg, S.L.4
  • 10
    • 75249095274 scopus 로고    scopus 로고
    • DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
    • Wang L, Feng Z, Wang X, Zhang X, (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26: 136-138.
    • (2010) Bioinformatics , vol.26 , pp. 136-138
    • Wang, L.1    Feng, Z.2    Wang, X.3    Zhang, X.4
  • 11
  • 12
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: identification of ortholog groups for eukaryotic genomes
    • Li L, Stoeckert CJ Jr, Roos DS, (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert Jr., C.J.2    Roos, D.S.3
  • 14
    • 78650991450 scopus 로고    scopus 로고
    • OrthoInspector: comprehensive orthology analysis and visual exploration
    • Linard B, Thompson JD, Poch O, Lecompte O, (2011) OrthoInspector: comprehensive orthology analysis and visual exploration. BMC Bioinformatics 12: 11.
    • (2011) BMC Bioinformatics , vol.12 , pp. 11
    • Linard, B.1    Thompson, J.D.2    Poch, O.3    Lecompte, O.4
  • 18
    • 79952314593 scopus 로고    scopus 로고
    • A pipeline for RNA-seq data processing and quality assessment
    • Goncalves A, Tikhonov A, Brazma A, Kapushesky M, (2011) A pipeline for RNA-seq data processing and quality assessment. Bioinformatics 27: 867-869.
    • (2011) Bioinformatics , vol.27 , pp. 867-869
    • Goncalves, A.1    Tikhonov, A.2    Brazma, A.3    Kapushesky, M.4
  • 19
    • 77955343193 scopus 로고    scopus 로고
    • Cloud-scale RNA-sequencing differential expression analysis with Myrna
    • Langmead B, Hansen KD, Leek JT, (2010) Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol 11: R83.
    • (2010) Genome Biol , vol.11
    • Langmead, B.1    Hansen, K.D.2    Leek, J.T.3
  • 21
    • 84863338285 scopus 로고    scopus 로고
    • Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity
    • He R, Kim MJ, Nelson W, Balbuena TS, Kim R, et al. (2012) Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity. Am J Bot 99: 232-247.
    • (2012) Am J Bot , vol.99 , pp. 232-247
    • He, R.1    Kim, M.J.2    Nelson, W.3    Balbuena, T.S.4    Kim, R.5
  • 22
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang X, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
    • (1999) Genome Res , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 25
    • 0033963089 scopus 로고    scopus 로고
    • The ENZYME database in 2000
    • Bairoch A, (2000) The ENZYME database in 2000. Nucleic Acids Res 28: 304-305.
    • (2000) Nucleic Acids Res , vol.28 , pp. 304-305
    • Bairoch, A.1
  • 28
    • 0034518635 scopus 로고    scopus 로고
    • The comparison of gene expression from multiple cDNA libraries
    • Stekel DJ, Git Y, Falciani F, (2000) The comparison of gene expression from multiple cDNA libraries. Genome Res 10: 2055-2061.
    • (2000) Genome Res , vol.10 , pp. 2055-2061
    • Stekel, D.J.1    Git, Y.2    Falciani, F.3
  • 29
    • 77955298482 scopus 로고    scopus 로고
    • baySeq: empirical Bayesian methods for identifying differential expression in sequence count data
    • Hardcastle TJ, Kelly KA, (2010) baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11: 422.
    • (2010) BMC Bioinformatics , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 32
    • 0033290515 scopus 로고    scopus 로고
    • ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences
    • Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol: 138-148.
    • (1999) Proc Int Conf Intell Syst Mol Biol , pp. 138-148
    • Iseli, C.1    Jongeneel, C.V.2    Bucher, P.3
  • 33
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 34
    • 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
  • 35
    • 78651337578 scopus 로고    scopus 로고
    • PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database
    • Zhang H, Jin J, Tang L, Zhao Y, Gu X, et al. (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res 39: D1114-1117.
    • (2011) Nucleic Acids Res , vol.39
    • Zhang, H.1    Jin, J.2    Tang, L.3    Zhao, Y.4    Gu, X.5
  • 36
    • 14644395503 scopus 로고    scopus 로고
    • wEMBOSS: a web interface for EMBOSS
    • Sarachu M, Colet M, (2005) wEMBOSS: a web interface for EMBOSS. Bioinformatics 21: 540-541.
    • (2005) Bioinformatics , vol.21 , pp. 540-541
    • Sarachu, M.1    Colet, M.2
  • 37
    • 81555234540 scopus 로고    scopus 로고
    • iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
    • Zheng Y, Zhao L, Gao J, Fei Z, (2011) iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12: 453.
    • (2011) BMC Bioinformatics , vol.12 , pp. 453
    • Zheng, Y.1    Zhao, L.2    Gao, J.3    Fei, Z.4
  • 38
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: multiple alignment of conserved genomic sequence with rearrangements
    • Darling AC, Mau B, Blattner FR, Perna NT, (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394-1403.
    • (2004) Genome Res , vol.14 , pp. 1394-1403
    • Darling, A.C.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 39
    • 79961194036 scopus 로고    scopus 로고
    • SyMAP v3.4: a turnkey synteny system with application to plant genomes
    • Soderlund C, Bomhoff M, Nelson WM, (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res 39: e68.
    • (2011) Nucleic Acids Res , vol.39
    • Soderlund, C.1    Bomhoff, M.2    Nelson, W.M.3
  • 40
    • 73349116606 scopus 로고    scopus 로고
    • Network visualization and analysis of gene expression data using BioLayout Express(3D)
    • Theocharidis A, van Dongen S, Enright AJ, Freeman TC, (2009) Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc 4: 1535-1550.
    • (2009) Nat Protoc , vol.4 , pp. 1535-1550
    • Theocharidis, A.1    van Dongen, S.2    Enright, A.J.3    Freeman, T.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.