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Volumn 13, Issue 1, 2012, Pages

Workflows for microarray data processing in the Kepler environment

Author keywords

[No Author keywords available]

Indexed keywords

AFFYMETRIX; ALGORITHM DEVELOPMENT; CHIP-CHIP; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL COMPONENTS; DATA-SOURCES; EXAMPLE-BASED; FILE PROCESSING; GENE EXPRESSION MICROARRAY; GRAPHICAL INTERFACE; KEPLER WORKFLOW; LOCAL RESOURCES; MICROARRAY DATA ANALYSIS; MICROARRAY DATA PROCESSING; PARAMETER VALUES; PIPELINE DESIGN; PRIMER DESIGN; PROGRAMMING PARADIGMS; REMOTE DATA; SCIENTIFIC RESEARCHES; SCIENTIFIC WORKFLOWS; WORK-FLOWS;

EID: 84861057273     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-102     Document Type: Article
Times cited : (11)

References (40)
  • 1
    • 84874615900 scopus 로고    scopus 로고
    • Bioconductor Annual Report 2011
    • Bioconductor Annual Report 2011. http://www.bioconductor.org/about/annual-reports/AnnRep2011.pdf.
  • 2
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • 10.1038/nature05874, 2212820, 17571346
    • Birney E, Stamatoyannopoulos JA, Dutta A, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816. 10.1038/nature05874, 2212820, 17571346.
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1    Stamatoyannopoulos, J.A.2    Dutta, A.3
  • 3
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, (455):1061-1068.
    • (2008) Nature , Issue.455 , pp. 1061-1068
  • 4
    • 69849112774 scopus 로고    scopus 로고
    • WebArrayDB: cross-platform microarray data analysis and public data repository
    • 10.1093/bioinformatics/btp430, 2735672, 19602526
    • Xia X-Q, McClelland M, Porwollik S, Song W, Cong X, Wang Y. WebArrayDB: cross-platform microarray data analysis and public data repository. Bioinformatics 2009, 25:2425-2429. 10.1093/bioinformatics/btp430, 2735672, 19602526.
    • (2009) Bioinformatics , vol.25 , pp. 2425-2429
    • Xia, X.-Q.1    McClelland, M.2    Porwollik, S.3    Song, W.4    Cong, X.5    Wang, Y.6
  • 5
    • 84934444122 scopus 로고    scopus 로고
    • Constructing computational pipelines
    • 10.1007/978-1-60327-429-6_24, 18712319
    • Halling-Brown M, Shepherd AJ. Constructing computational pipelines. Methods Mol Biol 2008, 453:451-470. 10.1007/978-1-60327-429-6_24, 18712319.
    • (2008) Methods Mol Biol , vol.453 , pp. 451-470
    • Halling-Brown, M.1    Shepherd, A.J.2
  • 11
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • 10.1186/gb-2010-11-8-r86, 2945788, 20738864
    • Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11:R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
    • (2010) Genome Biol , vol.11
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 12
    • 78650760428 scopus 로고    scopus 로고
    • Scientific workflow systems - can one size fit all? In Biomedical Engineering Conference, 2008. CIBEC, Cairo International
    • Curcin V, Ghanem M. Scientific workflow systems - can one size fit all? In Biomedical Engineering Conference, 2008. CIBEC, Cairo International. IEEE 2008, 2008:1-9.
    • (2008) IEEE , vol.2008 , pp. 1-9
    • Curcin, V.1    Ghanem, M.2
  • 17
    • 77949516139 scopus 로고    scopus 로고
    • JORCA: easily integrating bioinformatics Web Services
    • 10.1093/bioinformatics/btp709, 20047879
    • Martín-Requena V, Ríos J, García M, Ramírez S, Trelles O. jORCA: easily integrating bioinformatics Web Services. Bioinformatics 2010, 26:553-559. 10.1093/bioinformatics/btp709, 20047879.
    • (2010) Bioinformatics , vol.26 , pp. 553-559
    • Martín-Requena, V.1    Ríos, J.2    García, M.3    Ramírez, S.4    Trelles, O.5
  • 19
    • 84874590050 scopus 로고    scopus 로고
    • Beckman Coulter Genomics
    • Beckman Coulter Genomics. [http://www.beckmangenomics.com/ genomic_services/gene_expression.html].
  • 22
    • 77953313654 scopus 로고    scopus 로고
    • Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences
    • Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA. Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinforma 2010, 11:317.
    • (2010) BMC Bioinforma , vol.11 , pp. 317
    • Hartman, A.L.1    Riddle, S.2    McPhillips, T.3    Ludäscher, B.4    Eisen, J.A.5
  • 25
    • 84874602498 scopus 로고    scopus 로고
    • MyExperiment
    • myExperiment. 2006, [http://www.myexperiment.org/].
    • (2006)
  • 26
    • 33745140886 scopus 로고    scopus 로고
    • Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
    • 10.1101/gr.4887606, 1457046, 16606705
    • Bieda M, Xu X, Singer MA, Green R, Farnham PJ. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res 2006, 16:595-605. 10.1101/gr.4887606, 1457046, 16606705.
    • (2006) Genome Res , vol.16 , pp. 595-605
    • Bieda, M.1    Xu, X.2    Singer, M.A.3    Green, R.4    Farnham, P.J.5
  • 28
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Smyth G. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:3.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , pp. 3
    • Smyth, G.1
  • 29
    • 84874628161 scopus 로고    scopus 로고
    • GFF (General Feature Format) specifications document
    • GFF (General Feature Format) specifications document. 2005, [http://www. sanger.ac.uk/resources/software/gff/spec.html].
    • (2005)
  • 30
    • 24644512209 scopus 로고    scopus 로고
    • Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis
    • 10.1093/bioinformatics/bti605, 16076888
    • Wilson CL, Miller CJ. Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics 2005, 21:3683-3685. 10.1093/bioinformatics/bti605, 16076888.
    • (2005) Bioinformatics , vol.21 , pp. 3683-3685
    • Wilson, C.L.1    Miller, C.J.2
  • 31
    • 84874600508 scopus 로고    scopus 로고
    • GEO Accession viewer GSE718
    • GEO Accession viewer GSE718. [http://www.ncbi.nlm.nih.gov/projects/ geo/query/acc.cgi?acc=GSE7181].
  • 32
    • 34249332411 scopus 로고    scopus 로고
    • CD133(+) and CD133(-) glioblastoma-derived cancer stem cells show differential growth characteristics and molecular profiles
    • 10.1158/0008-5472.CAN-06-4180, 17483311
    • Beier D, Hau P, Proescholdt M, Lohmeier A, Wischhusen J, Oefner PJ, Aigner L, Brawanski A, Bogdahn U, Beier CP. CD133(+) and CD133(-) glioblastoma-derived cancer stem cells show differential growth characteristics and molecular profiles. Cancer Res 2007, 67:4010-4015. 10.1158/0008-5472.CAN-06-4180, 17483311.
    • (2007) Cancer Res , vol.67 , pp. 4010-4015
    • Beier, D.1    Hau, P.2    Proescholdt, M.3    Lohmeier, A.4    Wischhusen, J.5    Oefner, P.J.6    Aigner, L.7    Brawanski, A.8    Bogdahn, U.9    Beier, C.P.10
  • 33
  • 35
    • 41649107645 scopus 로고    scopus 로고
    • Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors
    • 10.1158/0008-5472.CAN-07-5590, 2567918, 18413731
    • Acevedo LG, Bieda M, Green R, Farnham PJ. Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Res 2008, 68:2641-2651. 10.1158/0008-5472.CAN-07-5590, 2567918, 18413731.
    • (2008) Cancer Res , vol.68 , pp. 2641-2651
    • Acevedo, L.G.1    Bieda, M.2    Green, R.3    Farnham, P.J.4
  • 36
    • 33846052176 scopus 로고    scopus 로고
    • QPrimerDepot: a primer database for quantitative real time PCR
    • 10.1093/nar/gkl767, 1635330, 17068075
    • Cui W, Taub DD, Gardner K. qPrimerDepot: a primer database for quantitative real time PCR. Nucleic Acids Res 2007, 35:D805-D809. 10.1093/nar/gkl767, 1635330, 17068075.
    • (2007) Nucleic Acids Res , vol.35
    • Cui, W.1    Taub, D.D.2    Gardner, K.3
  • 38
    • 33644779844 scopus 로고    scopus 로고
    • WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data
    • Yi M, Horton JD, Cohen JC, Hobbs HH, Stephens RM. WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data. BMC Bioinforma 2006, 7:30.
    • (2006) BMC Bioinforma , vol.7 , pp. 30
    • Yi, M.1    Horton, J.D.2    Cohen, J.C.3    Hobbs, H.H.4    Stephens, R.M.5
  • 39
    • 80053976986 scopus 로고    scopus 로고
    • Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA
    • 10.1093/bioinformatics/btr499, 21893519
    • Kamburov A, Cavill R, Ebbels TMD, Herwig R, Keun HC. Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. Bioinformatics 2011, 27:2917-2918. 10.1093/bioinformatics/btr499, 21893519.
    • (2011) Bioinformatics , vol.27 , pp. 2917-2918
    • Kamburov, A.1    Cavill, R.2    Ebbels, T.M.D.3    Herwig, R.4    Keun, H.C.5
  • 40
    • 84874604577 scopus 로고    scopus 로고
    • BioKepler
    • bioKepler. [http://sites.google.com/site/biokepler/].


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.