메뉴 건너뛰기




Volumn 9, Issue 1, 2018, Pages

Massive mining of publicly available RNA-seq data from human and mouse

Author keywords

[No Author keywords available]

Indexed keywords

CELL; GENE EXPRESSION; GENOME; MINING; PROTEIN; RNA; RODENT; VISUALIZATION;

EID: 85045272055     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-018-03751-6     Document Type: Article
Times cited : (458)

References (49)
  • 1
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter, J. C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
    • (2001) Science , vol.291 , pp. 1304-1351
    • Venter, J.C.1
  • 2
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 3
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • 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 Res. 18, 1509-1517 (2008).
    • (2008) Genome Res. , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 4
    • 0036081355 scopus 로고    scopus 로고
    • Gene expression omnibus: NCBI gene expression and hybridization array data repository
    • Edgar, R., Domrachev, M. & Lash, A. E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 5
    • 0037246058 scopus 로고    scopus 로고
    • ArrayExpress-A public repository for microarray gene expression data at the EBI
    • Brazma, A. et al. ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 68-71 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 68-71
    • Brazma, A.1
  • 6
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 7
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with burrows-wheeler transform
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 8
    • 84871809302 scopus 로고    scopus 로고
    • STAR: Ultrafast universal RNA-seq aligner
    • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 15-21
    • Dobin, A.1
  • 10
    • 84859048351 scopus 로고    scopus 로고
    • SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads
    • Liu, C.-M. et al. SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics 28, 878-879 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 878-879
    • Liu, C.-M.1
  • 11
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1
  • 12
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: An improved ultrafast tool for short read alignment
    • Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1
  • 13
    • 84899541625 scopus 로고    scopus 로고
    • Big data in biomedicine
    • Costa, F. F. Big data in biomedicine. Drug Discov. Today 19, 433-440 (2014).
    • (2014) Drug Discov. Today , vol.19 , pp. 433-440
    • Costa, F.F.1
  • 14
    • 84878682420 scopus 로고    scopus 로고
    • The genotype-tissue expression (GTEx) project
    • Lonsdale, J. et al. The genotype-tissue expression (GTEx) project. Nat. Genet. 45, 580-585 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 580-585
    • Lonsdale, J.1
  • 15
    • 84884994218 scopus 로고    scopus 로고
    • The cancer genome atlas pan-cancer analysis project
    • Weinstein, J. N. et al. The cancer genome atlas pan-cancer analysis project. Nat. Genet. 45, 1113-1120 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 1113-1120
    • Weinstein, J.N.1
  • 16
    • 85017352969 scopus 로고    scopus 로고
    • Toil enables reproducible, open source, big biomedical data analyses
    • Vivian, J. et al. Toil enables reproducible, open source, big biomedical data analyses. Nat. Biotechnol. 35, 314 (2017).
    • (2017) Nat. Biotechnol. , vol.35 , pp. 314
    • Vivian, J.1
  • 17
    • 84976878197 scopus 로고    scopus 로고
    • Expression atlas update-an integrated database of gene and protein expression in humans, animals and plants
    • Petryszak, R. et al. Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 44, D746-D752 (2015).
    • (2015) Nucleic Acids Res. , vol.44 , pp. D746-D752
    • Petryszak, R.1
  • 19
    • 85017363752 scopus 로고    scopus 로고
    • Reproducible RNA-seq analysis using recount2
    • Collado-Torres, L. et al. Reproducible RNA-seq analysis using recount2. Nat. Biotechnol. 35, 319-321 (2017).
    • (2017) Nat. Biotechnol. , vol.35 , pp. 319-321
    • Collado-Torres, L.1
  • 21
    • 0037236821 scopus 로고    scopus 로고
    • An elementary proof of a theorem of johnson and lindenstrauss
    • Dasgupta, S. & Gupta, A. An elementary proof of a theorem of Johnson and Lindenstrauss. Random Struct. Algorithms 22, 60-65 (2003).
    • (2003) Random Struct. Algorithms , vol.22 , pp. 60-65
    • Dasgupta, S.1    Gupta, A.2
  • 22
    • 77957243164 scopus 로고    scopus 로고
    • ChEA: Transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
    • Lachmann, A. et al. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 26, 2438-2444 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 2438-2444
    • Lachmann, A.1
  • 23
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia of DNA elements) project
    • Consortium, E. P. The ENCODE (ENCyclopedia of DNA elements) project. Science 306, 636-640 (2004).
    • (2004) Science , vol.306 , pp. 636-640
    • Consortium, E.P.1
  • 24
    • 61449203001 scopus 로고    scopus 로고
    • KEA: Kinase enrichment analysis
    • Lachmann, A. & Ma'ayan, A. KEA: kinase enrichment analysis. Bioinformatics 25, 684-686 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 684-686
    • Lachmann, A.1    Ma'Ayan, A.2
  • 25
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner, M. et al. Gene Ontology: tool for the unification of biology. Nat. Genet. 25, 25-29 (2000).
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 26
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 27
    • 26844450908 scopus 로고    scopus 로고
    • The mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information
    • Smith, C. L., Goldsmith, C.-A. W. & Eppig, J. T. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 6, R7 (2004).
    • (2004) Genome Biol. , vol.6 , pp. R7
    • Smith, C.L.1    Goldsmith, C.-A.W.2    Eppig, J.T.3
  • 28
    • 84876100615 scopus 로고    scopus 로고
    • Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool
    • Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).
    • (2013) BMC Bioinformatics , vol.14 , pp. 128
    • Chen, E.Y.1
  • 29
    • 84987663170 scopus 로고    scopus 로고
    • Enrichr: A comprehensive gene set enrichment analysis web server 2016 update
    • Kuleshov, M. V. et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44, W90-W97 (2016).
    • (2016) Nucleic Acids Res. , vol.44 , pp. W90-W97
    • Kuleshov, M.V.1
  • 30
    • 84954358609 scopus 로고    scopus 로고
    • The human phenotype ontology: A tool for annotating and analyzing human hereditary disease
    • Robinson, P. N. et al. The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am. J. Human Genet. 83, 610-615 (2008).
    • (2008) Am. J. Human Genet. , vol.83 , pp. 610-615
    • Robinson, P.N.1
  • 31
    • 85030995149 scopus 로고    scopus 로고
    • Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data
    • Fernandez, N. F. et al. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. Sci. Data 4, 170151 (2017).
    • (2017) Sci. Data , vol.4 , pp. 170151
    • Fernandez, N.F.1
  • 32
    • 85021320754 scopus 로고    scopus 로고
    • Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes
    • Drew, K. et al. Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Mol. Syst. Biol. 13, 932 (2017).
    • (2017) Mol. Syst. Biol. , vol.13 , pp. 932
    • Drew, K.1
  • 33
    • 33644873184 scopus 로고    scopus 로고
    • BioGRID: A general repository for interaction datasets
    • Stark, C. et al. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 34, D535-D539 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. D535-D539
    • Stark, C.1
  • 34
    • 84937213168 scopus 로고    scopus 로고
    • The BioPlex network: A systematic exploration of the human interactome
    • Huttlin, E. L. et al. The BioPlex network: a systematic exploration of the human interactome. Cell 162, 425-440 (2015).
    • (2015) Cell , vol.162 , pp. 425-440
    • Huttlin, E.L.1
  • 35
    • 84876571339 scopus 로고    scopus 로고
    • BioGPS and MyGene. Info: Organizing online, gene-centric information
    • Wu, C., MacLeod, I. & Su, A. I. BioGPS and MyGene. info: organizing online, gene-centric information. Nucleic Acids Res. 41, D561-D565 (2012).
    • (2012) Nucleic Acids Res. , vol.41 , pp. D561-D565
    • Wu, C.1    MacLeod, I.2    Su, A.I.3
  • 36
    • 78049480691 scopus 로고    scopus 로고
    • GeneCards version 3: The human gene integrator
    • Safran, M. et al. GeneCards Version 3: the human gene integrator. Database 2010, baq020 (2010).
    • (2010) Database , vol.2010 , pp. baq020
    • Safran, M.1
  • 37
    • 85011663517 scopus 로고    scopus 로고
    • The harmonizome: A collection of processed datasets gathered to serve and mine knowledge about genes and proteins
    • Rouillard, A. D. et al. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database 2016, baw100 (2016).
    • (2016) Database , vol.2016 , pp. baw100
    • Rouillard, A.D.1
  • 39
    • 84926444656 scopus 로고    scopus 로고
    • Docker: Lightweight linux containers for consistent development and deployment
    • Merkel, D. Docker: lightweight linux containers for consistent development and deployment. Linux J. 2014, 2 (2014).
    • (2014) Linux J. , vol.2014 , pp. 2
    • Merkel, D.1
  • 40
    • 34547871639 scopus 로고    scopus 로고
    • GEOquery: A bridge between the gene expression omnibus (GEO) and BioConductor
    • Davis, S. & Meltzer, P. S. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 23, 1846-1847 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 1846-1847
    • Davis, S.1    Meltzer, P.S.2
  • 41
    • 85045237456 scopus 로고    scopus 로고
    • (Manning Publications Co., Shelter Island, NY)
    • Ignazio, R. Mesos in Action (Manning Publications Co., Shelter Island, NY, 2016).
    • (2016) Mesos in Action
    • Ignazio, R.1
  • 43
    • 57249084011 scopus 로고    scopus 로고
    • Visualizing data using t-SNE
    • Maaten, Lvd & Hinton, G. Visualizing data using t-SNE. J. Mach. Learn. Res. 9, 2579-2605 (2008).
    • (2008) J. Mach. Learn. Res. , vol.9 , pp. 2579-2605
    • Maaten, L.1    Hinton, G.2
  • 47
    • 84859169877 scopus 로고    scopus 로고
    • The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity
    • Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012).
    • (2012) Nature , vol.483 , pp. 603-607
    • Barretina, J.1
  • 49
    • 84961371413 scopus 로고    scopus 로고
    • Lean big data integration in systems biology and systems pharmacology
    • Ma'ayan, A. et al. Lean Big Data integration in systems biology and systems pharmacology. Trends Pharmacol. Sci. 35, 450-460 (2014).
    • (2014) Trends Pharmacol. Sci. , vol.35 , pp. 450-460
    • Ma'Ayan, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.