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Volumn 15, Issue 6, 2014, Pages 361-369

Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing

Author keywords

[No Author keywords available]

Indexed keywords

INTERLEUKIN 13; LONG UNTRANSLATED RNA; RNA; SHORT HAIRPIN RNA; TRANSCRIPTOME; UNTRANSLATED RNA;

EID: 84908022585     PISSN: 14664879     EISSN: 14765470     Source Type: Journal    
DOI: 10.1038/gene.2014.27     Document Type: Article
Times cited : (126)

References (31)
  • 1
    • 79959830634 scopus 로고    scopus 로고
    • Genetic dissection of eosinophilic esophagitis provides insight into disease pathogenesis and treatment strategies
    • Sherrill JD, Rothenberg ME. Genetic dissection of eosinophilic esophagitis provides insight into disease pathogenesis and treatment strategies. J Allergy Clin Immunol 2011; 128: 23-32.
    • (2011) J Allergy Clin Immunol , vol.128 , pp. 23-32
    • Sherrill, J.D.1    Rothenberg, M.E.2
  • 4
    • 34247510590 scopus 로고    scopus 로고
    • Prevalence of oesophageal eosinophils and eosinophilic oesophagitis in adults: The population-based Kalixanda study
    • Ronkainen J, Talley NJ, Aro P, Storskrubb T, Johansson SE, Lind T et al. Prevalence of oesophageal eosinophils and eosinophilic oesophagitis in adults: The population-based Kalixanda study. Gut 2007; 56: 615-620.
    • (2007) Gut , vol.56 , pp. 615-620
    • Ronkainen, J.1    Talley, N.J.2    Aro, P.3    Storskrubb, T.4    Johansson, S.E.5    Lind, T.6
  • 6
    • 36849017952 scopus 로고    scopus 로고
    • IL-13 involvement in eosinophilic esophagitis: Transcriptome analysis and reversibility with glucocorticoids
    • Blanchard C, Mingler MK, Vicario M, Abonia JP, Wu YY, Lu TX et al. IL-13 involvement in eosinophilic esophagitis: Transcriptome analysis and reversibility with glucocorticoids. J Allergy Clin Immunol 2007; 120: 1292-1300.
    • (2007) J Allergy Clin Immunol , vol.120 , pp. 1292-1300
    • Blanchard, C.1    Mingler, M.K.2    Vicario, M.3    Abonia, J.P.4    Wu, Y.Y.5    Lu, T.X.6
  • 7
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008; 18: 1509-1517.
    • (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
  • 9
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature 2012; 482: 339-346.
    • (2012) Nature , vol.482 , pp. 339-346
    • Guttman, M.1    Rinn, J.L.2
  • 10
    • 84861881510 scopus 로고    scopus 로고
    • BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration
    • Flockhart RJ, Webster DE, Qu K, Mascarenhas N, Kovalski J, Kretz M et al. BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Genome Res 2012; 22: 1006-1014.
    • (2012) Genome Res , vol.22 , pp. 1006-1014
    • Flockhart, R.J.1    Webster, D.E.2    Qu, K.3    Mascarenhas, N.4    Kovalski, J.5    Kretz, M.6
  • 11
    • 84859159762 scopus 로고    scopus 로고
    • MicroRNA signature in patients with eosinophilic esophagitis, reversibility with glucocorticoids, and assessment as disease biomarkers
    • Lu TX, Sherrill JD, Wen T, Plassard AJ, Besse JA, Abonia JP et al. MicroRNA signature in patients with eosinophilic esophagitis, reversibility with glucocorticoids, and assessment as disease biomarkers. J Allergy Clin Immunol 2012; 129: 1064-75 e9.
    • (2012) J Allergy Clin Immunol , vol.129 , pp. 1064-75e9
    • Lu, T.X.1    Sherrill, J.D.2    Wen, T.3    Plassard, A.J.4    Besse, J.A.5    Abonia, J.P.6
  • 12
    • 84864859245 scopus 로고    scopus 로고
    • MiR-375 is downregulated in epithelial cells after IL-13 stimulation and regulates an IL-13-induced epithelial transcriptome
    • Lu TX, Lim EJ, Wen T, Plassard AJ, Hogan SP, Martin LJ et al. MiR-375 is downregulated in epithelial cells after IL-13 stimulation and regulates an IL-13-induced epithelial transcriptome. Mucosal Immunol 2012; 5: 388-396.
    • (2012) Mucosal Immunol , vol.5 , pp. 388-396
    • Lu, T.X.1    Lim, E.J.2    Wen, T.3    Plassard, A.J.4    Hogan, S.P.5    Martin, L.J.6
  • 13
    • 84863991618 scopus 로고    scopus 로고
    • MicroRNA profiling in mucosal biopsies of eosinophilic esophagitis patients pre and post treatment with steroids and relationship with mRNA targets
    • Lu S, Mukkada VA, Mangray S, Cleveland K, Shillingford N, Schorl C et al. MicroRNA profiling in mucosal biopsies of eosinophilic esophagitis patients pre and post treatment with steroids and relationship with mRNA targets. PLoS ONE 2012; 7: E40676.
    • (2012) PLoS ONE , vol.7 , pp. e40676
    • Lu, S.1    Mukkada, V.A.2    Mangray, S.3    Cleveland, K.4    Shillingford, N.5    Schorl, C.6
  • 14
    • 36549061966 scopus 로고    scopus 로고
    • Increased expression of eotaxin-3 distinguishes between eosinophilic esophagitis and gastroesophageal reflux disease
    • Bhattacharya B, Carlsten J, Sabo E, Kethu S, Meitner P, Tavares R et al. Increased expression of eotaxin-3 distinguishes between eosinophilic esophagitis and gastroesophageal reflux disease. Hum Pathol 2007; 38: 1744-1753.
    • (2007) Hum Pathol , vol.38 , pp. 1744-1753
    • Bhattacharya, B.1    Carlsten, J.2    Sabo, E.3    Kethu, S.4    Meitner, P.5    Tavares, R.6
  • 15
    • 84881478367 scopus 로고    scopus 로고
    • A long noncoding RNA mediates both activation and repression of immune response genes
    • Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL et al. A long noncoding RNA mediates both activation and repression of immune response genes. Science 2013; 341: 789-792.
    • (2013) Science , vol.341 , pp. 789-792
    • Carpenter, S.1    Aiello, D.2    Atianand, M.K.3    Ricci, E.P.4    Gandhi, P.5    Hall, L.L.6
  • 16
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res 2012; 22: 1775-1789.
    • (2012) Genome Res , vol.22 , pp. 1775-1789
    • Derrien, T.1    Johnson, R.2    Bussotti, G.3    Tanzer, A.4    Djebali, S.5    Tilgner, H.6
  • 18
    • 67650921949 scopus 로고    scopus 로고
    • Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    • Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 2009; 106: 11667-11672.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 11667-11672
    • Khalil, A.M.1    Guttman, M.2    Huarte, M.3    Garber, M.4    Raj, A.5    Rivea Morales, D.6
  • 19
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458: 223-227.
    • (2009) Nature , vol.458 , pp. 223-227
    • Guttman, M.1    Amit, I.2    Garber, M.3    French, C.4    Lin, M.F.5    Feldser, D.6
  • 20
    • 60349120914 scopus 로고    scopus 로고
    • Long non-coding RNAs: Insights into functions
    • Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: Insights into functions. Nat Rev Genet 2009; 10: 155-159.
    • (2009) Nat Rev Genet , vol.10 , pp. 155-159
    • Mercer, T.R.1    Dinger, M.E.2    Mattick, J.S.3
  • 21
    • 80053045739 scopus 로고    scopus 로고
    • Molecular mechanisms of long noncoding RNAs
    • Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43: 904-914.
    • (2011) Mol Cell , vol.43 , pp. 904-914
    • Wang, K.C.1    Chang, H.Y.2
  • 22
    • 84872135457 scopus 로고    scopus 로고
    • Control of somatic tissue differentiation by the long non-coding RNA TINCR
    • Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 2013; 493: 231-235.
    • (2013) Nature , vol.493 , pp. 231-235
    • Kretz, M.1    Siprashvili, Z.2    Chu, C.3    De, W.4    Zehnder, A.5    Qu, K.6
  • 23
    • 77951639698 scopus 로고    scopus 로고
    • Coordinate interaction between IL-13 and epithelial differentiation cluster genes in eosinophilic esophagitis
    • Blanchard C, Stucke EM, Burwinkel K, Caldwell JM, Collins MH, Ahrens A et al. Coordinate interaction between IL-13 and epithelial differentiation cluster genes in eosinophilic esophagitis. J Immunol 2010; 184: 4033-4041.
    • (2010) J Immunol , vol.184 , pp. 4033-4041
    • Blanchard, C.1    Stucke, E.M.2    Burwinkel, K.3    Caldwell, J.M.4    Collins, M.H.5    Ahrens, A.6
  • 24
    • 84897499193 scopus 로고    scopus 로고
    • Desmoglein-1 regulates esophageal epithelial barrier function and immune responses in eosinophilic esophagitis
    • Sherrill JD, Kc K, Wu D, Djukic Z, Caldwell JM, Stucke EM et al. Desmoglein-1 regulates esophageal epithelial barrier function and immune responses in eosinophilic esophagitis. Mucosal Immunol 2013; 7: 718-729.
    • (2013) Mucosal Immunol , vol.7 , pp. 718-729
    • Sherrill, J.D.1    Kc, K.2    Wu, D.3    Djukic, Z.4    Caldwell, J.M.5    Stucke, E.M.6
  • 25
    • 0037449752 scopus 로고    scopus 로고
    • Epidermal growth factor receptor mediates increased cell proliferation, migration, and aggregation in esophageal keratinocytes in vitro and in vivo
    • Andl CD, Mizushima T, Nakagawa H, Oyama K, Harada H, Chruma K et al. Epidermal growth factor receptor mediates increased cell proliferation, migration, and aggregation in esophageal keratinocytes in vitro and in vivo. J Biol Chem 2003; 278: 1824-1830.
    • (2003) J Biol Chem , vol.278 , pp. 1824-1830
    • Andl, C.D.1    Mizushima, T.2    Nakagawa, H.3    Oyama, K.4    Harada, H.5    Chruma, K.6
  • 26
    • 10744231069 scopus 로고    scopus 로고
    • Telomerase induces immortalization of human esophageal keratinocytes without p16INK4a inactivation
    • Harada H, Nakagawa H, Oyama K, Takaoka M, Andl CD, Jacobmeier B et al. Telomerase induces immortalization of human esophageal keratinocytes without p16INK4a inactivation. Mol Cancer Res 2003; 1: 729-738.
    • (2003) Mol Cancer Res , vol.1 , pp. 729-738
    • Harada, H.1    Nakagawa, H.2    Oyama, K.3    Takaoka, M.4    Andl, C.D.5    Jacobmeier, B.6
  • 27
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7: 562-578.
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6
  • 28
    • 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. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10: R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 29
    • 79957842166 scopus 로고    scopus 로고
    • Computational methods for transcriptome annotation and quantification using RNA-seq
    • Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 2011; 8: 469-477.
    • (2011) Nat Methods , vol.8 , pp. 469-477
    • Garber, M.1    Grabherr, M.G.2    Guttman, M.3    Trapnell, C.4
  • 31
    • 67849130563 scopus 로고    scopus 로고
    • ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
    • Web Server issue)
    • Chen J, Bardes EE, Aronow BJ, Jegga AG. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res 2009; 37(Web Server issue): W305-W311.
    • (2009) Nucleic Acids Res , vol.37 , pp. W305-W311
    • Chen, J.1    Bardes, E.E.2    Aronow, B.J.3    Jegga, A.G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.