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Volumn 43, Issue 1, 2015, Pages 225-236

Identifying causal regulatory SNPs in ChIP-seq enhancers

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EID: 84945187244     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1318     Document Type: Article
Times cited : (33)

References (63)
  • 1
    • 80052322958 scopus 로고    scopus 로고
    • Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA
    • Fehrmann, R. S. N., Jansen, R. C., Veldink, J. H., Westra, H.-J., Arends, D., Bonder, M. J., Fu, J., Deelen, P., Groen, H. J. M., Smolonska, A. et al. (2011) Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet., 7, e1002197.
    • (2011) PLoS Genet. , vol.7 , pp. e1002197
    • Fehrmann, R.S.N.1    Jansen, R.C.2    Veldink, J.H.3    Westra, H.-J.4    Arends, D.5    Bonder, M.J.6    Fu, J.7    Deelen, P.8    Groen, H.J.M.9    Smolonska, A.10
  • 2
    • 77952367694 scopus 로고    scopus 로고
    • Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations
    • Nica, A. C., Montgomery, S. B., Dimas, A. S., Stranger, B. E., Beazley, C., Barroso, I. And Dermitzakis, E. T. (2010) Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet., 6, e1000895.
    • (2010) PLoS Genet. , vol.6 , pp. e1000895
    • Nica, A.C.1    Montgomery, S.B.2    Dimas, A.S.3    Stranger, B.E.4    Beazley, C.5    Barroso, I.6    Dermitzakis, E.T.7
  • 4
    • 84872309911 scopus 로고    scopus 로고
    • Integrating GWAS and expression data for functional characterization of disease-associated SNPs: An application to follicular lymphoma
    • Conde, L., Bracci, P. M., Richardson, R., Montgomery, S. B. And Skibola, C. F. (2013) Integrating GWAS and expression data for functional characterization of disease-associated SNPs: An application to follicular lymphoma. Am. J. Hum. Genet., 92, 126-130.
    • (2013) Am. J. Hum. Genet. , vol.92 , pp. 126-130
    • Conde, L.1    Bracci, P.M.2    Richardson, R.3    Montgomery, S.B.4    Skibola, C.F.5
  • 5
    • 84922581297 scopus 로고    scopus 로고
    • Functional annotation of colon cancer risk SNPs
    • Yao, L., Tak, Y. G., Berman, B. P. And Farnham, P. J. (2014) Functional annotation of colon cancer risk SNPs. Nat Commun., 5, 1-13.
    • (2014) Nat Commun. , vol.5 , pp. 1-13
    • Yao, L.1    Tak, Y.G.2    Berman, B.P.3    Farnham, P.J.4
  • 8
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • The 1000 Genomes Project Consortium
    • The 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
    • (2010) Nature , vol.467 , pp. 1061-1073
  • 9
    • 74849111621 scopus 로고    scopus 로고
    • Identification of intergenic trans-regulatory RNAs containing a disease-linked SNP sequence and targeting cell cycle progression/differentiation pathways in multiple common human disorders
    • Glinskii, A. B., Ma, J., Ma, S., Grant, D., Lim, C.-U., Sell, S. And Glinsky, G. (2009) Identification of intergenic trans-regulatory RNAs containing a disease-linked SNP sequence and targeting cell cycle progression/differentiation pathways in multiple common human disorders. Cell Cycle, 8, 3925-3942.
    • (2009) Cell Cycle , vol.8 , pp. 3925-3942
    • Glinskii, A.B.1    Ma, J.2    Ma, S.3    Grant, D.4    Lim, C.-U.5    Sell, S.6    Glinsky, G.7
  • 10
    • 80055114535 scopus 로고    scopus 로고
    • Networks of intergenic long-range enhancers and snpRNAs drive castration-resistant phenotype of prostate cancer and contribute to pathogenesis of multiple common human disorders
    • Glinskii, A. B., Ma, S., Ma, J., Grant, D., Lim, C.-U., Guest, I., Sell, S., Buttyan, R. And Glinsky, G. V. (2011) Networks of intergenic long-range enhancers and snpRNAs drive castration-resistant phenotype of prostate cancer and contribute to pathogenesis of multiple common human disorders. Cell Cycle, 10, 3571-3597.
    • (2011) Cell Cycle , vol.10 , pp. 3571-3597
    • Glinskii, A.B.1    Ma, S.2    Ma, J.3    Grant, D.4    Lim, C.-U.5    Guest, I.6    Sell, S.7    Buttyan, R.8    Glinsky, G.V.9
  • 21
    • 84858779229 scopus 로고    scopus 로고
    • HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
    • Ward, L. D. And Kellis, M. (2012) HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res., 40, D930-D934.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D930-D934
    • Ward, L.D.1    Kellis, M.2
  • 22
    • 84873086126 scopus 로고    scopus 로고
    • Chromatin marks identify critical cell types for fine mapping complex trait variants
    • Trynka, G., Sandor, C., Han, B., Xu, H., Stranger, B. E., Liu, X. S. And Raychaudhuri, S. (2013) Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat. Genet., 45, 124-130.
    • (2013) Nat. Genet. , vol.45 , pp. 124-130
    • Trynka, G.1    Sandor, C.2    Han, B.3    Xu, H.4    Stranger, B.E.5    Liu, X.S.6    Raychaudhuri, S.7
  • 24
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M. And Shendure, J. (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet., 46, 310-315.
    • (2014) Nat. Genet. , vol.46 , pp. 310-315
    • Kircher, M.1    Witten, D.M.2    Jain, P.3    O'Roak, B.J.4    Cooper, G.M.5    Shendure, J.6
  • 26
    • 84868318661 scopus 로고    scopus 로고
    • Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
    • Gorkin, D. U., Lee, D., Reed, X., Fletez-Brant, C., Bessling, S. L., Loftus, S. K., Beer, M. A., Pavan, W. J. And McCallion, A. S. (2012) Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res., 22, 2290-2301.
    • (2012) Genome Res. , vol.22 , pp. 2290-2301
    • Gorkin, D.U.1    Lee, D.2    Reed, X.3    Fletez-Brant, C.4    Bessling, S.L.5    Loftus, S.K.6    Beer, M.A.7    Pavan, W.J.8    McCallion, A.S.9
  • 27
    • 34547569191 scopus 로고    scopus 로고
    • STAMP: A web tool for exploring DNA-binding motif similarities
    • Mahony, S. And Benos, P. V. (2007) STAMP: A web tool for exploring DNA-binding motif similarities. Nucleic Acids Res., 35, W253-W258.
    • (2007) Nucleic Acids Res. , vol.35 , pp. W253-W258
    • Mahony, S.1    Benos, P.V.2
  • 29
    • 0022293979 scopus 로고
    • Processed pseudogenes: Characteristics and evolution
    • Vanin, E. F. (1985) Processed pseudogenes: characteristics and evolution. Annu. Rev. Genet., 19, 253-272.
    • (1985) Annu. Rev. Genet. , vol.19 , pp. 253-272
    • Vanin, E.F.1
  • 32
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo, G. D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 36
    • 84891697734 scopus 로고    scopus 로고
    • Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
    • Corradin, O., Saiakhova, A., Akhtar-Zaidi, B., Myeroff, L., Willis, J., Cowper-Sallari, R., Lupien, M., Markowitz, S. And Scacheri, P. C. (2014) Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res., 24, 1-13.
    • (2014) Genome Res. , vol.24 , pp. 1-13
    • Corradin, O.1    Saiakhova, A.2    Akhtar-Zaidi, B.3    Myeroff, L.4    Willis, J.5    Cowper-Sallari, R.6    Lupien, M.7    Markowitz, S.8    Scacheri, P.C.9
  • 38
    • 33750857693 scopus 로고    scopus 로고
    • Foxa1-deficient mice exhibit impaired insulin secretion due to uncoupled oxidative phosphorylation
    • Vatamaniuk, M. Z., Gupta, R. K., Lantz, K. A., Doliba, N. M., Matschinsky, F. M. And Kaestner, K. H. (2006) Foxa1-deficient mice exhibit impaired insulin secretion due to uncoupled oxidative phosphorylation. Diabetes, 55, 2730-2736.
    • (2006) Diabetes , vol.55 , pp. 2730-2736
    • Vatamaniuk, M.Z.1    Gupta, R.K.2    Lantz, K.A.3    Doliba, N.M.4    Matschinsky, F.M.5    Kaestner, K.H.6
  • 39
    • 79952227694 scopus 로고    scopus 로고
    • Nuclear receptors in liver disease
    • Wagner, M., Zollner, G. And Trauner, M. (2011) Nuclear receptors in liver disease. Hepatology, 53, 1023-1034.
    • (2011) Hepatology , vol.53 , pp. 1023-1034
    • Wagner, M.1    Zollner, G.2    Trauner, M.3
  • 41
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • Sandelin, A., Alkema, W., Engström, P., Wasserman, W. W. And Lenhard, B. (2004) JASPAR: An open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32, D91-D94.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D91-D94
    • Sandelin, A.1    Alkema, W.2    Engström, P.3    Wasserman, W.W.4    Lenhard, B.5
  • 44
    • 0025690311 scopus 로고
    • Liver-enriched transcription factor HNF-4 is a novel member of the steroid hormone receptor superfamily
    • Sladek, F. M., Zhong, W. M., Lai, E. And Darnell, J. E. (1990) Liver-enriched transcription factor HNF-4 is a novel member of the steroid hormone receptor superfamily. Genes Dev., 4, 2353-2365.
    • (1990) Genes Dev. , vol.4 , pp. 2353-2365
    • Sladek, F.M.1    Zhong, W.M.2    Lai, E.3    Darnell, J.E.4
  • 45
    • 84896512186 scopus 로고    scopus 로고
    • HDAC2 provides a critical support to malignant progression of hepatocellular carcinoma through feedback control of mTORC1 and AKT
    • Noh, J. H., Bae, H. J., Eun, J. W., Shen, Q., Park, S. J., Kim, H. S., Nam, B., Shin, W. C., Lee, E. K., Lee, K. et al. (2014) HDAC2 provides a critical support to malignant progression of hepatocellular carcinoma through feedback control of mTORC1 and AKT. Cancer Res., 74, 1728-1738.
    • (2014) Cancer Res. , vol.74 , pp. 1728-1738
    • Noh, J.H.1    Bae, H.J.2    Eun, J.W.3    Shen, Q.4    Park, S.J.5    Kim, H.S.6    Nam, B.7    Shin, W.C.8    Lee, E.K.9    Lee, K.10
  • 48
    • 84898914140 scopus 로고    scopus 로고
    • Genome-wide analysis of functional and evolutional features of tele-enhancers
    • Huang, D. And Ovcharenko, I. (2014) Genome-wide analysis of functional and evolutional features of tele-enhancers. G3: Genes|Genomes|Genetics, 4, 579-593.
    • (2014) G3: Genes|Genomes|Genetics , vol.4 , pp. 579-593
    • Huang, D.1    Ovcharenko, I.2
  • 55
    • 77956182192 scopus 로고    scopus 로고
    • Association between posttraumatic stress disorder following myocardial infarction and liver enzyme levels: A prospective study
    • von KAñel, R., Abbas, C., Begré, S., Gander, M.-L., Saner, H. And Schmid, J.-P. (2010) Association between posttraumatic stress disorder following myocardial infarction and liver enzyme levels: A prospective study. Dig. Dis. Sci., 55, 2614-2623.
    • (2010) Dig. Dis. Sci. , vol.55 , pp. 2614-2623
    • Von Kañel, R.1    Abbas, C.2    Begré, S.3    Gander, M.-L.4    Saner, H.5    Schmid, J.-P.6
  • 59
    • 0025944323 scopus 로고
    • Multiple alpha-fetoprotein RNAs in adult rat liver: Cell type-specific expression and differential regulation
    • Lemire, J. M. And Fausto, N. (1991) Multiple alpha-fetoprotein RNAs in adult rat liver: cell type-specific expression and differential regulation. Cancer Res., 51, 4656-4664.
    • (1991) Cancer Res. , vol.51 , pp. 4656-4664
    • Lemire, J.M.1    Fausto, N.2
  • 60
    • 47649102850 scopus 로고    scopus 로고
    • Diagnosing and monitoring hepatocellular carcinoma with alpha-fetoprotein: New aspects and applications
    • Debruyne, E. N. And Delanghe, J. R. (2008) Diagnosing and monitoring hepatocellular carcinoma with alpha-fetoprotein: New aspects and applications. Clin. Chim. Acta, 395, 19-26.
    • (2008) Clin. Chim. Acta , vol.395 , pp. 19-26
    • Debruyne, E.N.1    Delanghe, J.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.