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Volumn 8, Issue 1, 2015, Pages

ASEQ: Fast allele-specific studies from next-generation sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE SPECIFIC EXPRESSION ANALYSIS; ARTICLE; COMPUTER PROGRAM; EXOME; NEXT GENERATION SEQUENCING; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; PROSTATE CANCER; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS; TUMOR GENE; ALLELE; BIOLOGY; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER SYSTEM; DNA SEQUENCE; FACTUAL DATABASE; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; GENOTYPE; HETEROZYGOTE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; MALE; METABOLISM; PROCEDURES; PROSTATE TUMOR; SOFTWARE;

EID: 84928166234     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/s12920-015-0084-2     Document Type: Article
Times cited : (48)

References (28)
  • 6
    • 0012789869 scopus 로고    scopus 로고
    • Allelic variation in gene expression is common in the human genome
    • Lo HS, Wang Z, Hu Y, Yang HH, Gere S, Buetow KH, et al. Allelic variation in gene expression is common in the human genome. Genome Res. 2003;13:1855-62.
    • (2003) Genome Res , vol.13 , pp. 1855-1862
    • Lo, H.S.1    Wang, Z.2    Hu, Y.3    Yang, H.H.4    Gere, S.5    Buetow, K.H.6
  • 8
    • 84862823843 scopus 로고
    • Allele-specific gene expression and epigenetic modifications and their application to understanding inheritance and cancer
    • Lee MP. Allele-specific gene expression and epigenetic modifications and their application to understanding inheritance and cancer. Biochim Biophys Acta BBA-Gene Regul Mech. 1819;2012:739-42.
    • (1819) Biochim Biophys Acta BBA-Gene Regul Mech , vol.2012 , pp. 739-742
    • Lee, M.P.1
  • 9
    • 84863082525 scopus 로고    scopus 로고
    • Monoallelic expression determines oncogenic progression and outcome in benign and malignant brain tumors
    • Walker EJ, Zhang C, Castelo-Branco P, Hawkins C, Wilson W, Zhukova N, et al. Monoallelic expression determines oncogenic progression and outcome in benign and malignant brain tumors. Cancer Res. 2012;72:636-44.
    • (2012) Cancer Res , vol.72 , pp. 636-644
    • Walker, E.J.1    Zhang, C.2    Castelo-Branco, P.3    Hawkins, C.4    Wilson, W.5    Zhukova, N.6
  • 10
    • 79953303842 scopus 로고    scopus 로고
    • RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression
    • Lalonde E, Ha KC, Wang Z, Bemmo A, Kleinman CL, Kwan T, et al. RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression. Genome Res. 2011;21:545-54.
    • (2011) Genome Res , vol.21 , pp. 545-554
    • Lalonde, E.1    Ha, K.C.2    Wang, Z.3    Bemmo, A.4    Kleinman, C.L.5    Kwan, T.6
  • 12
    • 84873821010 scopus 로고    scopus 로고
    • Germline allele-specific expression of DAPK1 in chronic lymphocytic leukemia
    • Wei Q-X, Claus R, Hielscher T, Mertens D, Raval A, Oakes CC, et al. Germline Allele-Specific Expression of DAPK1 in Chronic Lymphocytic Leukemia. PLoS One. 2013;8:e55261.
    • (2013) PLoS One , vol.8 , pp. e55261
    • Wei, Q.-X.1    Claus, R.2    Hielscher, T.3    Mertens, D.4    Raval, A.5    Oakes, C.C.6
  • 13
    • 80053522581 scopus 로고    scopus 로고
    • A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
    • Skelly DA, Johansson M, Madeoy J, Wakefield J, Akey JM. A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Res. 2011;21:1728-37.
    • (2011) Genome Res , vol.21 , pp. 1728-1737
    • Skelly, D.A.1    Johansson, M.2    Madeoy, J.3    Wakefield, J.4    Akey, J.M.5
  • 14
    • 84928114011 scopus 로고    scopus 로고
    • IASeq: Integrating multiple chip-seq datasets for detecting allele-specific binding
    • Wei Y, Li X, Wang Q, Ji H. iASeq: integrating multiple chip-seq datasets for detecting allele-specific binding. BMC Bioinformatics. 2012;13:A6.
    • (2012) BMC Bioinformatics , vol.13 , pp. A6
    • Wei, Y.1    Li, X.2    Wang, Q.3    Ji, H.4
  • 15
    • 84879419235 scopus 로고    scopus 로고
    • Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data
    • Pandey RV, Franssen SU, Futschik A, Schlötterer C. Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data. Mol Ecol Resour. 2013;13:740-5.
    • (2013) Mol Ecol Resour , vol.13 , pp. 740-745
    • Pandey, R.V.1    Franssen, S.U.2    Futschik, A.3    Schlötterer, C.4
  • 18
    • 70349910898 scopus 로고    scopus 로고
    • Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
    • Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, et al. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009;25:3207-12.
    • (2009) Bioinformatics , vol.25 , pp. 3207-3212
    • Degner, J.F.1    Marioni, J.C.2    Pai, A.A.3    Pickrell, J.K.4    Nkadori, E.5    Gilad, Y.6
  • 19
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297-303.
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4    Cibulskis, K.5    Kernytsky, A.6
  • 22
    • 78651426148 scopus 로고    scopus 로고
    • RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries
    • Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, et al. RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics. 2011;27:281-3.
    • (2011) Bioinformatics , vol.27 , pp. 281-283
    • Habegger, L.1    Sboner, A.2    Gianoulis, T.A.3    Rozowsky, J.4    Agarwal, A.5    Snyder, M.6
  • 23
    • 26444529054 scopus 로고    scopus 로고
    • A novel gene family NBPF: Intricate structure generated by gene duplications during primate evolution
    • Vandepoele K, Van Roy N, Staes K, Speleman F, Van Roy F. A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution. Mol Biol Evol. 2005;22:2265-74.
    • (2005) Mol Biol Evol , vol.22 , pp. 2265-2274
    • Vandepoele, K.1    Van Roy, N.2    Staes, K.3    Speleman, F.4    Van Roy, F.5
  • 25
    • 0035880481 scopus 로고    scopus 로고
    • Chromosomal imbalances in primary and metastatic melanomas revealed by comparative genomic hybridization
    • Balázs M, Ádám Z, Treszl A, Bégány Á, Hunyadi J, Adany R. Chromosomal imbalances in primary and metastatic melanomas revealed by comparative genomic hybridization. Cytometry. 2001;46:222-32.
    • (2001) Cytometry , vol.46 , pp. 222-232
    • Balázs, M.1    Ádám, Z.2    Treszl, A.3    Bégány Á.4    Hunyadi, J.5    Adany, R.6
  • 26
    • 0037564023 scopus 로고    scopus 로고
    • Malignancy-associated regions of transcriptional activation: Gene expression profiling identifies common chromosomal regions of a recurrent transcriptional activation in human prostate, breast, ovarian, and colon cancers
    • Glinsky GV, Krones-Herzig A, Glinskii AB. Malignancy-associated regions of transcriptional activation: gene expression profiling identifies common chromosomal regions of a recurrent transcriptional activation in human prostate, breast, ovarian, and colon cancers. Neoplasia. 2003;5:218-28.
    • (2003) Neoplasia , vol.5 , pp. 218-228
    • Glinsky, G.V.1    Krones-Herzig, A.2    Glinskii, A.B.3
  • 27
    • 0942301173 scopus 로고    scopus 로고
    • PMP24, a gene identified by MSRF, undergoes DNA hypermethylation-associated gene silencing during cancer progression in an LNCaP model
    • Wu M, Ho S-M. PMP24, a gene identified by MSRF, undergoes DNA hypermethylation-associated gene silencing during cancer progression in an LNCaP model. Oncogene. 2004;23:250-9.
    • (2004) Oncogene , vol.23 , pp. 250-259
    • Wu, M.1    Ho, S.-M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.