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Volumn 15, Issue 1, 2014, Pages

dCLIP: A computational approach for comparative CLIP-seq analyses

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN; MICRORNA; MIRN124 MICRORNA, HUMAN; MIRN155 MICRORNA, MOUSE;

EID: 84892171302     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-1-r11     Document Type: Article
Times cited : (40)

References (46)
  • 1
    • 34250735674 scopus 로고    scopus 로고
    • RNA regulons: coordination of post-transcriptional events
    • Keene JD: RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 2007, 8:533-543.
    • (2007) Nat Rev Genet , vol.8 , pp. 533-543
    • Keene, J.D.1
  • 2
    • 40449138572 scopus 로고    scopus 로고
    • Post-transcriptional gene regulation: from genome-wide studies to principles
    • Halbeisen RE, Galgano A, Scherrer T, Gerber AP: Post-transcriptional gene regulation: from genome-wide studies to principles. Cell Mol Life Sci 2008, 65:798-813.
    • (2008) Cell Mol Life Sci , vol.65 , pp. 798-813
    • Halbeisen, R.E.1    Galgano, A.2    Scherrer, T.3    Gerber, A.P.4
  • 5
    • 77953928753 scopus 로고    scopus 로고
    • HITS-CLIP: panoramic views of protein-RNA regulation in living cells
    • Darnell RB: HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA 2010, 1:266-286.
    • (2010) Wiley Interdiscip Rev RNA , vol.1 , pp. 266-286
    • Darnell, R.B.1
  • 8
    • 79960230895 scopus 로고    scopus 로고
    • Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    • Zhang C, Darnell RB: Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 2011, 29:607-614.
    • (2011) Nat Biotechnol , vol.29 , pp. 607-614
    • Zhang, C.1    Darnell, R.B.2
  • 10
    • 78651271270 scopus 로고    scopus 로고
    • CLIPZ: a database and analysis environment for experimentally determined binding sites of RNAbinding proteins
    • Khorshid M, Rodak C, Zavolan M: CLIPZ: a database and analysis environment for experimentally determined binding sites of RNAbinding proteins. Nucleic Acids Res 2011, 39:D245-D252.
    • (2011) Nucleic Acids Res , vol.39 , pp. D245-D252
    • Khorshid, M.1    Rodak, C.2    Zavolan, M.3
  • 12
    • 84869071915 scopus 로고    scopus 로고
    • Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data
    • Sievers C, Schlumpf T, Sawarkar R, Comoglio F, Paro R: Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data. Nucleic Acids Res 2012, 40:e160.
    • (2012) Nucleic Acids Res , vol.40
    • Sievers, C.1    Schlumpf, T.2    Sawarkar, R.3    Comoglio, F.4    Paro, R.5
  • 18
    • 84861133568 scopus 로고    scopus 로고
    • A computational pipeline for comparative ChIP-seq analyses
    • Bardet AF, He Q, Zeitlinger J, Stark A: A computational pipeline for comparative ChIP-seq analyses. Nat Protoc 2012, 7:45-61.
    • (2012) Nat Protoc , vol.7 , pp. 45-61
    • Bardet, A.F.1    He, Q.2    Zeitlinger, J.3    Stark, A.4
  • 19
    • 84877630587 scopus 로고    scopus 로고
    • Epigenetic change detection and pattern recognition via Bayesian hierarchical hidden Markov models
    • Wang X, Zang M, Xiao G: Epigenetic change detection and pattern recognition via Bayesian hierarchical hidden Markov models. Stat Med 2012, 32:2292-2307.
    • (2012) Stat Med , vol.32 , pp. 2292-2307
    • Wang, X.1    Zang, M.2    Xiao, G.3
  • 20
    • 84873801934 scopus 로고    scopus 로고
    • High-throughput sequencing for biology and medicine
    • Soon WW, Hariharan M, Snyder MP: High-throughput sequencing for biology and medicine. Mol Syst Biol 2013, 9:640.
    • (2013) Mol Syst Biol , vol.9 , pp. 640
    • Soon, W.W.1    Hariharan, M.2    Snyder, M.P.3
  • 21
    • 84878643203 scopus 로고    scopus 로고
    • High-throughput sequencing of cytosine methylation in plant DNA
    • Hardcastle TJ: High-throughput sequencing of cytosine methylation in plant DNA. Plant Methods 2013, 9:16.
    • (2013) Plant Methods , vol.9 , pp. 16
    • Hardcastle, T.J.1
  • 22
    • 84555179177 scopus 로고    scopus 로고
    • Identifying differential histone modification sites from ChIP-seq data
    • Xu H, Sung WK: Identifying differential histone modification sites from ChIP-seq data. Methods Mol Biol 2012, 802:293-303.
    • (2012) Methods Mol Biol , vol.802 , pp. 293-303
    • Xu, H.1    Sung, W.K.2
  • 23
    • 84864545388 scopus 로고    scopus 로고
    • ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries
    • Nair NU, Sahu AD, Bucher P, Moret BM: ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries. PLoS One 2012, 7:e39573.
    • (2012) PLoS One , vol.7
    • Nair, N.U.1    Sahu, A.D.2    Bucher, P.3    Moret, B.M.4
  • 24
    • 84862799740 scopus 로고    scopus 로고
    • MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
    • Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ: MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biol 2012, 13:R16.
    • (2012) Genome Biol , vol.13
    • Shao, Z.1    Zhang, Y.2    Yuan, G.C.3    Orkin, S.H.4    Waxman, D.J.5
  • 27
    • 84923901392 scopus 로고    scopus 로고
    • dCLIP
    • dCLIP. [http://qbrc.swmed.edu/software/]
  • 28
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • Smyth GK, Speed T: Normalization of cDNA microarray data. Methods 2003, 31:265-273.
    • (2003) Methods , vol.31 , pp. 265-273
    • Smyth, G.K.1    Speed, T.2
  • 29
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • Chi SW, Zang JB, Mele A, Darnell RB: Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009, 460:479-486.
    • (2009) Nature , vol.460 , pp. 479-486
    • Chi, S.W.1    Zang, J.B.2    Mele, A.3    Darnell, R.B.4
  • 30
    • 84885933908 scopus 로고
    • Alternatives to the median absolute deviation
    • Rousseeuw PJ, Croux C: Alternatives to the median absolute deviation. J Am Stat Assoc 1993, 88:1273-1283.
    • (1993) J Am Stat Assoc , vol.88 , pp. 1273-1283
    • Rousseeuw, P.J.1    Croux, C.2
  • 32
    • 18144365478 scopus 로고    scopus 로고
    • MicroRNA biogenesis and cancer
    • Gregory RI, Shiekhattar R: MicroRNA biogenesis and cancer. Cancer Res 2005, 65:3509-3512.
    • (2005) Cancer Res , vol.65 , pp. 3509-3512
    • Gregory, R.I.1    Shiekhattar, R.2
  • 33
    • 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
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 34
  • 36
    • 84859632747 scopus 로고    scopus 로고
    • miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay
    • Djuranovic S, Nahvi A, Green R: miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 2012, 336:237-240.
    • (2012) Science , vol.336 , pp. 237-240
    • Djuranovic, S.1    Nahvi, A.2    Green, R.3
  • 38
    • 84862778053 scopus 로고    scopus 로고
    • Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish
    • Bazzini AA, Lee MT, Giraldez AJ: Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 2012, 336:233-237.
    • (2012) Science , vol.336 , pp. 233-237
    • Bazzini, A.A.1    Lee, M.T.2    Giraldez, A.J.3
  • 42
    • 38449102667 scopus 로고    scopus 로고
    • Multiple roles of TDP-43 in gene expression, splicing regulation, and human disease
    • Buratti E, Baralle FE: Multiple roles of TDP-43 in gene expression, splicing regulation, and human disease. Front Biosci 2008, 13:867-878.
    • (2008) Front Biosci , vol.13 , pp. 867-878
    • Buratti, E.1    Baralle, F.E.2
  • 43
    • 84884777626 scopus 로고    scopus 로고
    • Pathological mechanisms underlying TDP-43 driven neurodegeneration in FTLD-ALS spectrum disorders
    • Janssens J, Van Broeckhoven C: Pathological mechanisms underlying TDP-43 driven neurodegeneration in FTLD-ALS spectrum disorders. Hum Mol Genet 2013, 22:R77-R87.
    • (2013) Hum Mol Genet , vol.22 , pp. R77-R87
    • Janssens, J.1    Van Broeckhoven, C.2
  • 44
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson MD, Oshlack A: A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 2010, 11:R25.
    • (2010) Genome Biol , vol.11
    • Robinson, M.D.1    Oshlack, A.2
  • 45
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • Bullard JH, Purdom E, Hansen KD, Dudoit S: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010, 11:94.
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.H.1    Purdom, E.2    Hansen, K.D.3    Dudoit, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.