메뉴 건너뛰기




Volumn 9, Issue 4, 2014, Pages

A model-based approach to identify binding sites in CLIP-seq data

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA; RNA BINDING PROTEIN;

EID: 84899497034     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093248     Document Type: Article
Times cited : (22)

References (44)
  • 1
    • 34250735674 scopus 로고    scopus 로고
    • RNA regulons: Coordination of post-transcriptional events
    • Keene JD (2007) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8: 533-543.
    • (2007) Nat Rev Genet , vol.8 , pp. 533-543
    • Keene, J.D.1
  • 2
    • 79953682552 scopus 로고    scopus 로고
    • Phosphorylation of human Argonaute proteins affects small RNA binding
    • Rudel S,Wang Y, Lenobel R, Korner R, Hsiao HH, et al. (2011) Phosphorylation of human Argonaute proteins affects small RNA binding. Nucleic Acids Res 39: 2330-2343.
    • (2011) Nucleic Acids Res , vol.39 , pp. 2330-2343
    • Rudel, S.1    Wang, Y.2    Lenobel, R.3    Korner, R.4    Hsiao, H.H.5
  • 4
    • 80052959701 scopus 로고    scopus 로고
    • FET proteins TAF15 and EWS are selective markers that distinguish FTLD with FUS pathology from amyotrophic lateral sclerosis with FUS mutations
    • Neumann M, Bentmann E, Dormann D, Jawaid A, DeJesus-Hernandez M, et al. (2011) FET proteins TAF15 and EWS are selective markers that distinguish FTLD with FUS pathology from amyotrophic lateral sclerosis with FUS mutations. Brain 134: 2595-2609.
    • (2011) Brain , vol.134 , pp. 2595-2609
    • Neumann, M.1    Bentmann, E.2    Dormann, D.3    Jawaid, A.4    DeJesus-Hernandez, M.5
  • 6
    • 27944508215 scopus 로고    scopus 로고
    • CLIP: A method for identifying protein-RNA interaction sites in living cells
    • DOI 10.1016/j.ymeth.2005.07.018, PII S1046202305001787, Post-transcriptional Regulation of Gene Expression
    • Ule J, Jensen K, Mele A, Darnell RB (2005) CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37: 376-386. (Pubitemid 41682508)
    • (2005) Methods , vol.37 , Issue.4 , pp. 376-386
    • Ule, J.1    Jensen, K.2    Mele, A.3    Darnell, R.B.4
  • 7
    • 0242497663 scopus 로고    scopus 로고
    • CLIP Identifies Nova-Regulated RNA Networks in the Brain
    • DOI 10.1126/science.1090095
    • Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, et al. (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science 302: 1212-1215. (Pubitemid 37421026)
    • (2003) Science , vol.302 , Issue.5648 , pp. 1212-1215
    • Ule, J.1    Jensen, K.B.2    Ruggiu, M.3    Mele, A.4    Ule, A.5    Darnell, R.B.6
  • 8
    • 79960230895 scopus 로고    scopus 로고
    • Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    • Zhang C, Darnell RB (2011) Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 29: 607-614.
    • (2011) Nat Biotechnol , vol.29 , pp. 607-614
    • Zhang, C.1    Darnell, R.B.2
  • 9
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 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
  • 10
    • 84870026823 scopus 로고    scopus 로고
    • Genome-wide identification of miRNA targets by PAR-CLIP
    • Hafner M, Lianoglou S, Tuschl T, Betel D (2012) Genome-wide identification of miRNA targets by PAR-CLIP. Methods 58: 94-105.
    • (2012) Methods , vol.58 , pp. 94-105
    • Hafner, M.1    Lianoglou, S.2    Tuschl, T.3    Betel, D.4
  • 11
    • 80055101895 scopus 로고    scopus 로고
    • PARCliP - A method to identify transcriptome-wide the binding sites of RNA binding proteins
    • Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, et al. (2010) PARCliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp.
    • (2010) J Vis Exp
    • Hafner, M.1    Landthaler, M.2    Burger, L.3    Khorshid, M.4    Hausser, J.5
  • 12
    • 77950920903 scopus 로고    scopus 로고
    • Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
    • Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141.
    • (2010) Cell , vol.141 , pp. 129-141
    • Hafner, M.1    Landthaler, M.2    Burger, L.3    Khorshid, M.4    Hausser, J.5
  • 13
    • 67649854477 scopus 로고    scopus 로고
    • Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs
    • Granneman S, Kudla G, Petfalski E, Tollervey D (2009) Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proc Natl Acad Sci U S A 106: 9613-9618.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 9613-9618
    • Granneman, S.1    Kudla, G.2    Petfalski, E.3    Tollervey, D.4
  • 14
    • 77954387023 scopus 로고    scopus 로고
    • iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
    • Konig J, Zarnack K, Rot G, Curk T, Kayikci M, et al. (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17: 909-915.
    • (2010) Nat Struct Mol Biol , vol.17 , pp. 909-915
    • Konig, J.1    Zarnack, K.2    Rot, G.3    Curk, T.4    Kayikci, M.5
  • 15
    • 78651271270 scopus 로고    scopus 로고
    • CLIPZ: A database and analysis environment for experimentally determined binding sites of RNA-binding proteins
    • Khorshid M, Rodak C, Zavolan M (2011) CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res 39: D245-252.
    • (2011) Nucleic Acids Res , vol.39
    • Khorshid, M.1    Rodak, C.2    Zavolan, M.3
  • 16
    • 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 (2012) Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data. Nucleic Acids Res.
    • (2012) Nucleic Acids Res
    • Sievers, C.1    Schlumpf, T.2    Sawarkar, R.3    Comoglio, F.4    Paro, R.5
  • 18
    • 84891818924 scopus 로고    scopus 로고
    • starBase v2.0: Decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from largescale CLIP-Seq data
    • Li JH, Liu S, Zhou H, Qu LH, Yang JH (2014) starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from largescale CLIP-Seq data. Nucleic Acids Res 42: D92-97.
    • (2014) Nucleic Acids Res , vol.42
    • Li, J.H.1    Liu, S.2    Zhou, H.3    Qu, L.H.4    Yang, J.H.5
  • 20
    • 84871166783 scopus 로고    scopus 로고
    • A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types
    • Xing H, Liao W, Mo Y, Zhang MQ (2012) A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types. J Vis Exp: e4273.
    • (2012) J Vis Exp
    • Xing, H.1    Liao, W.2    Mo, Y.3    Zhang, M.Q.4
  • 22
    • 0016526522 scopus 로고
    • Probabilistic Approach to Automatic Keyword Indexing.1. Distribution of Specialty Words in a Technical Literature
    • Harter SP (1975) Probabilistic Approach to Automatic Keyword Indexing .1. Distribution of Specialty Words in a Technical Literature. Journal of the American Society for Information Science 26: 197-206.
    • (1975) Journal of the American Society for Information Science , vol.26 , pp. 197-206
    • Harter, S.P.1
  • 23
    • 84935113569 scopus 로고
    • Error Bounds for Convolutional Codes and an Asymptotically Optimum Decoding Algorithm
    • Viterbi AJ (1967) Error Bounds for Convolutional Codes and an Asymptotically Optimum Decoding Algorithm. Ieee Transactions on Information Theory 13: 260-+.
    • (1967) Ieee Transactions on Information Theory , vol.13 , pp. 260
    • Viterbi, A.J.1
  • 24
    • 0033635967 scopus 로고    scopus 로고
    • Zero-inflated Poisson and binomial regression with random effects: A case study
    • Hall DB (2000) Zero-inflated Poisson and binomial regression with random effects: A case study. Biometrics 56: 1030-1039.
    • (2000) Biometrics , vol.56 , pp. 1030-1039
    • Hall, D.B.1
  • 25
    • 84920574625 scopus 로고    scopus 로고
    • A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing
    • Chou CH, Lin FM, Chou MT, Hsu SD, Chang TH, et al. (2013) A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics 14 Suppl 1: S2.
    • (2013) BMC Genomics , vol.14 , Issue.SUPPL. 1
    • Chou, C.H.1    Lin, F.M.2    Chou, M.T.3    Hsu, S.D.4    Chang, T.H.5
  • 27
    • 84864020005 scopus 로고    scopus 로고
    • Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain
    • Licatalosi DD, Yano M, Fak JJ, Mele A, Grabinski SE, et al. (2012) Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. Genes Dev 26: 1626-1642.
    • (2012) Genes Dev , vol.26 , pp. 1626-1642
    • Licatalosi, D.D.1    Yano, M.2    Fak, J.J.3    Mele, A.4    Grabinski, S.E.5
  • 28
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing
    • DOI 10.1016/j.molcel.2007.06.017, PII S1097276507004078
    • Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105. (Pubitemid 46991392)
    • (2007) Molecular Cell , vol.27 , Issue.1 , pp. 91-105
    • Grimson, A.1    Farh, K.K.-H.2    Johnston, W.K.3    Garrett-Engele, P.4    Lim, L.P.5    Bartel, D.P.6
  • 29
    • 57749206034 scopus 로고    scopus 로고
    • Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    • Wang Y, Juranek S, Li H, Sheng G, Tuschl T, et al. (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456: 921-926.
    • (2008) Nature , vol.456 , pp. 921-926
    • Wang, Y.1    Juranek, S.2    Li, H.3    Sheng, G.4    Tuschl, T.5
  • 30
    • 26444584579 scopus 로고    scopus 로고
    • Limitations and potentials of current motif discovery algorithms
    • DOI 10.1093/nar/gki791
    • Hu JJ, Li B, Kihara D (2005) Limitations and potentials of current motif discovery algorithms. Nucleic Acids Research 33: 4899-4913. (Pubitemid 41418889)
    • (2005) Nucleic Acids Research , vol.33 , Issue.15 , pp. 4899-4913
    • Hu, J.1    Li, B.2    Kihara, D.3
  • 31
    • 84860863700 scopus 로고    scopus 로고
    • Cell-free formation of RNA granules: Bound RNAs identify features and components of cellular assemblies
    • Han TW, Kato M, Xie S,Wu LC, Mirzaei H, et al. (2012) Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies. Cell 149: 768-779.
    • (2012) Cell , vol.149 , pp. 768-779
    • Han, T.W.1    Kato, M.2    Xie, S.3    Wu, L.C.4    Mirzaei, H.5
  • 33
    • 84871413198 scopus 로고    scopus 로고
    • FMRP targets distinct mRNA sequence elements to regulate protein expression
    • Ascano M, Jr., Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, et al. (2012) FMRP targets distinct mRNA sequence elements to regulate protein expression. Nature 492: 382-386.
    • (2012) Nature , vol.492 , pp. 382-386
    • Ascano Jr., M.1    Mukherjee, N.2    Bandaru, P.3    Miller, J.B.4    Nusbaum, J.D.5
  • 35
    • 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 (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 36
    • 84864957276 scopus 로고    scopus 로고
    • An analysis of substitution, deletion and insertion mutations in cancer genes
    • Iengar P (2012) An analysis of substitution, deletion and insertion mutations in cancer genes. Nucleic Acids Res 40: 6401-6413.
    • (2012) Nucleic Acids Res , vol.40 , pp. 6401-6413
    • Iengar, P.1
  • 38
    • 77955039075 scopus 로고    scopus 로고
    • Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model
    • Youn A, Reiss DJ, Stuetzle W (2010) Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model. Bioinformatics 26: 1879-1886.
    • (2010) Bioinformatics , vol.26 , pp. 1879-1886
    • Youn, A.1    Reiss, D.J.2    Stuetzle, W.3
  • 39
    • 77954838957 scopus 로고    scopus 로고
    • Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls
    • Zhang C, Frias MA, Mele A, Ruggiu M, Eom T, et al. (2010) Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science 329: 439-443.
    • (2010) Science , vol.329 , pp. 439-443
    • Zhang, C.1    Frias, M.A.2    Mele, A.3    Ruggiu, M.4    Eom, T.5
  • 40
    • 79953185674 scopus 로고    scopus 로고
    • Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43
    • Polymenidou M, Lagier-Tourenne C, Hutt KR, Huelga SC, Moran J, et al. (2011) Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat Neurosci 14: 459-468.
    • (2011) Nat Neurosci , vol.14 , pp. 459-468
    • Polymenidou, M.1    Lagier-Tourenne, C.2    Hutt, K.R.3    Huelga, S.C.4    Moran, J.5
  • 41
    • 79551647673 scopus 로고    scopus 로고
    • Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs
    • Leung AK, Young AG, Bhutkar A, Zheng GX, Bosson AD, et al. (2011) Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nat Struct Mol Biol 18: 237-244.
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 237-244
    • Leung, A.K.1    Young, A.G.2    Bhutkar, A.3    Zheng, G.X.4    Bosson, A.D.5
  • 42
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks J, Nekrutenko A, Taylor J, Galaxy T (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86.
    • (2010) Genome Biol , vol.11
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3    Galaxy, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.