메뉴 건너뛰기




Volumn 15, Issue 1, 2014, Pages

GraphProt: Modeling binding preferences of RNA-binding proteins

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE 2 PROTEIN; RNA BINDING PROTEIN; TRANSCRIPTOME;

EID: 84892636681     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-1-r17     Document Type: Article
Times cited : (217)

References (71)
  • 9
    • 67149098194 scopus 로고    scopus 로고
    • Current-generation high-throughput sequencing: deepening insights intomammalian transcriptomes
    • Blencowe BJ, Ahmad S, Lee LJ: Current-generation high-throughput sequencing: deepening insights intomammalian transcriptomes. Genes Dev 2009, 23:1379-1386.
    • (2009) Genes Dev , vol.23 , pp. 1379-1386
    • Blencowe, B.J.1    Ahmad, S.2    Lee, L.J.3
  • 12
    • 38549144819 scopus 로고    scopus 로고
    • A survey of DNA motif finding algorithms
    • Das MK, Dai HK: A survey of DNA motif finding algorithms. BMC Bioinformatics 2007, 8:S21.
    • (2007) BMC Bioinformatics , vol.8 , pp. S21
    • Das, M.K.1    Dai, H.K.2
  • 14
    • 33748191291 scopus 로고    scopus 로고
    • Statisticalmechanicalmodeling of genome-wide transcription factor occupancy data by MatrixREDUCE
    • Foat BC, Morozov AV, Bussemaker HJ: Statisticalmechanicalmodeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics 2006, 22:e141-e149.
    • (2006) Bioinformatics , vol.22 , pp. e141-e149
    • Foat, B.C.1    Morozov, A.V.2    Bussemaker, H.J.3
  • 15
    • 84883575302 scopus 로고    scopus 로고
    • DRIMust: a web server for discovering rank imbalanced motifs using suffix trees
    • Leibovich L, Paz I, Yakhini Z, Mandel-Gutfreund Y: DRIMust: a web server for discovering rank imbalanced motifs using suffix trees. Nucleic Acids Res 2013, 41:W174-W179.
    • (2013) Nucleic Acids Res , vol.41 , pp. W174-W179
    • Leibovich, L.1    Paz, I.2    Yakhini, Z.3    Mandel-Gutfreund, Y.4
  • 17
    • 78049275913 scopus 로고    scopus 로고
    • RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins
    • Kazan H, Ray D, Chan ET, Hughes TR, Morris Q: RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol 2010, 6:e1000832.
    • (2010) PLoS Comput Biol , vol.6
    • Kazan, H.1    Ray, D.2    Chan, E.T.3    Hughes, T.R.4    Morris, Q.5
  • 19
    • 37349056702 scopus 로고    scopus 로고
    • Pre-mRNA secondary, structures influence exon recognition
    • Hiller M, Zhang Z, Backofen R, Stamm S: Pre-mRNA secondary, structures influence exon recognition. PLoS Genet 2007, 3:e204.
    • (2007) PLoS Genet , vol.3
    • Hiller, M.1    Zhang, Z.2    Backofen, R.3    Stamm, S.4
  • 20
    • 25144478445 scopus 로고    scopus 로고
    • Amultiple-feature framework for modelling and predicting transcription factor binding sites
    • Pudimat R, Schukat-Talamazzini E, Backofen R: Amultiple-feature framework for modelling and predicting transcription factor binding sites. Bioinformatics 2005, 21:3082-3088.
    • (2005) Bioinformatics , vol.21 , pp. 3082-3088
    • Pudimat, R.1    Schukat-Talamazzini, E.2    Backofen, R.3
  • 21
    • 33750212480 scopus 로고    scopus 로고
    • Using RNA secondary structures to guide sequencemotif finding towards single-stranded regions
    • Hiller M, Pudimat R, Busch A, Backofen R: Using RNA secondary structures to guide sequencemotif finding towards single-stranded regions. Nucleic Acids Res 2006, 34:e117.
    • (2006) Nucleic Acids Res , vol.34
    • Hiller, M.1    Pudimat, R.2    Busch, A.3    Backofen, R.4
  • 22
    • 84883592184 scopus 로고    scopus 로고
    • RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins
    • Kazan H, Morris Q: RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. Nucleic Acids Res 2013, 41:W180-W186.
    • (2013) Nucleic Acids Res , vol.41 , pp. W180-W186
    • Kazan, H.1    Morris, Q.2
  • 23
    • 0037115895 scopus 로고    scopus 로고
    • Interaction of C5 protein with RNA, aptamers selected by SELEX
    • Lee JH, Kim H, Ko J, Lee Y: Interaction of C5 protein with RNA, aptamers selected by SELEX. Nucleic Acids Res 2002, 30:5360-5368.
    • (2002) Nucleic Acids Res , vol.30 , pp. 5360-5368
    • Lee, J.H.1    Kim, H.2    Ko, J.3    Lee, Y.4
  • 24
    • 0027478445 scopus 로고
    • Relatedness of an RNA-bindingmotif in human immunodeficiency virus type 1 TAR RNA-binding protein TRBP to human P1/dsI kinase and Drosophila staufen
    • Gatignol A, Buckler C, Jeang KT: Relatedness of an RNA-bindingmotif in human immunodeficiency virus type 1 TAR RNA-binding protein TRBP to human P1/dsI kinase and Drosophila staufen. Mol Cell Biol 1993, 13:2193-2202.
    • (1993) Mol Cell Biol , vol.13 , pp. 2193-2202
    • Gatignol, A.1    Buckler, C.2    Jeang, K.T.3
  • 25
    • 84884965371 scopus 로고    scopus 로고
    • CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
    • Lange SJ, Alkhnbashi OS, Rose D, Will S, Backofen R: CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res 2013, 41:8034-8044.
    • (2013) Nucleic Acids Res , vol.41 , pp. 8034-8044
    • Lange, S.J.1    Alkhnbashi, O.S.2    Rose, D.3    Will, S.4    Backofen, R.5
  • 26
    • 84855475577 scopus 로고    scopus 로고
    • Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a rulermechanism anchored at the precursor processing site
    • Hatoum-Aslan A, Maniv I, Marraffini LA: Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a rulermechanism anchored at the precursor processing site. Proc Natl Acad Sci USA 2121, 108:21218-21222.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 21218-21222
    • Hatoum-Aslan, A.1    Maniv, I.2    Marraffini, L.A.3
  • 27
    • 84878270899 scopus 로고    scopus 로고
    • RNA recognition by double-stranded RNA binding domains: amatter of shape and sequence
    • Masliah G, Barraud P, Allain FHT: RNA recognition by double-stranded RNA binding domains: amatter of shape and sequence. Cell Mol Life Sci 2013, 70:1875-1895.
    • (2013) Cell Mol Life Sci , vol.70 , pp. 1875-1895
    • Masliah, G.1    Barraud, P.2    Allain, F.H.T.3
  • 28
    • 84859947721 scopus 로고    scopus 로고
    • LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
    • Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R: LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA 2012, 18:900-914.
    • (2012) RNA , vol.18 , pp. 900-914
    • Will, S.1    Joshi, T.2    Hofacker, I.L.3    Stadler, P.F.4    Backofen, R.5
  • 29
    • 34247598415 scopus 로고    scopus 로고
    • Inferring non-coding RNA families and classes bymeans of genome-scale structure-based clustering
    • Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R: Inferring non-coding RNA families and classes bymeans of genome-scale structure-based clustering. PLoS Comput Biol 2007, 3:e65.
    • (2007) PLoS Comput Biol , vol.3
    • Will, S.1    Reiche, K.2    Hofacker, I.L.3    Stadler, P.F.4    Backofen, R.5
  • 31
    • 84255163357 scopus 로고    scopus 로고
    • Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1
    • Wang X, Juan L, Lv J, Wang K, Sanford JR, Liu Y: Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1. BMC Genomics 2011, 12:S8.
    • (2011) BMC Genomics , vol.12
    • Wang, X.1    Juan, L.2    Lv, J.3    Wang, K.4    Sanford, J.R.5    Liu, Y.6
  • 32
    • 77952671774 scopus 로고    scopus 로고
    • TargetSpy: a supervised machine learning approach formicroRNA target prediction
    • Sturm M, Hackenberg M, Langenberger D, Frishman D: TargetSpy: a supervised machine learning approach formicroRNA target prediction. BMC Bioinformatics 2010, 11:292.
    • (2010) BMC Bioinformatics , vol.11 , pp. 292
    • Sturm, M.1    Hackenberg, M.2    Langenberger, D.3    Frishman, D.4
  • 35
    • 34249753618 scopus 로고
    • Support-vector networks
    • Dordrecht: Kluwer Academic Publishers-Plenum Publishers
    • Cortes C, Vapnik V: Support-vector networks. In Machine Learning. Dordrecht: Kluwer Academic Publishers-Plenum Publishers; 1995:273-297.
    • (1995) Machine Learning , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 37
    • 33644878163 scopus 로고    scopus 로고
    • MulPSSM: a database of multiple position-specific scoring matrices of protein domain families
    • Gowri VS, Krishnadev O, Swamy CS, Srinivasan N: MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. Nucleic Acids Res 2006, 34:D243-D246.
    • (2006) Nucleic Acids Res , vol.34 , pp. D243-D246
    • Gowri, V.S.1    Krishnadev, O.2    Swamy, C.S.3    Srinivasan, N.4
  • 39
    • 72149117411 scopus 로고    scopus 로고
    • Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping
    • Xue Y, Zhou Y, Wu T, Zhu T, Ji X, Kwon YS, Zhang C, Yeo G, Black DL, Sun H, Fu XD, Zhang Y: Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol Cell 2009, 36:996-1006.
    • (2009) Mol Cell , vol.36 , pp. 996-1006
    • Xue, Y.1    Zhou, Y.2    Wu, T.3    Zhu, T.4    Ji, X.5    Kwon, Y.S.6    Zhang, C.7    Yeo, G.8    Black, D.L.9    Sun, H.10    Fu, X.D.11    Zhang, Y.12
  • 40
    • 0031037690 scopus 로고    scopus 로고
    • Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: creation of an SRp40-specific splicing enhancer
    • Tacke R, Chen Y, Manley JL: Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: creation of an SRp40-specific splicing enhancer. Proc Natl Acad Sci USA 1997, 94:1148-1153.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 1148-1153
    • Tacke, R.1    Chen, Y.2    Manley, J.L.3
  • 41
    • 0028054162 scopus 로고
    • Selection of a subset ofmRNAs, from combinatorial 3' untranslated region libraries using neuronal RNA-binding protein Hel-N1
    • Gao FB, Carson CC, Levine T, Keene JD: Selection of a subset ofmRNAs, from combinatorial 3' untranslated region libraries using neuronal RNA-binding protein Hel-N1. Proc Natl Acad Sci USA 1120, 91:7-11211.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 11207-11211
    • Gao, F.B.1    Carson, C.C.2    Levine, T.3    Keene, J.D.4
  • 42
    • 0030878682 scopus 로고    scopus 로고
    • Mutation of PTB binding sites causes misregulation of alternative 3' splice site selection in vivo
    • Perez I, Lin CH, McAfee JG, Patton JG: Mutation of PTB binding sites causes misregulation of alternative 3' splice site selection in vivo. RNA 1997, 3:764-778.
    • (1997) RNA , vol.3 , pp. 764-778
    • Perez, I.1    Lin, C.H.2    McAfee, J.G.3    Patton, J.G.4
  • 43
    • 84923886125 scopus 로고
    • TDP-43 and FUS RNA-binding proteins bind distinct sets of cytoplasmicmessenger RNAs and differently regulate their post-transcriptional fate in motoneuron-like cells
    • Colombrita C, Onesto E, Megiorni F, Pizzuti A, Baralle FE, Buratti E, Silani V, Ratti A: TDP-43 and FUS RNA-binding proteins bind distinct sets of cytoplasmicmessenger RNAs and differently regulate their post-transcriptional fate in motoneuron-like cells. J Biol Chem 1563, 287:5-15647.
    • (1563) J Biol Chem , vol.287 , pp. 5-15647
    • Colombrita, C.1    Onesto, E.2    Megiorni, F.3    Pizzuti, A.4    Baralle, F.E.5    Buratti, E.6    Silani, V.7    Ratti, A.8
  • 45
    • 0027992089 scopus 로고
    • The determinants of RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein C proteins
    • Gorlach M, Burd CG, Dreyfuss G: The determinants of RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein C proteins. J Biol Chem 2307, 269:4-23078.
    • (1994) J Biol Chem , vol.269 , pp. 23074-23078
    • Gorlach, M.1    Burd, C.G.2    Dreyfuss, G.3
  • 46
    • 0025243405 scopus 로고
    • A uridylate tractmediates efficient heterogeneous nuclear ribonucleoprotein C protein-RNA cross-linking and functionally substitutes for the downstream element of the polyadenylation signal
    • Wilusz J, Shenk T: A uridylate tractmediates efficient heterogeneous nuclear ribonucleoprotein C protein-RNA cross-linking and functionally substitutes for the downstream element of the polyadenylation signal. Mol Cell Biol 1990, 10:6397-6407.
    • (1990) Mol Cell Biol , vol.10 , pp. 6397-6407
    • Wilusz, J.1    Shenk, T.2
  • 47
    • 0030027575 scopus 로고    scopus 로고
    • Individual RNA recognitionmotifs of TIA-1 and TIAR have different RNA binding specificities
    • Dember L, Kim N, Liu K, Anderson P: Individual RNA recognitionmotifs of TIA-1 and TIAR have different RNA binding specificities. J Biol Chem 1996, 271:2783.
    • (1996) J Biol Chem , vol.271 , pp. 2783
    • Dember, L.1    Kim, N.2    Liu, K.3    Anderson, P.4
  • 49
    • 84856213943 scopus 로고    scopus 로고
    • Three RNA recognitionmotifs participate in RNA recognition and structural organization by the pro-apoptotic factor TIA-1
    • Bauer WJ, Heath J, Jenkins JL, Kielkopf CL: Three RNA recognitionmotifs participate in RNA recognition and structural organization by the pro-apoptotic factor TIA-1. JMol Biol 2012, 415:727-740.
    • (2012) JMol Biol , vol.415 , pp. 727-740
    • Bauer, W.J.1    Heath, J.2    Jenkins, J.L.3    Kielkopf, C.L.4
  • 51
    • 79951996054 scopus 로고    scopus 로고
    • U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression
    • Sharma S, Maris C, Allain FHT, Black DL: U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression. Mol Cell 2011, 41:579-588.
    • (2011) Mol Cell , vol.41 , pp. 579-588
    • Sharma, S.1    Maris, C.2    Allain, F.H.T.3    Black, D.L.4
  • 53
    • 33745616104 scopus 로고    scopus 로고
    • The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA
    • Law MJ, Rice AJ, Lin P, Laird-Offringa IA: The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA. RNA 2006, 12:1168-1178.
    • (2006) RNA , vol.12 , pp. 1168-1178
    • Law, M.J.1    Rice, A.J.2    Lin, P.3    Laird-Offringa, I.A.4
  • 57
    • 84881493949 scopus 로고    scopus 로고
    • Prediction of clustered RNA-binding protein motif sites in themammalian genome
    • Zhang C, Lee KY, Swanson MS, Darnell RB: Prediction of clustered RNA-binding protein motif sites in themammalian genome. Nucleic Acids Res 2013, 41:6793-6807.
    • (2013) Nucleic Acids Res , vol.41 , pp. 6793-6807
    • Zhang, C.1    Lee, K.Y.2    Swanson, M.S.3    Darnell, R.B.4
  • 62
    • 84863515320 scopus 로고    scopus 로고
    • GraphClust: alignment-free structural clustering of local RNA secondary structures
    • Heyne S, Costa F, Rose D, Backofen R: GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinformatics 2012, 28:i224-i232.
    • (2012) Bioinformatics , vol.28 , pp. i224-i232
    • Heyne, S.1    Costa, F.2    Rose, D.3    Backofen, R.4
  • 63
  • 64
  • 66
    • 84875627444 scopus 로고    scopus 로고
    • kLog: a language for logical and relational learning with kernels
    • abs/1205.3981
    • Frasconi P, Costa F, Raedt LD, Grave KD: kLog: a language for logical and relational learning with kernels. CoRR 2012. abs/1205.3981.
    • (2012) CoRR
    • Frasconi, P.1    Costa, F.2    Raedt, L.D.3    Grave, K.D.4
  • 67
    • 84923886124 scopus 로고    scopus 로고
    • Gene Expression Omnibus
    • Gene Expression Omnibus [www.ncbi.nih.gov/geo/]
  • 69
    • 79955702502 scopus 로고    scopus 로고
    • LIBSVM: A library for support vector machines
    • Chang CC, Lin CJ: LIBSVM: A library for support vector machines. ACM Trans Intell Syst Technol 2011, 2:27. [Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm].
    • (2011) ACM Trans Intell Syst Technol , vol.2 , pp. 27
    • Chang, C.C.1    Lin, C.J.2
  • 71
    • 84923886123 scopus 로고    scopus 로고
    • GraphProt
    • GraphProt [http://www.bioinf.uni-freiburg.de/Software/GraphProt]


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.