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Volumn 15, Issue 1, 2014, Pages

Sequence search and analysis of gene products containing RNA recognition motifs in the human genome

Author keywords

Domain architecture; Genome wide survey; Homo sapiens; RNA recognition motif; Splicing

Indexed keywords

PROTEIN BINDING; RNA; RNA BINDING PROTEIN;

EID: 85027923189     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-1159     Document Type: Article
Times cited : (9)

References (51)
  • 2
    • 85059954188 scopus 로고    scopus 로고
    • Analysing gene expression, edited by S. Lorkowski and P. Cullen
    • Le Jeune E, Ladurner AG: Analysing gene expression, edited by S. Lorkowski and P. Cullen. Protein Sci Publ Protein Soc 2004, 13:1950-1952.
    • (2004) Protein Sci Publ Protein Soc , vol.13 , pp. 1950-1952
    • Le Jeune, E.1    Ladurner, A.G.2
  • 3
    • 0033972791 scopus 로고    scopus 로고
    • The balance sheet for transcription: An analysis of nuclear RNA metabolism in mammalian cells
    • Jackson DA, Pombo A, Iborra F: The balance sheet for transcription: An analysis of nuclear RNA metabolism in mammalian cells. FASEB J Off Publ Fed Am Soc Exp Biol 2000, 14:242-254.
    • (2000) FASEB J off Publ Fed Am Soc Exp Biol , vol.14 , pp. 242-254
    • Jackson, D.A.1    Pombo, A.2    Iborra, F.3
  • 5
    • 84879853115 scopus 로고    scopus 로고
    • Cancer: Mutations close in on gene regulation
    • Aerts S, Cools J: Cancer: Mutations close in on gene regulation. Nature 2013, 499:35-36.
    • (2013) Nature , vol.499 , pp. 35-36
    • Aerts, S.1    Cools, J.2
  • 6
    • 84860280305 scopus 로고    scopus 로고
    • Gene regulatory network inference: Evaluation and application to ovarian cancer allows the prioritization of drug targets
    • Madhamshettiwar PB, Maetschke SR, Davis MJ, Reverter A, Ragan MA: Gene regulatory network inference: Evaluation and application to ovarian cancer allows the prioritization of drug targets. Genome Med 2012, 4:41.
    • (2012) Genome Med , vol.4 , pp. 41
    • Madhamshettiwar, P.B.1    Maetschke, S.R.2    Davis, M.J.3    Reverter, A.4    Ragan, M.A.5
  • 7
    • 44949179228 scopus 로고    scopus 로고
    • RNA recognition motifs: Boring? Not quite
    • Cléry A, Blatter M, Allain FH-T: RNA recognition motifs: Boring? Not quite. Curr Opin Struct Biol 2008, 18:290-298.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 290-298
    • Cléry, A.1    Blatter, M.2    Fh-T, A.3
  • 8
    • 0028129989 scopus 로고
    • Conserved structures and diversity of functions of RNA-binding proteins
    • Burd CG, Dreyfuss G: Conserved structures and diversity of functions of RNA-binding proteins. Science 1994, 265:615-621.
    • (1994) Science , vol.265 , pp. 615-621
    • Burd, C.G.1    Dreyfuss, G.2
  • 10
    • 84862151933 scopus 로고    scopus 로고
    • The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease
    • King OD, Gitler AD, Shorter J: The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease. Brain Res 2012, 1462:61-80.
    • (2012) Brain Res , vol.1462 , pp. 61-80
    • King, O.D.1    Gitler, A.D.2    Shorter, J.3
  • 11
    • 0027753933 scopus 로고
    • Analysis of the RNA-recognition motif and RS and RGG domains: Conservation in metazoan pre-mRNA splicing factors
    • Birney E, Kumar S, Krainer AR: Analysis of the RNA-recognition motif and RS and RGG domains: Conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res 1993, 21:5803-5816.
    • (1993) Nucleic Acids Res , vol.21 , pp. 5803-5816
    • Birney, E.1    Kumar, S.2    Krainer, A.R.3
  • 13
    • 79961091137 scopus 로고    scopus 로고
    • Evolution of RNA-binding proteins in animals: Insights from genome-wide analysis in the sponge Amphimedon queenslandica
    • Kerner P, Degnan SM, Marchand L, Degnan BM, Vervoort M: Evolution of RNA-binding proteins in animals: Insights from genome-wide analysis in the sponge Amphimedon queenslandica. Mol Biol Evol 2011, 28:2289-2303.
    • (2011) Mol Biol Evol , vol.28 , pp. 2289-2303
    • Kerner, P.1    Degnan, S.M.2    Marchand, L.3    Degnan, B.M.4    Vervoort, M.5
  • 14
    • 84883151591 scopus 로고    scopus 로고
    • A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels
    • Tamburino AM, Ryder SP, Walhout AJM: A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 Bethesda Md 2013, 3:297-304.
    • (2013) G3 Bethesda Md , vol.3 , pp. 297-304
    • Tamburino, A.M.1    Ryder, S.P.2    Walhout, A.J.M.3
  • 15
    • 0036464536 scopus 로고    scopus 로고
    • Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana
    • Lorković ZJ, Barta A: Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana. Nucleic Acids Res 2002, 30:623-635.
    • (2002) Nucleic Acids Res , vol.30 , pp. 623-635
    • Lorković, Z.J.1    Barta, A.2
  • 16
    • 24344452361 scopus 로고    scopus 로고
    • A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain
    • McKee AE, Minet E, Stern C, Riahi S, Stiles CD, Silver PA: A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. BMC Dev Biol 2005, 5:14.
    • (2005) BMC Dev Biol , vol.5 , pp. 14
    • McKee, A.E.1    Minet, E.2    Stern, C.3    Riahi, S.4    Stiles, C.D.5    Silver, P.A.6
  • 21
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 23
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O: New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst Biol 2010, 59:307-321.
    • (2010) Syst Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.-F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 24
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC: MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 30
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy SR: Accelerated profile HMM searches. PLoS Comput Biol 2011, 7:e1002195.
    • (2011) PLoS Comput Biol , vol.7 , pp. e1002195
    • Eddy, S.R.1
  • 31
    • 85084916252 scopus 로고    scopus 로고
    • BLASTclust
    • BLASTclust. http://toolkit.tuebingen.mpg.de/blastclust#.
  • 34
  • 35
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 36
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang DW, Sherman BT, Lempicki RA: Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37:1-13.
    • (2009) Nucleic Acids Res , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 37
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 40
    • 84883514164 scopus 로고    scopus 로고
    • Structural disorder and the loss of RNA homeostasis in aging and neurodegenerative disease
    • Gray DA, Woulfe J: Structural disorder and the loss of RNA homeostasis in aging and neurodegenerative disease. Front Genet 2013, 4:149.
    • (2013) Front Genet , vol.4 , pp. 149
    • Gray, D.A.1    Woulfe, J.2
  • 41
    • 84887043259 scopus 로고    scopus 로고
    • Role of stress granules and RNA-binding proteins in neurodegeneration: A mini-review
    • Vanderweyde T, Youmans K, Liu-Yesucevitz L, Wolozin B: Role of stress granules and RNA-binding proteins in neurodegeneration: A mini-review. Gerontology 2013, 59:524-533.
    • (2013) Gerontology , vol.59 , pp. 524-533
    • Vanderweyde, T.1    Youmans, K.2    Liu-Yesucevitz, L.3    Wolozin, B.4
  • 42
    • 84869192353 scopus 로고    scopus 로고
    • Regulated protein aggregation: Stress granules and neurodegeneration
    • Wolozin B: Regulated protein aggregation: Stress granules and neurodegeneration. Mol Neurodegener 2012, 7:56.
    • (2012) Mol Neurodegener , vol.7 , pp. 56
    • Wolozin, B.1
  • 43
    • 84873521914 scopus 로고    scopus 로고
    • RRM-RNA recognition: NMR or crystallography and new findings
    • [Folding and Binding/Protein-Nucleic Acid Interactions]
    • Daubner GM, Cléry A, Allain FH-T: RRM-RNA recognition: NMR or crystallography and new findings. Curr Opin Struct Biol 2013, 23:100-108 [Folding and Binding/Protein-Nucleic Acid Interactions].
    • (2013) Curr Opin Struct Biol , vol.23 , pp. 100-108
    • Daubner, G.M.1    Cléry, A.2    Fh-T, A.3
  • 44
    • 18544377013 scopus 로고    scopus 로고
    • The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression
    • Maris C, Dominguez C, Allain FH-T: The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J 2005, 272:2118-2131.
    • (2005) FEBS J , vol.272 , pp. 2118-2131
    • Maris, C.1    Dominguez, C.2    Fh-T, A.3
  • 46
    • 3442902456 scopus 로고    scopus 로고
    • The role of structural disorder in the function of RNA and protein chaperones
    • Tompa P, Csermely P: The role of structural disorder in the function of RNA and protein chaperones. FASEB J 2004, 18:1169-1175.
    • (2004) FASEB J , vol.18 , pp. 1169-1175
    • Tompa, P.1    Csermely, P.2
  • 47
    • 84866076924 scopus 로고    scopus 로고
    • Intrinsic disorder in the human spliceosomal proteome
    • Korneta I, Bujnicki JM: Intrinsic disorder in the human spliceosomal proteome. PLoS Comput Biol 2012, 8:e1002641.
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002641
    • Korneta, I.1    Bujnicki, J.M.2
  • 49
    • 85084922153 scopus 로고    scopus 로고
    • FigTree
    • FigTree. http://tree.bio.ed.ac.uk/software/figtree/.
  • 50
    • 59449110909 scopus 로고    scopus 로고
    • DOG 1.0: Illustrator of protein domain structures
    • Ren J, Wen L, Gao X, Jin C, Xue Y, Yao X: DOG 1.0: Illustrator of protein domain structures. Cell Res 2009, 19:271-273.
    • (2009) Cell Res , vol.19 , pp. 271-273
    • Ren, J.1    Wen, L.2    Gao, X.3    Jin, C.4    Xue, Y.5    Yao, X.6
  • 51
    • 13444266370 scopus 로고    scopus 로고
    • Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    • Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005, 33(suppl 1):D514-D517.
    • (2005) Nucleic Acids Res , vol.33 , pp. D514-D517
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3    Bocchini, C.A.4    McKusick, V.A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.