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Volumn 2, Issue 3, 2012, Pages 273-284

FiRePat-Finding regulatory patterns between sRNAs and genes

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; LARGE DATASET; RNA;

EID: 84869497932     PISSN: 19424787     EISSN: 19424795     Source Type: Journal    
DOI: 10.1002/widm.1053     Document Type: Article
Times cited : (5)

References (59)
  • 1
    • 33646137364 scopus 로고    scopus 로고
    • The diversity of RNA silencing pathways in plants
    • Brodersen P, Voinnet O. The diversity of RNA silencing pathways in plants. Trends Genet 2006, 22:268-280
    • (2006) Trends Genet , vol.22 , pp. 268-280
    • Brodersen, P.1    Voinnet, O.2
  • 2
    • 70449715574 scopus 로고    scopus 로고
    • Deciphering the diversity of small RNAs in plants: the long and short of it
    • Schwach F, Moxon S, Moulton V, Dalmay T. Deciphering the diversity of small RNAs in plants: the long and short of it. Brief Funct Genomic Proteomic 2009, 8:472-481
    • (2009) Brief Funct Genomic Proteomic , vol.8 , pp. 472-481
    • Schwach, F.1    Moxon, S.2    Moulton, V.3    Dalmay, T.4
  • 3
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
    • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811
    • (1998) Nature , vol.391 , pp. 806-811
    • Fire, A.1    Xu, S.2    Montgomery, M.K.3    Kostas, S.A.4    Driver, S.E.5    Mello, C.C.6
  • 4
    • 0032506226 scopus 로고    scopus 로고
    • Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA
    • Waterhouse PM, Graham MW, Wang MB. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci USA 1998, 95:13959-13964
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 13959-13964
    • Waterhouse, P.M.1    Graham, M.W.2    Wang, M.B.3
  • 5
    • 0030087727 scopus 로고    scopus 로고
    • Gene silencing mediated by promoter homology occurs at the level of transcription and results in meiotically heritable alterations in methylation and gene activity
    • Park YD, Papp I, Moscone EA, Iglesias VA, Vaucheret H, Matzke AJ, Matzke MA. Gene silencing mediated by promoter homology occurs at the level of transcription and results in meiotically heritable alterations in methylation and gene activity. Plant J 1996, 9:183-194
    • (1996) Plant J , vol.9 , pp. 183-194
    • Park, Y.D.1    Papp, I.2    Moscone, E.A.3    Iglesias, V.A.4    Vaucheret, H.5    Matzke, A.J.6    Matzke, M.A.7
  • 6
    • 0029111346 scopus 로고
    • Homology-dependent resistance: transgenic virus resistance in plants related to homologydependent gene silencing
    • Mueller E. Homology-dependent resistance: transgenic virus resistance in plants related to homologydependent gene silencing. Plant J 1995, 7:1001-1013
    • (1995) Plant J , vol.7 , pp. 1001-1013
    • Mueller, E.1
  • 7
    • 10644294519 scopus 로고    scopus 로고
    • The roles of histone modifications and small RNA in centromere function
    • Ekwall K. The roles of histone modifications and small RNA in centromere function. Chromosome Res 2004, 12:535-542
    • (2004) Chromosome Res , vol.12 , pp. 535-542
    • Ekwall, K.1
  • 8
  • 11
    • 77956496359 scopus 로고    scopus 로고
    • Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data
    • Bonnet E, Michoel T, Van de Peer Y. Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics 2010, 26:i638-i644
    • (2010) Bioinformatics , vol.26
    • Bonnet, E.1    Michoel, T.2    Van de Peer, Y.3
  • 13
    • 38349169664 scopus 로고    scopus 로고
    • Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?
    • FilipowiczW, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 2008, 9:102-114
    • (2008) Nat Rev Genet , vol.9 , pp. 102-114
    • Filipowicz, W.1    Bhattacharyya, S.N.2    Sonenberg, N.3
  • 14
    • 43349093418 scopus 로고    scopus 로고
    • RNA secondary structure analysis using the Vienna RNA package
    • 12.2.1-12.2.16
    • Hofacker IL. RNA secondary structure analysis using the Vienna RNA package. Curr Protoc Bioinform 2009, 12:12.2.1-12.2.16
    • (2009) Curr Protoc Bioinform , vol.12
    • Hofacker, I.L.1
  • 15
    • 50649087826 scopus 로고    scopus 로고
    • Activity range of Arabidopsis small RNAs derived from different biogenesis pathways
    • Tretter EM, Alvarez JP, Eshed Y, Bowman JL. Activity range of Arabidopsis small RNAs derived from different biogenesis pathways. Plant Physiol 2008, 147:58-62
    • (2008) Plant Physiol , vol.147 , pp. 58-62
    • Tretter, E.M.1    Alvarez, J.P.2    Eshed, Y.3    Bowman, J.L.4
  • 16
    • 42549096814 scopus 로고    scopus 로고
    • PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis
    • USA
    • Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci USA 2008, 105:3145-3150
    • (2008) Proc Natl Acad Sci , vol.105 , pp. 3145-3150
    • Mosher, R.A.1    Schwach, F.2    Studholme, D.3    Baulcombe, D.C.4
  • 17
    • 4644286235 scopus 로고    scopus 로고
    • SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of transacting siRNAs in Arabidopsis
    • Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of transacting siRNAs in Arabidopsis. Genes Dev 2004, 18:2368-2379
    • (2004) Genes Dev , vol.18 , pp. 2368-2379
    • Peragine, A.1    Yoshikawa, M.2    Wu, G.3    Albrecht, H.L.4    Poethig, R.S.5
  • 18
    • 29244490062 scopus 로고    scopus 로고
    • Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
    • Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2005, 123:1279-1291
    • (2005) Cell , vol.123 , pp. 1279-1291
    • Borsani, O.1    Zhu, J.2    Verslues, P.E.3    Sunkar, R.4    Zhu, J.K.5
  • 20
    • 60149086351 scopus 로고    scopus 로고
    • Origin, biogenesis, and activity of plant microRNAs
    • Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136:669-687
    • (2009) Cell , vol.136 , pp. 669-687
    • Voinnet, O.1
  • 23
    • 79961001437 scopus 로고    scopus 로고
    • Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis
    • Ahmed I, Sarazin A, Bowler C, Colot V, Quesneville H. Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res 2011
    • (2011) Nucleic Acids Res
    • Ahmed, I.1    Sarazin, A.2    Bowler, C.3    Colot, V.4    Quesneville, H.5
  • 25
    • 58849093262 scopus 로고    scopus 로고
    • Revisiting the principles of microRNA target recognition and mode of action
    • Brodersen P, Voinnet O. Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 2009, 10:141-148
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 141-148
    • Brodersen, P.1    Voinnet, O.2
  • 26
    • 59149086907 scopus 로고    scopus 로고
    • Identification of genes targeted by microRNAs
    • Dalmay T. Identification of genes targeted by microRNAs. Biochem Soc Trans 2008, 36:1194-1196
    • (2008) Biochem Soc Trans , vol.36 , pp. 1194-1196
    • Dalmay, T.1
  • 29
    • 33845755467 scopus 로고    scopus 로고
    • Illuminating the silence: understanding the structure and function of small RNAs
    • Rana TM. Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol 2007, 8:23-36
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 23-36
    • Rana, T.M.1
  • 31
    • 0037249498 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
    • Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, et al. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 2003, 31:224-228
    • (2003) Nucleic Acids Res , vol.31 , pp. 224-228
    • Rhee, S.Y.1    Beavis, W.2    Berardini, T.Z.3    Chen, G.4    Dixon, D.5    Doyle, A.6    Garcia-Hernandez, M.7    Huala, E.8    Lander, G.9    Montoya, M.10
  • 34
    • 11244251011 scopus 로고    scopus 로고
    • Plant and animal microRNAs: similarities and differences
    • Millar AA, Waterhouse PM. Plant and animal microRNAs: similarities and differences. Funct IntegrGenomics 2005, 5:129-135
    • (2005) Funct IntegrGenomics , vol.5 , pp. 129-135
    • Millar, A.A.1    Waterhouse, P.M.2
  • 35
    • 33845688601 scopus 로고    scopus 로고
    • A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006, 20:3407-3425
    • (2006) Genes Dev , vol.20 , pp. 3407-3425
    • Rajagopalan, R.1    Vaucheret, H.2    Trejo, J.3    Bartel, D.P.4
  • 36
    • 78149443144 scopus 로고    scopus 로고
    • The microRNA and messengerRNA profile of the RNA-induced silencing complex in human primary astrocyte and astrocytoma cells
    • DOI:10.1371/journal.pone.001344
    • Moser JJ, Fritzler MJ. The microRNA and messengerRNA profile of the RNA-induced silencing complex in human primary astrocyte and astrocytoma cells. PLoS One 2010, 5:e13445. DOI:10.1371/ journal.pone.001344. http://www.plosone.org/article/ info:doi%2F10.1371%2Fjournal.pone.0013445
    • (2010) PLoS One , vol.5
    • Moser, J.J.1    Fritzler, M.J.2
  • 37
    • 34347355440 scopus 로고    scopus 로고
    • miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii
    • Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 2007, 447:1126-1129
    • (2007) Nature , vol.447 , pp. 1126-1129
    • Molnar, A.1    Schwach, F.2    Studholme, D.J.3    Thuenemann, E.C.4    Baulcombe, D.C.5
  • 38
    • 1342288026 scopus 로고    scopus 로고
    • affy-analysis of Affymetrix GeneChip data at the probe level
    • Gautier L, Cope L, Bolstad BM, Irizarry RA. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315
    • (2004) Bioinformatics , vol.20 , pp. 307-315
    • Gautier, L.1    Cope, L.2    Bolstad, B.M.3    Irizarry, R.A.4
  • 42
    • 28644449917 scopus 로고    scopus 로고
    • How does gene expression clustering work?
    • D'Haeseleer P. How does gene expression clustering work? Nat Biotechnol 2005, 23:1499-1501
    • (2005) Nat Biotechnol , vol.23 , pp. 1499-1501
    • D'Haeseleer, P.1
  • 44
    • 0000950204 scopus 로고    scopus 로고
    • Cluster analysis and mathematical programming
    • Hansen P, Jaumard B. Cluster analysis and mathematical programming. Math Program 1997, 79:191-215
    • (1997) Math Program , vol.79 , pp. 191-215
    • Hansen, P.1    Jaumard, B.2
  • 45
    • 30344442460 scopus 로고    scopus 로고
    • Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm
    • Grotkjaer T, Winther O, Regenberg B, Nielsen J, Hansen LK. Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm. Bioinformatics 2006, 22:58-67
    • (2006) Bioinformatics , vol.22 , pp. 58-67
    • Grotkjaer, T.1    Winther, O.2    Regenberg, B.3    Nielsen, J.4    Hansen, L.K.5
  • 46
    • 84857058733 scopus 로고    scopus 로고
    • Choosing the number of clusters
    • Mirkin B. Choosing the number of clusters. WIREs Data Min Knowl Discov 2011, 1:252-260
    • (2011) WIREs Data Min Knowl Discov , vol.1 , pp. 252-260
    • Mirkin, B.1
  • 50
    • 0037144457 scopus 로고    scopus 로고
    • Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
    • Llave C, Xie Z, Kasschau KD, Carrington JC. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297:2053-2056
    • (2002) Science , vol.297 , pp. 2053-2056
    • Llave, C.1    Xie, Z.2    Kasschau, K.D.3    Carrington, J.C.4
  • 51
    • 34547135690 scopus 로고    scopus 로고
    • Pentatricopeptide repeat proteins and their emerging roles in plants
    • Saha D, Prasad AM, Srinivasan R. Pentatricopeptide repeat proteins and their emerging roles in plants. Plant Physiol Biochem 2007, 45:521-534
    • (2007) Plant Physiol Biochem , vol.45 , pp. 521-534
    • Saha, D.1    Prasad, A.M.2    Srinivasan, R.3
  • 52
    • 33845608810 scopus 로고    scopus 로고
    • The multifarious roles of PPR proteins in plantmitochondrial gene expression
    • Andres C. The multifarious roles of PPR proteins in plantmitochondrial gene expression. Physiologia Plantarum 2007, 129:14-22
    • (2007) Physiologia Plantarum , vol.129 , pp. 14-22
    • Andres, C.1
  • 53
    • 56549095978 scopus 로고    scopus 로고
    • Pentatricopeptide repeat proteins: a socket set for organelle gene expression
    • Schmitz-Linneweber C, Small I. Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 2008, 13:663-670
    • (2008) Trends Plant Sci , vol.13 , pp. 663-670
    • Schmitz-Linneweber, C.1    Small, I.2
  • 54
    • 79953002266 scopus 로고    scopus 로고
    • MicroRNAs-10a and -10b contribute to retinoic acid-induced differentiation of neuroblastoma cells and target the alternative splicing regulatory factor SFRS1 (SF2/ASF)
    • Meseguer S, Mudduluru G, Escamilla JM, Allgayer H, Barettino D. MicroRNAs-10a and -10b contribute to retinoic acid-induced differentiation of neuroblastoma cells and target the alternative splicing regulatory factor SFRS1 (SF2/ASF). J Biol Chem 2011, 286:4150-4164
    • (2011) J Biol Chem , vol.286 , pp. 4150-4164
    • Meseguer, S.1    Mudduluru, G.2    Escamilla, J.M.3    Allgayer, H.4    Barettino, D.5
  • 55
    • 35148886434 scopus 로고    scopus 로고
    • Tumour invasion and metastasis initiated by microRNA-10b in breast cancer
    • Ma L, Teruya-Feldstein J, Weinberg RA. Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 2007, 449:682-688
    • (2007) Nature , vol.449 , pp. 682-688
    • Ma, L.1    Teruya-Feldstein, J.2    Weinberg, R.A.3
  • 56
    • 78449234396 scopus 로고    scopus 로고
    • Hyaluronan-CD44 interaction promotes c-Src-mediated twist signaling, microRNA-10b expression, and RhoA/RhoC up-regulation, leading to Rhokinase-associated cytoskeleton activation and breast tumor cell invasion
    • Bourguignon LY, Wong G, Earle C, Krueger K, Spevak CC. Hyaluronan-CD44 interaction promotes c-Src-mediated twist signaling, microRNA-10b expression, and RhoA/RhoC up-regulation, leading to Rhokinase-associated cytoskeleton activation and breast tumor cell invasion. J Biol Chem 2010, 285:36721-36735
    • (2010) J Biol Chem , vol.285 , pp. 36721-36735
    • Bourguignon, L.Y.1    Wong, G.2    Earle, C.3    Krueger, K.4    Spevak, C.C.5
  • 57
    • 43449091567 scopus 로고    scopus 로고
    • Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
    • Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 2008, 18:758-762
    • (2008) Curr Biol , vol.18 , pp. 758-762
    • Addo-Quaye, C.1    Eshoo, T.W.2    Bartel, D.P.3    Axtell, M.J.4
  • 58
    • 0141958996 scopus 로고    scopus 로고
    • Microarrays-guilt by association
    • Quackenbush J. Genomics. Microarrays-guilt by association. Science 2003, 302:240-241
    • (2003) Science , vol.302 , pp. 240-241
    • Quackenbush, J.G.1


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