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Volumn 5, Issue 1, 2012, Pages

MicroRNA Targets, a new AthaMap web-tool for genome-wide identification of miRNA targets in Arabidopsis thaliana

Author keywords

Arabidopsis thaliana; AthaMap; MicroRNAs; Post transcriptional regulation; Small RNAs

Indexed keywords

MICRORNA; TRANSCRIPTOME;

EID: 84864748399     PISSN: None     EISSN: 17560381     Source Type: Journal    
DOI: 10.1186/1756-0381-5-7     Document Type: Article
Times cited : (20)

References (42)
  • 1
    • 78049263858 scopus 로고    scopus 로고
    • MiRNAs in the biogenesis of trans-acting siRNAs in higher plants
    • 10.1016/j.semcdb.2010.03.008 20359543
    • miRNAs in the biogenesis of trans-acting siRNAs in higher plants. Allen E, Howell MD, Semin Cell Dev Biol 2010 21 798 804 10.1016/j.semcdb.2010.03.008 20359543
    • (2010) Semin Cell Dev Biol , vol.21 , pp. 798-804
    • Allen, E.1    Howell, M.D.2
  • 2
    • 33645525893 scopus 로고    scopus 로고
    • MicroRNAs and their regulatory roles in plants
    • DOI 10.1146/annurev.arplant.57.032905.105218
    • MicroRNAS and their regulatory roles in plants. Jones-Rhoades MW, Bartel DP, Bartel B, Annu Rev Plant Biol 2006 57 19 53 10.1146/annurev.arplant.57. 032905.105218 16669754 (Pubitemid 44061017)
    • (2006) Annual Review of Plant Biology , vol.57 , pp. 19-53
    • Jones-Rhoades, M.W.1    Bartel, D.P.2    Bartel, B.3
  • 3
    • 0347755643 scopus 로고    scopus 로고
    • The microRNA Registry
    • 10.1093/nar/gkh023 14681370
    • The microRNA Registry. Griffiths-Jones S, Nucleic Acids Res 2004 32 109 111 10.1093/nar/gkh023 14681370
    • (2004) Nucleic Acids Res , vol.32 , pp. 4109-4111
    • Griffiths-Jones, S.1
  • 5
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: Integrating microRNA annotation and deep-sequencing data
    • 10.1093/nar/gkq1027 21037258
    • miRBase: integrating microRNA annotation and deep-sequencing data. Kozomara A, Griffiths-Jones S, Nucleic Acids Res 2011 39 152 157 10.1093/nar/gkq1027 21037258
    • (2011) Nucleic Acids Res , vol.39 , pp. 4152-4157
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 8
    • 33846120020 scopus 로고    scopus 로고
    • CSRDB: A small RNA integrated database and browser resource for cereals
    • DOI 10.1093/nar/gkl991
    • CSRDB: a small RNA integrated database and browser resource for cereals. Johnson C, Bowman L, Adai AT, Vance V, Sundaresan V, Nucleic Acids Res 2007 35 829 833 10.1093/nar/gkl991 17169981 (Pubitemid 46056317)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Johnson, C.1    Bowman, L.2    Adai, A.T.3    Vance, V.4    Sundaresan, V.5
  • 10
    • 84861526539 scopus 로고    scopus 로고
    • SoMART, a web server for plant miRNA, tasiRNA and target gene analysis
    • SoMART, a web server for plant miRNA, tasiRNA and target gene analysis. Li F, Orban R, Baker B, Plant J 70 891 901
    • Plant J , vol.70 , pp. 891-901
    • Li, F.1    Orban, R.2    Baker, B.3
  • 11
    • 79953137130 scopus 로고    scopus 로고
    • Computational analysis of miRNA targets in plants: Current status and challenges
    • 10.1093/bib/bbq065 20858738
    • Computational analysis of miRNA targets in plants: current status and challenges. Dai X, Zhuang Z, Zhao PX, Brief Bioinform 2011 12 115 121 10.1093/bib/bbq065 20858738
    • (2011) Brief Bioinform , vol.12 , pp. 115-121
    • Dai, X.1    Zhuang, Z.2    Zhao, P.X.3
  • 12
    • 23144458275 scopus 로고    scopus 로고
    • MiRU: An automated plant miRNA target prediction server
    • DOI 10.1093/nar/gki383
    • miRU: an automated plant miRNA target prediction server. Zhang Y, Nucleic Acids Res 2005 33 701 704 10.1093/nar/gki383 15980567 (Pubitemid 44530014)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
    • Zhang, Y.1
  • 13
    • 77954184918 scopus 로고    scopus 로고
    • TAPIR, a web server for the prediction of plant microRNA targets, including target mimics
    • 10.1093/bioinformatics/btq233 20430753
    • TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bonnet E, He Y, Billiau K, Van de Peer Y, Bioinformatics 2010 26 1566 1568 10.1093/bioinformatics/btq233 20430753
    • (2010) Bioinformatics , vol.26 , pp. 1566-1568
    • Bonnet, E.1    He, Y.2    Billiau, K.3    Van De Peer, Y.4
  • 14
    • 78449293356 scopus 로고    scopus 로고
    • Target-align: A tool for plant microRNA target identification
    • 10.1093/bioinformatics/btq568 20934992
    • Target-align: a tool for plant microRNA target identification. Xie F, Zhang B, Bioinformatics 2010 26 3002 3003 10.1093/bioinformatics/btq568 20934992
    • (2010) Bioinformatics , vol.26 , pp. 3002-3003
    • Xie, F.1    Zhang, B.2
  • 15
    • 79959967431 scopus 로고    scopus 로고
    • PsRNATarget: A plant small RNA target analysis server
    • 10.1093/nar/gkr319 21622958
    • psRNATarget: a plant small RNA target analysis server. Dai X, Zhao PX, Nucleic Acids Res 2011 39 155 159 10.1093/nar/gkr319 21622958
    • (2011) Nucleic Acids Res , vol.39 , pp. 23155-23159
    • Dai, X.1    Zhao, P.X.2
  • 16
    • 0037162702 scopus 로고    scopus 로고
    • Prediction of plant microRNA targets
    • DOI 10.1016/S0092-8674(02)00863-2
    • Prediction of plant microRNA targets. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP, Cell 2002 110 513 520 10.1016/S0092-8674(02) 00863-2 12202040 (Pubitemid 35232294)
    • (2002) Cell , vol.110 , Issue.4 , pp. 513-520
    • Rhoades, M.W.1    Reinhart, B.J.2    Lim, L.P.3    Burge, C.B.4    Bartel, B.5    Bartel, D.P.6
  • 17
    • 16244398080 scopus 로고    scopus 로고
    • Specific effects of microRNAs on the plant transcriptome
    • DOI 10.1016/j.devcel.2005.01.018, PII S1534580705000225
    • Specific effects of microRNAs on the plant transcriptome. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D, Dev Cell 2005 8 517 527 10.1016/j.devcel.2005.01.018 15809034 (Pubitemid 40450741)
    • (2005) Developmental Cell , vol.8 , Issue.4 , pp. 517-527
    • Schwab, R.1    Palatnik, J.F.2    Riester, M.3    Schommer, C.4    Schmid, M.5    Weigel, D.6
  • 20
    • 79953231729 scopus 로고    scopus 로고
    • AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana
    • 10.1093/database/baq034
    • AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana. Bülow L, Brill Y, Hehl R, Database (Oxford) 2010 2010 aq034 10.1093/database/baq034
    • (2010) Database (Oxford) , vol.2010
    • Bülow, L.1    Brill, Y.2    Hehl, R.3
  • 21
    • 78651339097 scopus 로고    scopus 로고
    • AGRIS: The Arabidopsis Gene Regulatory Information Server, an update
    • 10.1093/nar/gkq1120 21059685
    • AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E, Nucleic Acids Res 2011 39 1118 1122 10.1093/nar/gkq1120 21059685
    • (2011) Nucleic Acids Res , vol.39 , pp. 41118-41122
    • Yilmaz, A.1    Mejia-Guerra, M.K.2    Kurz, K.3    Liang, X.4    Welch, L.5    Grotewold, E.6
  • 22
    • 0345863918 scopus 로고    scopus 로고
    • AthaMap: An online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
    • 10.1093/nar/gkh017 14681436
    • AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. Steffens NO, Galuschka C, Schindler M, Bülow L, Hehl R, Nucleic Acids Res 2004 32 368 372 10.1093/nar/gkh017 14681436
    • (2004) Nucleic Acids Res , vol.32 , pp. 4368-4372
    • Steffens, N.O.1    Galuschka, C.2    Schindler, M.3    Bülow, L.4    Hehl, R.5
  • 23
    • 58149200922 scopus 로고    scopus 로고
    • AthaMap, integrating transcriptional and post-transcriptional data
    • 10.1093/nar/gkn709 18842622
    • AthaMap, integrating transcriptional and post-transcriptional data. Bülow L, Engelmann S, Schindler M, Hehl R, Nucleic Acids Res 2009 37 983 986 10.1093/nar/gkn709 18842622
    • (2009) Nucleic Acids Res , vol.37 , pp. 4983-4986
    • Bülow, L.1    Engelmann, S.2    Schindler, M.3    Hehl, R.4
  • 24
    • 24644490196 scopus 로고    scopus 로고
    • Genetics: Elucidation of the small RNA component of the transcriptome
    • DOI 10.1126/science.1114112
    • Elucidation of the small RNA component of the transcriptome. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ, Science 2005 309 1567 1569 10.1126/science.1114112 16141074 (Pubitemid 41266483)
    • (2005) Science , vol.309 , Issue.5740 , pp. 1567-1569
    • Lu, C.1    Tej, S.S.2    Luo, S.3    Haudenschild, C.D.4    Meyers, B.C.5    Green, P.J.6
  • 26
    • 33750440526 scopus 로고    scopus 로고
    • A Two-Hit Trigger for siRNA Biogenesis in Plants
    • DOI 10.1016/j.cell.2006.09.032, PII S009286740601292X
    • A two-hit trigger for siRNA biogenesis in plants. Axtell MJ, Jan C, Rajagopalan R, Bartel DP, Cell 2006 127 565 577 10.1016/j.cell.2006.09.032 17081978 (Pubitemid 44647429)
    • (2006) Cell , vol.127 , Issue.3 , pp. 565-577
    • Axtell, M.J.1    Jan, C.2    Rajagopalan, R.3    Bartel, D.P.4
  • 27
    • 33845688601 scopus 로고    scopus 로고
    • A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    • DOI 10.1101/gad.1476406
    • A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP, Genes Dev 2006 20 3407 3425 10.1101/gad.1476406 17182867 (Pubitemid 44969159)
    • (2006) Genes and Development , vol.20 , Issue.24 , pp. 3407-3425
    • Rajagopalan, R.1    Vaucheret, H.2    Trejo, J.3    Bartel, D.P.4
  • 30
    • 34250717043 scopus 로고    scopus 로고
    • Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting
    • DOI 10.1105/tpc.107.050062
    • Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC, Plant Cell 2007 19 926 942 10.1105/tpc.107.050062 17400893 (Pubitemid 46953238)
    • (2007) Plant Cell , vol.19 , Issue.3 , pp. 926-942
    • Howell, M.D.1    Fahlgren, N.2    Chapman, E.J.3    Cumbie, J.S.4    Sullivan, C.M.5    Givan, S.A.6    Kasschau, K.D.7    Carrington, J.C.8
  • 32
    • 23144456815 scopus 로고    scopus 로고
    • AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana
    • DOI 10.1093/nar/gki395
    • AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. Steffens NO, Galuschka C, Schindler M, Bülow L, Hehl R, Nucleic Acids Res 2005 33 397 402 10.1093/nar/gki395 15980498 (Pubitemid 44529951)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
    • Steffens, N.O.1    Galuschka, C.2    Schindler, M.3    Bulow, L.4    Hehl, R.5
  • 33
    • 33846105271 scopus 로고    scopus 로고
    • AthaMap web tools for the analysis and identification of co-regulated genes
    • DOI 10.1093/nar/gkl1006
    • AthaMap web-tools for the analysis and identification of co-regulated genes. Galuschka C, Schindler M, Bülow L, Hehl R, Nucleic Acids Res 2007 35 857 D862 10.1093/nar/gkl1006 17148485 (Pubitemid 46056322)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Galuschka, C.1    Schindler, M.2    Bulow, L.3    Hehl, R.4
  • 34
    • 33748132234 scopus 로고    scopus 로고
    • MicroRNA promoter element discovery in Arabidopsis
    • DOI 10.1261/rna.130506
    • MicroRNA promoter element discovery in Arabidopsis. Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG, RNA 2006 12 1612 1619 10.1261/rna.130506 16888323 (Pubitemid 44316025)
    • (2006) RNA , vol.12 , Issue.9 , pp. 1612-1619
    • Megraw, M.1    Baev, V.2    Rusinov, V.3    Jensen, S.T.4    Kalantidis, K.5    Hatzigeorgiou, A.G.6
  • 35
    • 42449109504 scopus 로고    scopus 로고
    • Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana
    • DOI 10.1261/rna.895308
    • Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. Liu HH, Tian X, Li YJ, Wu CA, Zheng CC, RNA 2008 14 836 843 10.1261/rna.895308 18356539 (Pubitemid 351574905)
    • (2008) RNA , vol.14 , Issue.5 , pp. 836-843
    • Liu, H.-H.1    Tian, X.2    Li, Y.-J.3    Wu, C.-A.4    Zheng, C.-C.5
  • 36
    • 0347492019 scopus 로고    scopus 로고
    • AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
    • DOI 10.1186/1471-2105-4-25
    • AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E, BMC Bioinforma 2003 4 25 10.1186/1471-2105-4-25 (Pubitemid 38751245)
    • (2003) BMC Bioinformatics , vol.4 , pp. 25
    • Davuluri, R.V.1    Sun, H.2    Palaniswamy, S.K.3    Matthews, N.4    Molina, C.5    Kurtz, M.6    Grotewold, E.7
  • 37
    • 33646907417 scopus 로고    scopus 로고
    • AGRIS and AtRegNet. A platform to link cis-regulatory elements and transcription factors into regulatory networks
    • DOI 10.1104/pp.105.072280
    • AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Palaniswamy SK, James S, Sun H, Lamb RS, Davuluri RV, Grotewold E, Plant Physiol 2006 140 818 829 10.1104/pp.105.072280 16524982 (Pubitemid 43956237)
    • (2006) Plant Physiology , vol.140 , Issue.3 , pp. 818-829
    • Palaniswamy, S.K.1    James, S.2    Sun, H.3    Lamb, R.S.4    Davuluri, R.V.5    Grotewold, E.6
  • 38
    • 60549111213 scopus 로고    scopus 로고
    • PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups
    • 10.1186/1471-2164-9-561 19036138
    • PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. Chang WC, Lee TY, Huang HD, Huang HY, Pan RL, BMC Genomics 2008 9 561 10.1186/1471-2164-9-561 19036138
    • (2008) BMC Genomics , vol.9 , pp. 561
    • Chang, W.C.1    Lee, T.Y.2    Huang, H.D.3    Huang, H.Y.4    Pan, R.L.5
  • 39
    • 28944448612 scopus 로고    scopus 로고
    • Athena: A resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences
    • DOI 10.1093/bioinformatics/bti714
    • Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. O'Connor TR, Dyreson C, Wyrick JJ, Bioinformatics 2005 21 4411 4413 10.1093/bioinformatics/bti714 16223790 (Pubitemid 41782933)
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4411-4413
    • O'Connor, T.R.1    Dyreson, C.2    Wyrick, J.J.3
  • 40
    • 33846061087 scopus 로고    scopus 로고
    • ATTED-II: A database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
    • DOI 10.1093/nar/gkl783
    • ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H, Nucleic Acids Res 2007 35 863 869 10.1093/nar/gkl783 17130150 (Pubitemid 46056323)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Obayashi, T.1    Kinoshita, K.2    Nakai, K.3    Shibaoka, M.4    Hayashi, S.5    Saeki, M.6    Shibata, D.7    Saito, K.8    Ohta, H.9
  • 41
    • 58149197587 scopus 로고    scopus 로고
    • ATTED-II provides coexpressed gene networks for Arabidopsis
    • 10.1093/nar/gkn807 18953027
    • ATTED-II provides coexpressed gene networks for Arabidopsis. Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K, Nucleic Acids Res 2009 37 987 991 10.1093/nar/gkn807 18953027
    • (2009) Nucleic Acids Res , vol.37 , pp. 4987-4991
    • Obayashi, T.1    Hayashi, S.2    Saeki, M.3    Ohta, H.4    Kinoshita, K.5
  • 42
    • 79951562208 scopus 로고    scopus 로고
    • ATTED-II updates: Condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
    • 10.1093/pcp/pcq203 21217125
    • ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Obayashi T, Nishida K, Kasahara K, Kinoshita K, Plant Cell Physiol 2011 52 213 219 10.1093/pcp/pcq203 21217125
    • (2011) Plant Cell Physiol , vol.52 , pp. 213-219
    • Obayashi, T.1    Nishida, K.2    Kasahara, K.3    Kinoshita, K.4


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