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Volumn 57, Issue 1, 2016, Pages e8-

CANTATAdb: A collection of plant long non-coding RNAs

Author keywords

Database; Long non coding RNAs; MicroRNAs; RNA RNA interactions; Splicing

Indexed keywords

LONG UNTRANSLATED RNA; MICRORNA; PLANT RNA;

EID: 84964843315     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcv201     Document Type: Article
Times cited : (130)

References (37)
  • 2
    • 41149112564 scopus 로고    scopus 로고
    • A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition
    • Beltran, M., Puig, I., Peña, C., García, J.M., Alvarez, A.B., Peña, R., et al. (2008) A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev. 22: 756-769.
    • (2008) Genes Dev , vol.22 , pp. 756-769
    • Beltran, M.1    Puig, I.2    Peña, C.3    García, J.M.4    Alvarez, A.B.5    Peña, R.6
  • 3
    • 61449126060 scopus 로고    scopus 로고
    • Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
    • Ben Amor, B., Wirth, S., Merchan, F., Laporte, P., d'Aubenton-Carafa, Y., Hirsch, J., et al. (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res. 19: 57-69.
    • (2009) Genome Res , vol.19 , pp. 57-69
    • Ben Amor, B.1    Wirth, S.2    Merchan, F.3    Laporte, P.4    D'Aubenton-Carafa, Y.5    Hirsch, J.6
  • 4
    • 84869088820 scopus 로고    scopus 로고
    • Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat
    • Carrieri, C., Cimatti, L., Biagioli, M., Beugnet, A., Zucchelli, S., Fedele, S., et al. (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491: 454-457.
    • (2012) Nature , vol.491 , pp. 454-457
    • Carrieri, C.1    Cimatti, L.2    Biagioli, M.3    Beugnet, A.4    Zucchelli, S.5    Fedele, S.6
  • 5
    • 84862209063 scopus 로고    scopus 로고
    • PlantNATsDB: A comprehensive database of plant natural antisense transcripts
    • Chen, D., Yuan, C., Zhang, J., Zhang, Z., Bai, L., Meng, Y., et al. (2012) PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Res. 40: D1187-D1193.
    • (2012) Nucleic Acids Res , vol.40 , pp. D1187-D1193
    • Chen, D.1    Yuan, C.2    Zhang, J.3    Zhang, Z.4    Bai, L.5    Meng, Y.6
  • 7
    • 79959967431 scopus 로고    scopus 로고
    • PsRNATarget: A plant small RNA target analysis server
    • Dai, X. and Zhao, P.X. (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 39: W155-W159.
    • (2011) Nucleic Acids Res , vol.39 , pp. W155-W159
    • Dai, X.1    Zhao, P.X.2
  • 8
    • 84863115947 scopus 로고    scopus 로고
    • A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice
    • Ding, J., Lu, Q., Ouyang, Y., Mao, H., Zhang, P., Yao, J., et al. (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc. Natl. Acad. Sci. USA 109: 2654-2659.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 2654-2659
    • Ding, J.1    Lu, Q.2    Ouyang, Y.3    Mao, H.4    Zhang, P.5    Yao, J.6
  • 9
    • 57149107578 scopus 로고    scopus 로고
    • Differentiating protein-coding and noncoding RNA: Challenges and ambiguities
    • Dinger, M.E., Pang, K.C., Mercer, T.R. and Mattick, J.S. (2008) Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput. Biol. 4: e1000176.
    • (2008) PLoS Comput. Biol , vol.4
    • Dinger, M.E.1    Pang, K.C.2    Mercer, T.R.3    Mattick, J.S.4
  • 10
    • 46749083733 scopus 로고    scopus 로고
    • Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of betasecretase
    • Faghihi, M.A., Modarresi, F., Khalil, A.M., Wood, D.E., Sahagan, B.G., Morgan, T.E., et al. (2008) Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of betasecretase. Nat. Med. 14: 723-730.
    • (2008) Nat. Med , vol.14 , pp. 723-730
    • Faghihi, M.A.1    Modarresi, F.2    Khalil, A.M.3    Wood, D.E.4    Sahagan, B.G.5    Morgan, T.E.6
  • 11
    • 84886252113 scopus 로고    scopus 로고
    • RNA in unexpected places: Long non-coding RNA functions in diverse cellular contexts
    • Geisler, S. and Coller, J. (2013) RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat. Rev. Mol. Cell Biol. 14: 699-712.
    • (2013) Nat. Rev. Mol. Cell Biol , vol.14 , pp. 699-712
    • Geisler, S.1    Coller, J.2
  • 12
    • 79951495822 scopus 로고    scopus 로고
    • LncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 30 UTRs via Alu elements
    • Gong, C. and Maquat, L.E. (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 30 UTRs via Alu elements. Nature 470: 284-288.
    • (2011) Nature , vol.470 , pp. 284-288
    • Gong, C.1    Maquat, L.E.2
  • 13
    • 84880266648 scopus 로고    scopus 로고
    • De novo transcript sequence reconstruction from RNAseq using the Trinity platform for reference generation and analysis
    • Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P.D., Bowden, J., et al. (2013) De novo transcript sequence reconstruction from RNAseq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8: 1494-1512.
    • (2013) Nat. Protoc , vol.8 , pp. 1494-1512
    • Haas, B.J.1    Papanicolaou, A.2    Yassour, M.3    Grabherr, M.4    Blood, P.D.5    Bowden, J.6
  • 14
    • 79957536771 scopus 로고    scopus 로고
    • Encoding memory of winter by noncoding RNAs
    • Heo, J.B. and Sung, S. (2011) Encoding memory of winter by noncoding RNAs. Epigenetics 6: 544-547.
    • (2011) Epigenetics , vol.6 , pp. 544-547
    • Heo, J.B.1    Sung, S.2
  • 15
    • 84888406718 scopus 로고    scopus 로고
    • A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness
    • Jabnoune, M., Secco, D., Lecampion, C., Robaglia, C., Shu, Q.Y. and Poirier, Y. (2013) A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness. Plant Cell 25: 4166-4182.
    • (2013) Plant Cell , vol.25 , pp. 4166-4182
    • Jabnoune, M.1    Secco, D.2    Lecampion, C.3    Robaglia, C.4    Shu, Q.Y.5    Poirier, Y.6
  • 16
    • 84876219082 scopus 로고    scopus 로고
    • PLncDB: Plant long non-coding RNA database
    • Jin, J., Liu, J., Wang, H., Wong, L. and Chua, N.H. (2013) PLncDB: plant long non-coding RNA database. Bioinformatics 29: 1068-1071.
    • (2013) Bioinformatics , vol.29 , pp. 1068-1071
    • Jin, J.1    Liu, J.2    Wang, H.3    Wong, L.4    Chua, N.H.5
  • 19
    • 34547582418 scopus 로고    scopus 로고
    • CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine
    • Kong, L., Zhang, Y., Ye, Z.Q., Liu, X.Q., Zhao, S.Q., Wei, L., et al. (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35: W345-W349.
    • (2007) Nucleic Acids Res , vol.35 , pp. W345-W349
    • Kong, L.1    Zhang, Y.2    Ye, Z.Q.3    Liu, X.Q.4    Zhao, S.Q.5    Wei, L.6
  • 20
    • 0033118515 scopus 로고    scopus 로고
    • Rice ENOD40: Isolation and expression analysis in rice and transgenic soybean root nodules
    • Kouchi, H., Takane, K., So, R.B., Ladha, J.K. and Reddy, P.M. (1999) Rice ENOD40: isolation and expression analysis in rice and transgenic soybean root nodules. Plant J. 18: 121-129.
    • (1999) Plant J , vol.18 , pp. 121-129
    • Kouchi, H.1    Takane, K.2    So, R.B.3    Ladha, J.K.4    Reddy, P.M.5
  • 21
    • 84891818318 scopus 로고    scopus 로고
    • MiRBase: Annotating high confidence microRNAs using deep sequencing data
    • Kozomara, A. and Griffiths-Jones, S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 42: D68-D73.
    • (2014) Nucleic Acids Res , vol.42 , pp. D68-D73
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 22
    • 84859512866 scopus 로고    scopus 로고
    • Non-coding RNAs: Key regulators of mammalian transcription
    • Kugel, J.F. and Goodrich, J.A. (2012) Non-coding RNAs: key regulators of mammalian transcription. Trends Biochem Sci. 37: 144-151.
    • (2012) Trends Biochem Sci , vol.37 , pp. 144-151
    • Kugel, J.F.1    Goodrich, J.A.2
  • 23
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 25
    • 84946013175 scopus 로고    scopus 로고
    • LncRNAdb v2.0: Expanding the reference database for functional long noncoding RNAs
    • Quek, X.C., Thomson, D.W., Maag, J.L., Bartonicek, N., Signal, B., Clark, M.B., et al. (2015) lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res. 43: D168-D173.
    • (2015) Nucleic Acids Res , vol.43 , pp. D168-D173
    • Quek, X.C.1    Thomson, D.W.2    Maag, J.L.3    Bartonicek, N.4    Signal, B.5    Clark, M.B.6
  • 26
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 27
    • 79961170994 scopus 로고    scopus 로고
    • A ceRNA hypothesis: The Rosetta stone of a hidden RNA language?
    • Salmena, L., Poliseno, L., Tay, Y., Kats, L. and Pandolfi, P.P. (2011) A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? Cell 146: 353-358.
    • (2011) Cell , vol.146 , pp. 353-358
    • Salmena, L.1    Poliseno, L.2    Tay, Y.3    Kats, L.4    Pandolfi, P.P.5
  • 29
    • 84884915826 scopus 로고    scopus 로고
    • Utilizing sequence intrinsic composition to classify protein-coding and long noncoding transcripts
    • Sun, L., Luo, H., Bu, D., Zhao, G., Yu, K., Zhang, C., et al. (2013) Utilizing sequence intrinsic composition to classify protein-coding and long noncoding transcripts. Nucleic Acids Res. 41: e166.
    • (2013) Nucleic Acids Res , vol.41 , pp. e166
    • Sun, L.1    Luo, H.2    Bu, D.3    Zhao, G.4    Yu, K.5    Zhang, C.6
  • 30
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-11.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 31
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7: 562-578.
    • (2012) Nat. Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6
  • 32
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: A hub for protein information
    • UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res. 43: D204-D212.
    • (2015) Nucleic Acids Res , vol.43 , pp. D204-D212
    • Consortium, U.1
  • 33
    • 84904310301 scopus 로고    scopus 로고
    • Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light
    • Wang, Y., Fan, X., Lin, F., He, G., Terzaghi, W., Zhu, D., et al. (2014) Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc. Natl. Acad. Sci. USA 111: 10359-10364.
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 10359-10364
    • Wang, Y.1    Fan, X.2    Lin, F.3    He, G.4    Terzaghi, W.5    Zhu, D.6
  • 34
    • 84875750847 scopus 로고    scopus 로고
    • Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants
    • Wu, H.J., Wang, Z.M., Wang, M. and Wang, X.J. (2013) Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol. 161: 1875-1884.
    • (2013) Plant Physiol , vol.161 , pp. 1875-1884
    • Wu, H.J.1    Wang, Z.M.2    Wang, M.3    Wang, X.J.4
  • 35
    • 84891798006 scopus 로고    scopus 로고
    • NONCODEv4: Exploring the world of long non-coding RNA genes
    • Xie, C., Yuan, J., Li, H., Li, M., Zhao, G., Bu, D. et al. (2014) NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res. 42: D98-D103.
    • (2014) Nucleic Acids Res , vol.42 , pp. D98-D103
    • Xie, C.1    Yuan, J.2    Li, H.3    Li, M.4    Zhao, G.5    Al Et, B.D.6
  • 36
    • 84941934451 scopus 로고    scopus 로고
    • PLNlncRbase: A resource for experimentally identified lncRNAs in plants
    • Xuan, H., Zhang, L., Liu, X., Han, G., Li, J., Li, X., et al. (2015) PLNlncRbase: a resource for experimentally identified lncRNAs in plants. Gene 573: 328-332.
    • (2015) Gene , vol.573 , pp. 328-332
    • Xuan, H.1    Zhang, L.2    Liu, X.3    Han, G.4    Li, J.5    Li, X.6
  • 37
    • 84941107874 scopus 로고    scopus 로고
    • PNRD: A plant noncoding RNA database
    • Yi, X., Zhang, Z., Ling, Y., Xu, W. and Su, Z. (2015) PNRD: a plant noncoding RNA database. Nucleic Acids Res. 43: D982-D989.
    • (2015) Nucleic Acids Res , vol.43 , pp. D982-D989
    • Yi, X.1    Zhang, Z.2    Ling, Y.3    Xu, W.4    Su, Z.5


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