PLncDB: Plant long non-coding RNA database

Bioinformatics

Volumn 29, Issue 8, 2013, Pages 1068-1071

  Jin, Jingjing ^a,b   Liu, Jun ^a   Wang, Huan ^a   Wong, Limsoon ^b   Chua, Nam Hai ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS;

LONG UNTRANSLATED RNA; PLANT RNA; SMALL INTERFERING RNA;

ARABIDOPSIS; ARTICLE; GENE EXPRESSION PROFILING; GENE LOCUS; GENETIC EPIGENESIS; GENETICS; GENOMICS; METABOLISM; NUCLEIC ACID DATABASE; PLANT GENOME;

ARABIDOPSIS; DATABASES, NUCLEIC ACID; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENETIC LOCI; GENOME, PLANT; GENOMICS; RNA, LONG UNTRANSLATED; RNA, PLANT; RNA, SMALL INTERFERING;

EID: 84876219082     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt107     Document Type: Review

References (37)

1. Amaral, P.P. et al. (2011) lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res., 39, D146-D151.
2. Boerner, S. and McGinnis, K.M. (2012) Computational identification and functional predictions of long noncoding RNA in Zea mays. PLoS One, 7, e43047.
3. Bu, D. et al. (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res., 40, D210-D215.
4. Cabianca, D.S. et al. (2012) A long ncRNA links copy number variation to a poly- comb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell, 149, 819-831.
5. Cabili, M.N. et al. (2011) Integrative annotation of human large intergenic noncod- ing RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
6. Chen, D. et al. (2012) PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Res., 40, D1187-D1193.
7. Dinger, M.E. et al. (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res., 18, 1433-1445.
8. Dinger, M.E. et al. (2009) NRED: a database oflong noncoding RNA expression. Nucleic Acids Res., 37, D122-D126.
9. Gerhard, D.S. et al. (2004) The status, quality, and expansion of theNIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res., 14, 2121-2127.
10. Gupta, R.A. et al. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 464, 1071-1076.
11. Guttman, M. et al. (2009) Chromatin signature reveals over a thousand highly con- served large non-coding RNAs in mammals. Nature, 458, 223-227.
12. Hu, W. et al. (2011) Long noncoding RNA-mediated anti-apoptotic activity in murine erythroid terminal differentiation. Genes Dev., 25, 2573-2578.
13. Kent, WJ. et al. (2010) BigWig and BigBed: enabling browsing oflarge distributed datasets. Bioinformatics, 26, 2204-2207.
14. Khalil, A.M. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA, 106, 11667-11672.
15. Liao, Q. et al. (2011a) Large-scale prediction oflong non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res., 39, 3864-3878.
16. Liao, Q. et al. (2011b) ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res., 39, W118-W124.
17. Liu, J. et al. (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell, 24, 4333-4345.
18. Luo, Q.J. et al. (2009) Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis. PLoS Genet., 5, e1000457.
19. MacIntosh, G.C. et al. (2001) Identification and analysis of Arabidopsis ex- pressed sequence tags characteristic ofnon-coding RNAs. Plant Physiol., 127, 765-776.
20. Managadze, D. et al. (2011) Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol. Evol., 3, 1390-1404.
21. Marker, C. et al. (2002) Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr Biol., 12, 2002-2013.
22. Matsui, A. et al. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol., 49, 1135-1149.
23. Oh, S. et al. (2008) Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet., 4, e1000077.
24. Rymarquis, L.A. et al. (2008) Diamonds in the rough: mRNA-like non-coding RNAs. Trends Plant Sci., 13, 329-334.
25. Song, D. et al. (2009) Computational prediction of novel non-coding RNAs in Arabidopsis thaliana. BMC Bioinformatics, 10 (Suppl. 1), S36.
26. Stein, L.D. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.
27. Swarbreck, D. et al. (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res., 36, D1009-D1014.
28. Tupy, J.L. et al. (2005) Identification of putative noncoding polyadenylated tran- scripts in Drosophilamelanogaster. Proc. Natl. Acad. Sci. USA, 102, 5495-5500.
29. Wang, XJ. et al. (2005) Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol., 6, R30.
30. Wang, H. et al. (2006) Prediction oftrans-antisense transcripts in Arabidopsis thali- ana. Genome Biol., 7, R92.
31. Wang, H. et al. (2011) Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J., 67, 292-304.
32. Wen, J. et al. (2007) In Silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula. In Silico Biol., 7, 485-505.
33. Wilusz, J.E. et al. (2009) Long noncoding RNAs: functional surprises from the RNA world. GenesDev., 23, 1494-1504.
34. Xin, M. et al. (2011) Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol., 11, 61.
35. Zhang, X. et al. (2009) Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol., 10, R62.
36. Zhang, Y. et al. (2010) ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs. RNA, 16, 1889-1901.
37. Zhang, X. et al. (2012) Genome-wide analysis ofplant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol., 13, R20.