CoRAL: Predicting non-coding RNAs from small RNA-sequencing data

Nucleic Acids Research

Volumn 41, Issue 14, 2013, Pages

  Leung, Yuk Yee ^a   Ryvkin, Paul ^a   Ungar, Lyle H ^a,b   Gregory, Brian D ^a,c   Wang, Li San ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; SMALL NUCLEAR RNA; UNTRANSLATED RNA;

ACCESS TO INFORMATION; ACCURACY; ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; HUMAN; HUMAN TISSUE; INTERNET; MACHINE LEARNING; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RNA ANALYSIS; RNA CLEAVAGE; RNA SEQUENCE; RNA STRUCTURE; TRANSPOSON;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CLASSIFICATION; HUMANS; RNA, SMALL UNTRANSLATED; SEQUENCE ANALYSIS, RNA;

EID: 84881516445     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt426     Document Type: Article

References (29)

1. Eddy S.R. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet., 2, 919-929
2. Todd G. and Karbstein K. (2007) RNA takes center stage. Biopolymers, 87, 275-278
3. Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser D., Huarte M., Zuk O., Carey B.W., Cassady J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227
4. Khalil A.M., Guttman M., Huarte M., Garber M., Raj A., Rivea Morales D., Thomas K., Presser A., Bernstein B.E., Van Oudenaarden A. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. U.S.A., 106, 11667-11672
5. Black D.L., Chabot B. and Steitz J.A. (1985) U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing. Cell, 42, 737-750
6. Maxwell E.S. and Fournier M.J. (1995) The small nucleolar RNAs. Annu. Rev. Biochem., 64, 897-934
7. Carninci P., Yasuda J. and Hayashizaki Y. (2008) Multifaceted mammalian transcriptome. Curr. Opin. Cell Biol., 20, 274-280
8. Bu D., Yu K., Sun S., Xie C., Skogerbø G., Miao R., Xiao H., Liao Q., Luo H., Zhao G. et al. (2012) NONCODE v3.0: Integrative annotation of long noncoding RNAs. Nucleic Acids Res., 40, D210-D215
9. Landgraf P., Rusu M., Sheridan R., Sewer A., Iovino N., Aravin A., Pfeffer S., Rice A., Kamphorst A.O., Landthaler M. et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 129, 1401-1414
10. Friedlä nder M.R., Mackowiak S.D., Li N., Chen W. and Rajewsky N. (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res., 40, 37-52
11. Langenberger D., Bermudez-Santana C.I., Stadler P.F. and Hoffmann S. (2010) Identification and classification of small rnas in transcriptome sequence data. Pac. Symp. Biocomput., 2010, 80-87
12. Fasold M., Langenberger D., Binder H., Stadler P.F. and Hoffmann S. (2011) DARIO: A ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 39, W112-W117
13. Erhard F. and Zimmer R. (2010) Classification of ncRNAs using position and size information in deep sequencing data. Bioinformatics, 26, i426-i432
14. Li F., Ryvkin P., Childress D.M., Valladares O., Gregory B.D. and Wang L-S. (2012) SAVoR: A server for sequencing annotation and visualization of RNA structures. Nucleic Acids Res., 40, W59-W64
15. Joyce C.E., Zhou X., Xia J., Ryan C., Thrash B., Menter A., Zhang W. and Bowcock A.M. (2011) Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome. Hum. Mol. Genet., 20, 4025-4040
16. Faghihi M.A., Zhang M., Huang J., Modarresi F., Van der Brug M.P., Nalls M.A., Cookson M.R., St-Laurent G. III and Wahlestedt C. (2010) Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol., 11, R56
17. Martin M. (2011) Cutadapt removes adapter sequences from high-Throughput sequencing reads. EMBnet J., 17, 10-12
18. 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
19. Habegger L., Sboner A., Gianoulis T.A., Rozowsky J., Agarwal A., Snyder M. and Gerstein M. (2011) RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics, 27, 281-283
20. Fujita P.A., Rhead B., Zweig A.S., Hinrichs A.S., Karolchik D., Cline M.S., Goldman M., Barber G.P., Clawson H., Coelho A. et al. (2011) The UCSC Genome Browser database: Update 2011. Nucleic Acids Res., 39, D876-D882
21. Bartel D.P. (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-297
22. Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer L.S., Tacker M. and Schuster P. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125, 167-188
23. Díaz-Uriarte R. and De Andres S.A. (2006) Gene selection and classification of microarray data using random forest. BMC Bioinformatics, 7, 3
24. Statnikov A., Wang L. and Aliferis C.F. (2008) A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification. BMC Bioinformatics, 9, 319
25. Cabili M.N., Trapnell C., Goff L., Koziol M., Tazon-Vega B., Regev A. and Rinn J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927
26. Tiedge H., Chen W. and Brosius J. (1993) Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. J. Neurosci., 13, 2382-2390
27. Ebhardt H.A., Tsang H.H., Dai D.C., Liu Y., Bostan B. and Fahlman R.P. (2009) Meta-Analysis of small RNA-sequencing errors reveals ubiquitous post-Transcriptional RNA modifications. Nucleic Acids Res., 37, 2461-2470
28. Verhagen A.P.M. and Pruijn G.J.M. (2011) Are the Ro RNP-Associated Y RNAs concealing microRNAs? Y RNA-derived miRNAs may be involved in autoimmunity. BioEssays, 33, 674-682
29. Menzel P., Gorodkin J. and Stadler P.F. (2009) The tedious task of finding homologous noncoding RNA genes. RNA, 15, 2075-2082