The identification and characterization of novel transcripts from RNA-seq data

Briefings in Bioinformatics

Volumn 17, Issue 4, 2016, Pages 678-685

  Weirick, Tyler ^a   Militello, Giuseppe ^a   Müller, Raphael ^a   John, David ^a   Dimmeler, Stefanie ^a   Uchida, Shizuka ^a  

^a Institute of Cardiovascular Regeneration (Uchida Lab)   (Germany)

Author keywords

Gene expression; lncRNA; Novel transcripts; RNA seq; Transcriptome assembly

Indexed keywords

RNA; TRANSCRIPTOME;

GENETICS; HIGH THROUGHPUT SEQUENCING; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

BASE SEQUENCE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; RNA; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84991401479     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbv067     Document Type: Article

References (17)

1. Uchida S, Dimmeler S. Long noncoding RNAs in cardiovascular diseases. Circ Res 2015;116:737-50.
2. Uchida S, Gellert P, Braun T. Deeply dissecting stemness: making sense to non-coding RNAs in stem cells. Stem Cell Rev 2012;8:78-86.
3. Ezkurdia I, Juan D, Rodriguez JM, et al. Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes. Hum Mol Genet 2014;23:5866-78.
4. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25:1105-11.
5. Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010;28:511-15.
6. Iyer MK, Niknafs YS, Malik R, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 2015;47:199-208.
7. Sun L, Zhang Z, Bailey TL, et al. Prediction of novel long noncoding RNAs based on RNA-Seq data of mouse Klf1 knockout study. BMC Bioinformatics 2012;13:331.
8. Wang L, Park HJ, Dasari S, et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res 2013;41:e74.
9. Nielsen MM, Tehler D, Vang S, et al. Identification of expressed and conserved human noncoding RNAs. RNA 2014;20:236-51.
10. Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621-8.
11. Bidichandani SI, Ashizawa T, Patel PI. The GAA triplet-repeat expansion in Friedreich ataxia interferes with transcription and may be associated with an unusual DNA structure. Am J Hum Genet 1998;62:111-21.
12. Hasler J, Strub K. Alu elements as regulators of gene expression. Nucleic Acids Res 2006;34:5491-7.
13. Belan E. LINEs of evidence: noncanonical DNA replication as an epigenetic determinant. Biol Direct 2013;8:22.
14. McCarthy EM, McDonald JF. Long terminal repeat retrotransposons of Mus musculus. Genome Biol 2004;5:R14.
15. Xie C, Yuan J, Li H, et al. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 2014;42:D98-103.
16. Rollins RA, Haghighi F, Edwards JR, et al. Large-scale structure of genomic methylation patterns. Genome Res 2006;16:157-63.
17. Matylla-Kulinska K, Tafer H, Weiss A, et al. Functional repeatderived RNAs often originate from retrotransposonpropagated ncRNAs. Wiley Interdiscip Rev RNA 2014;5:591-600.