Methods to detect transcribed pseudogenes: Rna-seq discovery allows learning through features

Methods in Molecular Biology

Volumn 1167, Issue , 2014, Pages 157-183

  Valdes, Camilo ^a   Capobianco, Enrico ^a,b  

^a UNIVERSITY OF MIAMI   (United States)

^b INSTITUTE OF CLINICAL PHYSIOLOGY   (Italy)

Author keywords

Feature matrix; Predictive inference; Pseudogenes; RNA Seq; Transcriptomes

Indexed keywords

TRANSCRIPTOME; UNTRANSLATED RNA;

ARTICLE; GENE CONTROL; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; MACHINE LEARNING; PRIORITY JOURNAL; PSEUDOGENE; REPRODUCIBILITY; RNA SEQUENCE; BIOLOGY; BRAIN; GENETICS; GENOMICS; METABOLISM; NUCLEIC ACID DATABASE; PROCEDURES; SEQUENCE ANALYSIS;

BRAIN; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENOMICS; HUMANS; PSEUDOGENES; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84922309101     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0835-6_11     Document Type: Article

References (32)

1. Tang F, Lao K, Surani MA (2011) Development and applications of single cell transcriptome analysis. Nat Methods 8(4 Suppl):S6–S11
2. Jacquier A (2009) The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 10(12):833–844
3. Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ et al (2011) The reality of pervasive transcription. PLoS Biol 9(7):e1000625
4. Huarte M, Rinn JL (2010) Large non-coding RNAs: missing links in cancer? Hum Mol Genet 19(2):R152–R161
5. Ponjavic J, Ponting CP, Lunter G (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 17(5):556–565
6. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235): 223–227
7. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106(28):11667–11672
8. Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143(1):46–58
9. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
10. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63
11. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantifi cation by RNA-Seq reveals unanno-tated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511–515
12. Balakirev L, Ayala F (2003) Pseudogenes: are they “junk” or functional DNA? Annu Rev Genet 37:123–151
13. Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei C-L, Thomas R, Gingeras TR, Guigó R, Harrow J, Gerstein MB (2007) Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 17(6):839–851
14. Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu JX, Harte R, Balasubramanian S, Tanzer A, Mark Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB (2012) The GENCODE pseudogene resource. Genome Biol 13:R51
15. Kalyana-Sundaram S et al (2012) Expressed pseudogenes in the transcriptional landscape of human cancers. Cell 149(7):1622–1634
16. Muro EM, Mah N, Andrade-Navarro MA (2011) Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie 93(11):1916–1921
17. Poliseno L (2012) Pseudogenes: newly discovered players in human cancer. Sci Signal 5(242):re5
18. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26(4):493–500
19. Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A (2011) Differential expression in RNA-seq: a matter of depth. Genome Res 21(12):2213–2223
20. Rung J, Brazma A (2013) Reuse of public genome-wide expression data. Nat Rev Genet 14(2):89–99
21. Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M (2006) PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics 22(12):1437–1439
22. van Baren MJ, Brent MR (2006) Iterative gene prediction and pseudogene removal improves genome annotation. Genome Res 16(5):678–685
23. Lam HYK, Khurana E, Fang G, Cayting P, Carriero N, Cheung K-H, Gerstein M (2009) Pseudofam: the pseudogene families database. Nucl Acids Res 37(Suppl 1):D738–D743
24. Kang HJ et al (2011) Spatio-temporal tran-scriptome of the human brain. Nature 478(7370):483–489
25. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12(10): 671–682
26. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantifi cation by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515
27. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A (2010) Ab initio reconstruction of cell type-specifi c transcriptomes in mouse reveals the conserved multi-exonic structure of lin-cRNAs. Nat Biotechnol 28(5):503–510
28. Robertson G et al (2010) De novo assembly and analysis of RNA-seq data. Nat Meth 7(11):909–912
29. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18(9):1509–1517, Date published
30. Licatalosi DD, Darnell RB (2010) RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 11(1): 75–87
31. Flicek P et al (2013) Ensembl 2013. Nucleic Acids Res 41(Database):D48–D55
32. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111