Differential expression in RNA-seq: A matter of depth

Genome Research

Volumn 21, Issue 12, 2011, Pages 2213-2223

  Tarazona, Sonia ^a,b   García Alcalde, Fernando ^a   Dopazo, Joaquín ^a   Ferrer, Alberto ^b   Conesa, Ana ^a  

^a CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^b UNIVERSITAT POLITÈCNICA DE VALÈNCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOTYPE; DATA ANALYSIS SOFTWARE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; HUMAN; METHODOLOGY; PRIORITY JOURNAL; RNA SEQUENCE; SIGNAL NOISE RATIO; TRANSCRIPTOMICS;

ALGORITHMS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 83055192078     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.124321.111     Document Type: Article

References (38)

1. Anders S. 2010. Htseq: analysing high-throughput sequencing data with python. http://www-huber.embl.de/users/anders/HTSeq/.
2. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106. doi: 10.1186/gb-2010-11-10-r106.
3. Anderson J. 2005. RNA turnover: unexpected consequences of being tailed. Curr Biol 15: R635-R638. (Pubitemid 41187481)
4. Argout X, Salse J, Aury J, Guiltinan M, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova S, et al. 2010. The genome of Theobroma cacao. Nat Genet 43: 101-108.
5. Blencowe BJ, Ahmad S, Lee LJ. 2009. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev 23: 1379-1386.
6. Bloom J, Khan Z, Kruglyak L, Singh M, Caudy A. 2009. Measuring differential gene expression by short read sequencing: quantitative comparison to two-channel gene expression microarrays. BMC Genomics 10: 221. doi: 10.1186/1471-2164-10-221.
7. Bullard JH, Purdom E, Hansen KD, Dudoit S. 2010. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11: 94. doi: 10.1186/1471-2164-10- 221.
8. Carninci P, Kasukawa T, Katayama S, Gough J, Frith M, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
9. Davis J, Goadrich M. 2006. The relationship between precision-recall and ROC curves. In Proceedings of the 23rd International Conference onMachine Learning, pp. 233-240. ACM, New York.
10. Durbin RM, Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Collins FS, De La Vega FM, Donnelly P, et al. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
11. Flicek P, Amode M, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, et al. 2011. Ensembl 2011. Nucleic Acids Res 39: D800-D806.
12. Graveley B, Brooks A, Carlson J, Duff M, Landolin J, Yang L, Artieri C, van Baren M, Boley N, Booth B, et al. 2010. The developmental transcriptome of Drosophila melanogaster. Nature 471: 473-479.
13. Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, TangMJ, Hou YC, Pugh TJ, et al. 2010. Alternative expression analysis by RNA sequencing. Nat Methods 7: 843-847.
14. Grzechnik P, Kufel J. 2008. Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast. Mol Cell 32: 247-258.
15. Hardcastle T, Kelly K. 2010. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11: 422. doi: 10.1186/1471-2105-11-422.
16. Illumina. 2009. Preparing samples for sequencing mRNA. http://icom.illumina.com/.
17. Kim V, Han J, Siomi M. 2009. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10: 126-139.
18. Leinonen R, Sugawara H, Shumway M. 2011. The sequence read archive. Nucleic Acids Res 39: D19-D21.
19. Lemay J, D'Amours A, Lemieux C, Lackner D, St-Sauveur V, Bähler J, Bachand F. 2010. The nuclear poly (A)-binding protein interacts with the exosome to promote synthesis of noncoding small nucleolar RNAs. Mol Cell 37: 34-45.
20. Li N, Ye M, Li Y, Yan Z, Butcher L, Sun J, Han X, Chen Q, Zhang X,Wang J. 2010. Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods 52: 203-212.
21. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, et al. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469: 529-533.
22. 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: 1509-1517.
23. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
24. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. (Pubitemid 351929471)
25. Oshlack A, Wakefield M. 2009. Transcript length bias in RNA-seq data confounds systems biology. Biol Direct 4: 14. doi: 10.1186/1745-6150-4- 14.
26. Oshlack A, Robinson M, Young M. 2010. From RNA-seq reads to differential expression results. Genome Biol 11: 220. doi: 10.1186/gb-2010-11-12- 220.
27. Park P. 2009. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
28. Robinson MD, Oshlack A. 2010. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11: R25. doi: 10.1186/gb-2010-11-3-r25.
29. Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
30. Shi L, Reid L, Jones W, Shippy R, Warrington J, Baker S, Collins P, De Longueville F, Kawasaki E, Lee K, et al. 2006. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24: 1151-1161. (Pubitemid 44359727)
31. Slomovic S, Laufer D, Geiger D, Schuster G. 2006. Polyadenylation of ribosomal RNA in human cells. Nucleic Acids Res 34: 2966-2975. (Pubitemid 44540424)
32. Srivastava S, Chen L. 2010. A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Res 38: e170. doi: 10.1093/nar/gkq670.
33. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, et al. 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
34. Trapnell C, Pachter L, Salzberg S. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
35. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
36. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, et al. 2010. The genome of the domesticated apple (Malus domestica Borkh). Nat Genet 42: 833-839.
37. Young MD, Wakefield MJ, Smyth GK, Oshlack A. 2010. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11: R14. doi: 10.1186/gb-2010-11-2-r14.
38. Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo S, Lu Y, Denoeud F, Antonarakis S, Snyder M, et al. 2007. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 17: 839-851. (Pubitemid 46919719)