Differential analysis of gene regulation at transcript resolution with RNA-seq

Nature Biotechnology

Volumn 31, Issue 1, 2013, Pages 46-53

  Trapnell, Cole ^a,b   Hendrickson, David G ^a,b   Sauvageau, Martin ^a,b   Goff, Loyal ^a,b,c   Rinn, John L ^a,b   Pachter, Lior ^d  

^a Harvard University   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CYCLE; DIFFERENTIAL ANALYSIS; EXPRESSION LEVELS; HELA CELL; HIGH-THROUGHPUT; HIGH-THROUGHPUT TECHNOLOGIES; ISOFORMS; KEY REGULATORS; RNA SEQUENCING;

BIOLOGICAL ORGANS; CELL CULTURE; FIBROBLASTS; GENES; TRANSCRIPTION FACTORS;

RNA;

TRANSCRIPTION FACTOR HOXA10; TRANSCRIPTOME;

ALGORITHM; ARTICLE; CELL CYCLE PROGRESSION; CELL SURVIVAL; CELL VIABILITY; CUTDIFF 2; DNA BINDING; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HELA CELL; HUMAN; HUMAN CELL; LUNG FIBROBLAST; PRIORITY JOURNAL; RNA SEQUENCE; RNA SPLICING;

FIBROBLASTS; GENE EXPRESSION REGULATION; HELA CELLS; HOMEODOMAIN PROTEINS; HUMANS; LUNG; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS;

EID: 84872198346     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2450     Document Type: Article

References (50)

1. Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613-619 (2008 (Pubitemid 351911866)
2. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621-628 (2008 (Pubitemid 351911867)
3. Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010
4. Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010
5. Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M. Gilad, Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509-1517 (2008
6. Fu, X. et al. Estimating accuracy of RNA-seq and microarrays with proteomics. BMC Genomics 10, 161 (2009
7. Graveley, B.R. et al. The developmental transcriptome of Drosophila melanogaster. Nature 471, 473-479 (2011
8. Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68-73 (2011
9. Pickrell, J.K. et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768-772 (2010
10. Montgomery, S.B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773-777 (2010
11. Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008 (Pubitemid 352759009)
12. Pan, Q., Shai, O., Lee, L.J., Frey, B.J. Blencowe, B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413-1415 (2008
13. Jiang, H. & Wong, W.H. Statistical inferences for isoform expression in RNA-seq. Bioinformatics 25, 1026-1032 (2009
14. Katz, Y., Wang, E.T., Airoldi, E.M. & Burge, C.B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009-1015 (2010
15. Nicolae, M., Mangul, S., Mandoiu, I.I. & Zelikovsky, A. Estimation of alternative splicing isoform frequencies from RNA-seq data. Algorithms Mol. Biol. 6, 9 (2011
16. Lee, S. et al. Accurate quantification of transcriptome from RNA-seq data by effective length normalization. Nucleic Acids Res. 39, e9 (2011
17. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010
18. Langmead, B., Hansen, K.D. & Leek, J.T. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 11, R83 (2010
19. Oshlack, A., Robinson, M.D. & Young, M.D. From RNA-seq reads to differential expression results. Genome Biol. 11, 220 (2010
20. Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010
21. Wang, L., Feng, Z., Wang, X., Wang, X. & Zhang, X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26, 136-138 (2010
22. Hardcastle, T.J. & Kelly, K.A. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11, 422 (2010
23. Griffith, M. et al. Alternative expression analysis by RNA sequencing. Nat. Methods 7, 843-847 (2010
24. Glaus, P., Honkela, A. & Rattray, M. Identifying differentially expressed transcripts from RNA-seq data with biological variation. Bioinformatics 28, 1721-1728 (2012
25. Anders, S., Reyes, A. & Huber, W. Detecting differential usage of exons from RNA-seq data. Genome Res. 22, 2008-2017 (2012
26. Pearson, J.C., Lemons, D. & McGinnis, W. Modulating Hox gene functions during animal body patterning. Nat. Rev. Genet. 6, 893-904 (2005 (Pubitemid 41782157)
27. Xi, W., WU, Z. & Zhang, X. Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq. J. Bioinform. Comput. Biol. 08, 177 (2010
28. Tarazona, S., García-Alcalde, F., Dopazo, J., Ferrer, A. & Conesa, A. Differential expression in RNA-seq: a matter of depth. Genome Res. 21, 2213-2223 (2011
29. Hiller, D., Jiang, H., Xu, W. & Wong, W.H. Identifiability of isoform deconvolution from junction arrays and RNA-seq. Bioinformatics 25, 3056-3059 (2009
30. Roberts, A., Trapnell, C., Donaghey, J., Rinn, J.L. & Pachter, L. Improving RNA-seq expression estimates by correcting for fragment bias. Genome Biol. 12, R22 (2011
31. Rinn, J.L., Bondre, C., Gladstone, H.B., Brown, P.O. & Chang, H.Y. Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet. 2, e119 (2006
32. Wu, J.Q. et al. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc. Natl. Acad. Sci. USA 107, 5254-5259 (2010
33. Cabili, M.N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. (2011
34. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550 (2005 (Pubitemid 41528093)
35. Morgan, D.O. & Morgan, D.O. Cyclin-dependent kinases: engines, clocks, and microprocessors. Annu. Rev. Cell Dev. Biol. 13, 261-291 (1997 (Pubitemid 28034527)
36. Liu, S. et al. Structural analysis of human Orc6 protein reveals a homology with transcription factor TFIIB. Proc. Natl. Acad. Sci. USA 108, 7373-7378 (2011
37. Dhar, S.K. & Dhar, S.K. Identification and characterization of the human ORC6 homolog. J. Biol. Chem. 275, 34983-34988 (2000
38. Guillamot, M. et al. Cdc14b regulates mammalian RNA polymerase II and represses cell cycle transcription. Scientific Reports 1, 189 (2011
39. Washkowitz, A.J., Gavrilov, S., Begum, S. & Papaioannou, V.E. Diverse functional networks of Tbx3 in development and disease. Wiley Interdisciplinary Rev. Syst. Biol. Med. 4, 273-283 (2012
40. Wilson, V., Wilson, V., Conlon, F.L. & Conlon, F.L. The T-box family. Genome Biol. 3, S3008 (2002
41. Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012
42. Bradley, R.K., Merkin, J., Lambert, N.J. & Burge, C.B. Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol. 10, e1001229 (2012
43. Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007 (Pubitemid 46906620)
44. Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007 (Pubitemid 47206934)
45. Crawford, G.E. et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16, 123-131 (2006 (Pubitemid 43048941)
46. Giresi, P.G. & Lieb, J.D. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (formaldehyde assisted isolation of regulatory elements). Methods 48, 233-239 (2009
47. Fullwood, M.J. et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462, 58-64 (2009
48. Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939-953 (2010
49. Licatalosi, D.D. et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456, 464-469 (2008 (Pubitemid 352759008)
50. Wang, E.T. et al. Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 150, 710-724 (2012)