Flexible expressed region analysis for RNA-seq with derfinder

Nucleic Acids Research

Volumn 45, Issue 2, 2017, Pages e9-

  Collado Torres, Leonardo ^a,b,c   Nellore, Abhinav ^a,b   Frazee, Alyssa C ^a,b   Wilks, Christopher ^b   Love, Michael I ^d,e   Langmead, Ben ^a,b   Irizarry, Rafael A ^d,e   Leek, Jeffrey T ^a,b   Jaffe, Andrew E ^a,b,c  

^a JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^b Johns Hopkins University   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

^d HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^e HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DIFFERENTIALLY EXPRESSED REGION; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; NUCLEIC ACID STRUCTURE; RNA SEQUENCE; SEQUENCE ANALYSIS; SIMULATION; SOFTWARE; STATISTICAL MODEL; ANTIBODY SPECIFICITY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; PROCEDURES; WEB BROWSER;

TRANSCRIPTOME;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; ORGAN SPECIFICITY; SOFTWARE; TRANSCRIPTOME; WEB BROWSER;

EID: 85014052295     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw852     Document Type: Article

References (47)

1. Farrell,C.M., O'Leary,N.A., Harte,R.A., Loveland,J.E., Wilming,L.G., Wallin,C., Diekhans,M., Barrell,D., Searle,S. M.J., Aken,B. et al. (2014) Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res., 42, D865-D872.
2. GTEx Consortium (2013) The Genotype-Tissue Expression (GTEx) project. Nat. Genet., 45, 580-585.
3. GTEx Consortium (2015) Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science, 348, 648-660.
4. ENCODE Project Consortium, Bernstein,B.E., Birney,E., Dunham,I., Green,E.D., Gunter,C. and Snyder,M. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
5. Lappalainen,T., Sammeth,M., Friedländer,M.R., 't Hoen,P.A.C., Monlong,J., Rivas,M.A., Gonzàlez-Porta,M., Kurbatova,N., Griebel,T., Ferreira,P.G. et al. (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature, 501, 506-511.
6. Dillman,A.A., Hauser,D.N., Gibbs,J.R., Nalls,M.A., McCoy,M.K., Rudenko,I.N., Galter,D. and Cookson,M.R. (2013) mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex. Nat. Neurosci., 16, 499-506.
7. Daines,B., Wang,H., Wang,L., Li,Y., Han,Y., Emmert,D., Gelbart,W., Wang,X., Li,W., Gibbs,R. et al. (2011) The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res., 21, 315-324.
8. Steijger,T., Abril,J.F., Engström,P.G., Kokocinski,F., Abril,J.F., Akerman,M., Alioto,T., Ambrosini,G., Antonarakis,S.E., RGASP Consortium et al. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods, 10, 1177-1184.
9. Anders,S., Pyl,P.T. and Huber,W. (2015) HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169.
10. Robinson,M.D., McCarthy,D.J. and Smyth,G.K. (2010) edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
11. Anders,S. and Huber,W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
12. McCarthy,D.J., Chen,Y. and Smyth,G.K. (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res., 40, 4288-4297.
13. Liao,Y., Smyth,G.K. and Shi,W. (2014) featureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30, 923-930.
14. Love,M.I., Huber,W. and Anders,S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 1-21.
15. Ritchie,M.E., Phipson,B., Wu,D., Hu,Y., Law,C.W., Shi,W. and Smyth,G.K. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, e47.
16. Smyth,G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, 1-25.
17. Law,C.W., Chen,Y., Shi,W. and Smyth,G.K. (2014) Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol., 15, R29.
18. Zhou,X., Lindsay,H. and Robinson,M.D. (2014) Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Res., 42, e91.
19. Frazee,A.C., Sabunciyan,S., Hansen,K.D., Irizarry,R.A. and Leek,J.T. (2014) Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics, 15, 413-426.
20. Jaffe,A.E., Shin,J., Collado-Torres,L., Leek,J.T., Tao,R., Li,C., Gao,Y., Jia,Y., Maher,B.J., Hyde,T.M. et al. (2015) Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nat. Neurosci., 18, 154-161.
21. BrainSpan Atlas of the Developing Human Brain (2011) Funded by ARRA Awards 1RC2MH089921-01, 1RC2MH090047-01, and 1RC2MH089929-01, http://www.brainspan.org/.
22. Frazee,A.C., Pertea,G., Jaffe,A.E., Langmead,B., Salzberg,S.L. and Leek,J.T. (2015) Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat. Biotechnol., 33, 243-246.
23. Pertea,M., Pertea,G.M., Antonescu,C.M., Chang,T.-C., Mendell,J.T. and Salzberg,S.L. (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol., 33, 290-295.
24. Rainer,J. (2015) EnsDb.Hsapiens.v75: Ensembl based annotation package. R package version 0.99.12, http://bioconductor.org/packages/EnsDb.Hsapiens.v75.
25. Falcon,S. and Gentleman,R. (2007) Using GOstats to test gene lists for GO term association. Bioinformatics, 23, 257-258.
26. Nellore,A., Collado-Torres,L., Jaffe,A. E., Alquicira-Hernández,J., Wilks,C., Pritt,J., Morton,J., Leek,J.T. and Langmead,B. (2016) Rail-RNA: Scalable analysis of RNA-seq splicing and coverage. Bioinformatics, btw575.
27. Lawrence,M., Huber,W., Pagès,H., Aboyoun,P., Carlson,M., Gentleman,R., Morgan,M. and Carey,V. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput. Biol., 9, e1003118.
28. Frazee,A.C., Jaffe,A.E., Langmead,B. and Leek,J.T. (2015) Polyester: simulating RNA-seq datasets with differential transcript expression. Bioinformatics, 31, 2778-2784.
29. Kim,D., Langmead,B. and Salzberg,S.L. (2015) HISAT: A fast spliced aligner with low memory requirements. Nat. Methods, 12, 357-360.
30. Kim,D., Pertea,G., Trapnell,C., Pimentel,H., Kelley,R. and Salzberg,S.L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, R36.
31. Kent,W.J., Zweig,A.S., Barber,G., Hinrichs,A.S. and Karolchik,D. (2010) BigWig and BigBed: Enabling browsing of large distributed datasets. Bioinformatics, 26, 2204-2207.
32. Li,H., Handsaker,B., Wysoker,A., Fennell,T., Ruan,J., Homer,N., Marth,G., Abecasis,G., Durbin,R. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
33. Jaffe,A.E., Murakami,P., Lee,H., Leek,J.T., Fallin,M.D., Feinberg,A.P. and Irizarry,R.A. (2012) Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int. J. Epidemiol., 41, 200-209.
34. Selcen,D. and Engel,A.G. (2005) Mutations in ZASP define a novel form of muscular dystrophy in humans. Ann. Neurol., 57, 269-276.
35. Osio,A., Tan,L., Chen,S.N., Lombardi,R., Nagueh,S.F., Shete,S., Roberts,R., Willerson,J.T. and Marian,A.J. (2007) Myozenin 2 is a novel gene for human hypertrophic cardiomyopathy. Circ. Res., 100, 766-768.
36. Duncan,A.W., Hanlon Newell,A.E., Bi,W., Finegold,M.J., Olson,S.B., Beaudet,A.L. and Grompe,M. (2012) Aneuploidy as a mechanism for stress-induced liver adaptation. J. Clin. Investig., 122, 3307-3315.
37. Sakamoto,T., Sakata,S.F., Matsuda,K., Horikawa,Y. and Tamaki,N. (2001) Expression and properties of human liver beta-ureidopropionase. J. Nutr. Sci. Vitaminol (Tokyo), 47, 132-138.
38. Collado-Torres,L., Jaffe,A.E. and Leek,J.T. (2016) regionReport: Interactive reports for region-level and feature-level genomic analyses [version2; referees: 2 approved, 1 approved with reservations]. F1000Research, 4, 1-10.
39. Pickrell,J.K., Pai,A.A., Gilad,Y. and Pritchard,J.K. (2010) Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet., 6, e1001236.
40. Leek,J.T., Scharpf,R.B., Bravo,H.C., Simcha,D., Langmead,B., Johnson,W.E., Geman,D., Baggerly,K. and Irizarry,R.A. (2010) Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet., 11, 733-739.
41. Ouimet,C.C., Hemmings,H.C. and Greengard,P. (1989) ARPP-21, a cyclic AMP-regulated phosphoprotein enriched in dopamine-innervated brain regions. II. Immunocytochemical localization in rat brain. J. Neurosci., 9, 865-875.
42. Cachope,R. and Cheer,J.F. (2014) Local control of striatal dopamine release. Front. Behav. Neurosci., 8, 1-7.
43. Melchior,K., Weiss,J., Zaehres,H., Kim,Y.-m., Lutzko,C., Roosta,N., Hescheler,J. and Müschen,M. (2008) The WNT receptor FZD7 contributes to self-renewal signaling of human embryonic stem cells. Biol. Chem., 389, 897-903.
44. Tatard,V.M., Xiang,C., Biegel,J.A. and Dahmane,N. (2010) ZNF238 is expressed in postmitotic brain cells and inhibits brain tumor growth. Cancer Res., 70, 1236-1246.
45. Poulin,G., Turgeon,B. and Drouin,J. (1997) NeuroD1/beta2 contributes to cell-specific transcription of the proopiomelanocortin gene. Mol. Cell. Biol., 17, 6673-6682.
46. Gallego Romero,I., Pai,A.A., Tung,J. and Gilad,Y. (2014) RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol., 12, 1-13.
47. Cunningham,F., Amode,M.R., Barrell,D., Beal,K., Billis,K., Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G., Fitzgerald,S. et al. (2015) Ensembl 2015. Nucleic Acids Res., 43, D662-D669.