Survey and Summary: How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets

Nucleic Acids Research

Volumn 43, Issue 16, 2015, Pages 7664-7674

  Peixoto, Lucia ^a,e   Risso, Davide ^b   Poplawski, Shane G ^a,f   Wimmer, Mathieu E ^a,g   Speed, Terence P ^c   Wood, Marcelo A ^d   Abel, Ted ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e WASHINGTON STATE UNIVERSITY   (United States)

^f Ibis Biosciences Inc   (United States)

^g UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ADULT; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; GENE EXPRESSION; MALE; MEASUREMENT; MEASUREMENT ACCURACY; MEASUREMENT POWER; MOUSE; NONHUMAN; NUCLEIC ACID DATABASE; PRIORITY JOURNAL; REPRODUCIBILITY; RNA SEQUENCE; ANIMAL; C57BL MOUSE; EVALUATION STUDY; GENE EXPRESSION PROFILING; GENETIC VARIATION; NEUROSCIENCE; PROCEDURES; SEQUENCE ANALYSIS;

ANIMALS; GENE EXPRESSION PROFILING; GENETIC VARIATION; MALE; MICE, INBRED C57BL; NEUROSCIENCES; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, RNA;

EID: 84942292053     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv736     Document Type: Article

References (45)

1. 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.
2. Bullard,J. H., Purdom,E., Hansen,K. D. And Dudoit,S. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics, 11, 94.
3. Dillies,M. A., Rau,A., Aubert,J., Hennequet-Antier,C., Jeanmougin,M., Servant,N., Keime,C., Marot,G., Castel,D., Estelle,J. et al. (2013) A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief. Bioinformatics, 14, 671-683.
4. Robinson,M. D. And Oshlack,A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol., 11, R25.
5. Mortazavi,A.,Williams,B. A., McCue,K., Schaeffer,L. And Wold,B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628.
6. Risso,D., Ngai,J., Speed,T. P. And Dudoit,S. (2014) Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol., 32, 896-902.
7. Suzuki,A., Josselyn,S. A., Frankland,P. W., Masushige,S., Silva,A. J. And Kida,S. (2004) Memory reconsolidation and extinction have distinct temporal and biochemical signatures. J. Neurosci., 24, 4787-4795.
8. von Hertzen,L. S. J. And Giese,K. P. (2005) Memory reconsolidation engages only a subset of immediate-early genes induced during consolidation. J. Neurosci., 25, 1935-1942.
9. Vogel-Ciernia,A. And Wood,M. A. (2014) Examining object location and object recognition memory in mice. Curr. Protoc. Neurosci., 69, 8. 31. 1-8. 31. 17.
10. Wu,T. D. And Watanabe,C. K. (2005) GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859-1875.
11. Anders,S., Pyl,P. T. And Huber,W. (2015) HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169.
12. Gentleman,R. C., Carey,V. J., Bates,D. M., Bolstad,B., Dettling,M., Dudoit,S., Ellis,B., Gautier,L., Ge,Y., Gentry,J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
13. Risso,D., Schwartz,K., Sherlock,G. And Dudoit,S. (2011) GC-content normalization for RNA-Seq data. BMC Bioinformatics, 12, 480.
14. 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.
15. Peixoto,L., Wimmer,M. E., Poplawski,S. G., Tudor,J. C., Kenworthy,C. A., Liu,S., Mizuno,K., Garcia,B. A., Zhang,N. R., Giese,K. P. et al. (2015) Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression. BMC Genomics, 16(Suppl. 5), S5.
16. Dennis,G. Jr, Sherman,B. T., Hosack,D. A., Yang,J., Gao,W., Lane,H. C. And Lempicki,R. A. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol., 4, P3.
17. Mardia,K. V., Kent,J. T. And Bibby,J. M. (1979) Multivariate Analysis. Academic Press, London; NY.
18. Agranoff,B. W., Davis,R. E., Casola,L. And Lim,R. (1967) Actinomycin D blocks formation of memory of shock-avoidance in goldfish. Science, 158, 1600-1601.
19. Igaz,L. M., Vianna,M. R., Medina,J. H. And Izquierdo,I. (2002) Two time periods of hippocampal mRNA synthesis are required for memory consolidation of fear-motivated learning. J. Neurosci., 22, 6781-6789.
20. Keeley,M. B., Wood,M. A., Isiegas,C., Stein,J., Hellman,K., Hannenhalli,S. And Abel,T. (2006) Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus. Learn. Mem., 13, 135-142.
21. Levenson,J. M., Choi,S., Lee,S. Y., Cao,Y. A., Ahn,H. J., Worley,K. C., Pizzi,M., Liou,H. C. And Sweatt,J. D. (2004) A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel. J. Neurosci., 24, 3933-3943.
22. Barnes,P., Kirtley,A. And Thomas,K. L. (2012) Quantitatively and qualitatively different cellular processes are engaged in CA1 during the consolidation and reconsolidation of contextual fear memory. Hippocampus, 22, 149-171.
23. Hawk,J. D., Bookout,A. L., Poplawski,S. G., Bridi,M., Rao,A. J., Sulewski,M. E., Kroener,B. T., Manglesdorf,D. J. And Abel,T. (2012) NR4A nuclear receptors support memory enhancement by histone deacetylase inhibitors. J. Clin. Invest., 122, 3593-3602.
24. Vogel-Ciernia,A., Matheos,D. P., Barrett,R. M., Kramar,E. A., Azzawi,S., Chen,Y., Magnan,C. N., Zeller,M., Sylvain,A., Haettig,J. et al. (2013) The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. Nat. Neurosci., 16, 552-561.
25. Bolstad,B. M., Collin,F., Brettschneider,J., Simpson,K., Cope,L., Irizarry,R. A. And Speed,T. P. (2005) In: Gentleman,R, Carey,V, Huber,W, Irizarry,R and Dudoit,S (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer, NY, pp. 33-47.
26. Gagnon-Bartsch,J. A. And Speed,T. P. (2012) Using control genes to correct for unwanted variation in microarray data. Biostatistics, 13, 539-552.
27. Stegle,O., Parts,L., Durbin,R. And Winn,J. (2010) A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLoS Comput. Biol., 6, e1000770.
28. t Hoen,P. A., Friedlander,M. R., Almlof,J., Sammeth,M., Pulyakhina,I., Anvar,S. Y., Laros,J. F., Buermans,H. P., Karlberg,O., Brannvall,M. et al. (2013) Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat. Biotechnol., 31, 1015-1022.
29. Leek,J. T. And Storey,J. D. (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet., 3, 1724-1735.
30. Leek,J. T. (2014) svaseq: removing batch effects and other unwanted noise from sequencing data. Nucleic Acids Res., 42, doi:10. 1093/nar/gku864.
31. Schug,J., Schuller,W. P., Kappen,C., Salbaum,J. M., Bucan,M. And Stoeckert,C. J. Jr. (2005) Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol., 6, R33.
32. Anders,S., McCarthy,D. J., Chen,Y., Okoniewski,M., Smyth,G. K., Huber,W. And Robinson,M. D. (2013) Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc., 8, 1765-1786.
33. Sakamoto,K., Karelina,K. And Obrietan,K. (2011) CREB: a multifaceted regulator of neuronal plasticity and protection. J. Neurochem., 116, 1-9.
34. Oikawa,K., Odero,G. L., Platt,E., Neuendorff,M., Hatherell,A., Bernstein,M. J. And Albensi,B. C. (2012) NF-kappaB p50 subunit knockout impairs late LTP and alters long term memory in the mouse hippocampus. BMC Neurosci., 13, 45.
35. Stern,S. A., Chen,D. Y. And Alberini,C. M. (2014) The effect of insulin and insulin-like growth factors on hippocampus-and amygdala-dependent long-term memory formation. Learn. Mem., 21, 556-563.
36. Donzis,E. J. And Tronson,N. C. (2014) Modulation of learning and memory by cytokines: signaling mechanisms and long term consequences. Neurobiol. Learn. Mem., 115, 68-77.
37. Atkins,C. M., Selcher,J. C., Petraitis,J. J., Trzaskos,J. M. And Sweatt,J. D. (1998) The MAPK cascade is required for mammalian associative learning. Nat. Neurosci., 1, 602-609.
38. Smyth,G. K. (2005) In: Gentleman,R, Carey,V, Huber,W, Irizarry,R and Dudoit,S (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer, NY, pp. 397-420.
39. Nicolas,C. S., Peineau,S., Amici,M., Csaba,Z., Fafouri,A., Javalet,C., Collett, Valerie,J., Hildebrandt,L., Seaton,G., Choi,S.-L. et al. The JAK/STAT pathway is involved in synaptic plasticity. Neuron, 73, 374-390.
40. Fiorenza,A., Lopez-Atalaya,J. P., Rovira,V., Scandaglia,M., Geijo-Barrientos,E. And Barco,A. (2015) Blocking miRNA biogenesis in adult forebrain neurons enhances seizure susceptibility, fear memory, and food intake by increasing neuronal responsiveness. Cerebral Cortex, doi:10. 1093/cercor/bhu332.
41. Zovkic,I. B., Paulukaitis,B. S., Day,J. J., Etikala,D. M. And Sweatt,J. D. (2014) Histone H2A. Z subunit exchange controls consolidation of recent and remote memory. Nature, 515, 582-586.
42. Stilling,R. M., Benito,E., Gertig,M., Barth,J., Capece,V., Burkhardt,S., Bonn,S. And Fischer,A. (2014) De-regulation of gene expression and alternative splicing affects distinct cellular pathways in the aging hippocampus. Front. Cell. Neurosci., 8, 373.
43. Stilling,R. M., Ronicke,R., Benito,E., Urbanke,H., Capece,V., Burkhardt,S., Bahari-Javan,S., Barth,J., Sananbenesi,F., Schutz,A. L. et al. (2014) K-Lysine acetyltransferase 2a regulates a hippocampal gene expression network linked to memory formation. EMBO J., 33, 1912-1927.
44. Gjoneska,E., Pfenning,A. R., Mathys,H., Quon,G., Kundaje,A., Tsai,L. H. And Kellis,M. (2015) Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature, 518, 365-369.
45. Ainsley,J. A., Drane,L., Jacobs,J., Kittelberger,K. A. And Reijmers,L. G. (2014) Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience. Nat. Commun., 5, 4510.