Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates - PubMed (original) (raw)
. 2012 Oct 22;11(5):/j/sagmb.2012.11.issue-5/1544-6115.1826/1544-6115.1826.xml.
doi: 10.1515/1544-6115.1826.
Affiliations
- PMID: 23104842
- DOI: 10.1515/1544-6115.1826
Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
Steven P Lund et al. Stat Appl Genet Mol Biol. 2012.
Abstract
Next generation sequencing technology provides a powerful tool for measuring gene expression (mRNA) levels in the form of RNA-sequence data. Method development for identifying differentially expressed (DE) genes from RNA-seq data, which frequently includes many low-count integers and can exhibit severe overdispersion relative to Poisson or binomial distributions, is a popular area of ongoing research. Here we present quasi-likelihood methods with shrunken dispersion estimates based on an adaptation of Smyth's (2004) approach to estimating gene-specific error variances for microarray data. Our suggested methods are computationally simple, analogous to ANOVA and compare favorably versus competing methods in detecting DE genes and estimating false discovery rates across a variety of simulations based on real data.
Similar articles
- Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys.
Su Z, Li Z, Chen T, Li QZ, Fang H, Ding D, Ge W, Ning B, Hong H, Perkins RG, Tong W, Shi L. Su Z, et al. Chem Res Toxicol. 2011 Sep 19;24(9):1486-93. doi: 10.1021/tx200103b. Epub 2011 Aug 23. Chem Res Toxicol. 2011. PMID: 21834575 - Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors.
Van De Wiel MA, Leday GG, Pardo L, Rue H, Van Der Vaart AW, Van Wieringen WN. Van De Wiel MA, et al. Biostatistics. 2013 Jan;14(1):113-28. doi: 10.1093/biostatistics/kxs031. Epub 2012 Sep 17. Biostatistics. 2013. PMID: 22988280 - A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data.
Kvam VM, Liu P, Si Y. Kvam VM, et al. Am J Bot. 2012 Feb;99(2):248-56. doi: 10.3732/ajb.1100340. Epub 2012 Jan 20. Am J Bot. 2012. PMID: 22268221 Review. - BALLI: Bartlett-adjusted likelihood-based linear model approach for identifying differentially expressed genes with RNA-seq data.
Park K, An J, Gim J, Seo M, Lee W, Park T, Won S. Park K, et al. BMC Genomics. 2019 Jul 2;20(1):540. doi: 10.1186/s12864-019-5851-6. BMC Genomics. 2019. PMID: 31266443 Free PMC article. - Statistical detection of differentially expressed genes based on RNA-seq: from biological to phylogenetic replicates.
Gu X. Gu X. Brief Bioinform. 2016 Mar;17(2):243-8. doi: 10.1093/bib/bbv035. Epub 2015 Jun 24. Brief Bioinform. 2016. PMID: 26108230 Review.
Cited by
- Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons.
Signal B, Phipps AJ, Giles KA, Huskins SN, Mercer TR, Robinson MD, Woodhouse A, Taberlay PC. Signal B, et al. Cells. 2024 Aug 21;13(16):1393. doi: 10.3390/cells13161393. Cells. 2024. PMID: 39195281 Free PMC article. - Circulating small RNA signatures differentiate accurately the subtypes of muscular dystrophies: small-RNA next-generation sequencing analytics and functional insights.
Kakouri AC, Koutalianos D, Koutsoulidou A, Oulas A, Tomazou M, Nikolenko N, Turner C, Roos A, Lusakowska A, Janiszewska K, Papadimas GK, Papadopoulos C, Kararizou E, Papanicolaou EZ, Gorman G, Lochmüller H, Spyrou GM, Phylactou LA. Kakouri AC, et al. RNA Biol. 2022;19(1):507-518. doi: 10.1080/15476286.2022.2058817. Epub 2021 Dec 31. RNA Biol. 2022. PMID: 35388741 Free PMC article. - Partition: a surjective mapping approach for dimensionality reduction.
Millstein J, Battaglin F, Barrett M, Cao S, Zhang W, Stintzing S, Heinemann V, Lenz HJ. Millstein J, et al. Bioinformatics. 2020 Feb 1;36(3):676-681. doi: 10.1093/bioinformatics/btz661. Bioinformatics. 2020. PMID: 31504178 Free PMC article. - Case Report: Hypoglycemia Due to a Novel Activating Glucokinase Variant in an Adult - a Molecular Approach.
Koneshamoorthy A, Seniveratne-Epa D, Calder G, Sawyer M, Kay TWH, Farrell S, Loudovaris T, Mariana L, McCarthy D, Lyu R, Liu X, Thorn P, Tong J, Chin LK, Zacharin M, Trainer A, Taylor S, MacIsaac RJ, Sachithanandan N, Thomas HE, Krishnamurthy B. Koneshamoorthy A, et al. Front Endocrinol (Lausanne). 2022 Mar 17;13:842937. doi: 10.3389/fendo.2022.842937. eCollection 2022. Front Endocrinol (Lausanne). 2022. PMID: 35370948 Free PMC article. - Molecular fingerprint of female bovine embryos produced in vitro with high competence to establish and maintain pregnancy†.
Zolini AM, Block J, Rabaglino MB, Tríbulo P, Hoelker M, Rincon G, Bromfield JJ, Hansen PJ. Zolini AM, et al. Biol Reprod. 2020 Feb 14;102(2):292-305. doi: 10.1093/biolre/ioz190. Biol Reprod. 2020. PMID: 31616926 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources