voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Charity W. Law,Charity W. Law,Yunshun Chen,Yunshun Chen,Wei Shi,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TLDR
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments, and the voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline.Abstract:
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods.read more
Citations
More filters
Journal ArticleDOI
Tissue specific regulation of transcription in endometrium and association with disease.
Sally Mortlock,Raden I Kendarsari,Jenny N. Fung,Greg Gibson,Fei Yang,Restuadi Restuadi,Jane E. Girling,Jane E. Girling,Sarah J Holdsworth-Carson,Wan Tinn Teh,Samuel W. Lukowski,Martin Healey,Ting Qi,Peter Rogers,Jian Yang,Brett McKinnon,Grant W. Montgomery +16 more
TL;DR: The statistical approaches used in this study identify the likely gene targets for specific genetic risk factors, but not the functional mechanism by which changes in gene expression may influence disease risk.
Journal ArticleDOI
TFAP2 transcription factors are regulators of lipid droplet biogenesis.
TL;DR: It is reported that Wnt-induced lipid droplet biogenesis does not depend on the canonical TCF/LEF transcription factors, and it is found that TFAP2 family members mediate the pro-lipid droplet signal induced by Wnt3a, leading to the notion that theTFAP2 transcription factor may function as a ‘master’ regulator of lipid droplets biogenesis.
Journal ArticleDOI
Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons
Priscilla Turelli,Christopher Playfoot,Dephine Grun,Charlène Raclot,Julien Pontis,Alexandre Coudray,Christian W. Thorball,Julien Duc,Eugenia V. Pankevich,Eugenia V. Pankevich,Bart Deplancke,Volker Busskamp,Volker Busskamp,Didier Trono +13 more
TL;DR: ZNF417 and ZNF587 are identified as primate-specific KZFPs repressing HERVK and SVA and preventing the induction of neurotoxic retroviral proteins and an interferon-like response in human embryonic stem cells and brain organoids.
Journal ArticleDOI
Serotonergic system antagonists target breast tumor initiating cells and synergize with chemotherapy to shrink human breast tumor xenografts
William D. Gwynne,Robin M. Hallett,Adele Girgis-Gabardo,Bojana Bojovic,Anna Dvorkin-Gheva,Craig Aarts,Kay Dias,Anita Bane,John A. Hassell +8 more
TL;DR: The data suggest that antidepressants in combination with cytotoxic anticancer therapies may be an appropriate treatment regimen for testing in clinical trials.
Journal ArticleDOI
Transcriptome analysis of callus from Picea balfouriana
TL;DR: It is found that somatic embryogenesis receptor kinase (SERK), arabinogalactan proteins, and members of the WUS-related homeobox protein family may play important roles and could act as molecular markers in the early stage of somatic embryosogenesis, as reported previously.
References
More filters
Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Book
Generalized Linear Models
Peter McCullagh,John A. Nelder +1 more
TL;DR: In this paper, a generalization of the analysis of variance is given for these models using log- likelihoods, illustrated by examples relating to four distributions; the Normal, Binomial (probit analysis, etc.), Poisson (contingency tables), and gamma (variance components).
Journal ArticleDOI
featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features
TL;DR: FeatureCounts as discussed by the authors is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments, which implements highly efficient chromosome hashing and feature blocking techniques.
Journal ArticleDOI
Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.