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
A selective peptide inhibitor of Frizzled 7 receptors disrupts intestinal stem cells.
Aaron H. Nile,Felipe De Sousa E Melo,Susmith Mukund,Robert Piskol,Simon Hansen,Lijuan Zhou,Yingnan Zhang,Yue Fu,Emily B. Gogol,László G. Kömüves,Zora Modrusan,Stephane Angers,Yvonne Franke,Christopher M. Koth,Wayne J. Fairbrother,Weiru Wang,Frederic J. de Sauvage,Rami N. Hannoush +17 more
TL;DR: The identification of a potent peptide that selectively binds to the FZD7 CRD at a previously uncharacterized site and alters the conformation of the CRD and the architecture of its lipid-binding groove illustrates that targeting the lipid- binding groove holds promise as an approach for achieving isoform-selective FZd receptor inhibition.
Journal ArticleDOI
Dynamic changes in Id3 and E-protein activity orchestrate germinal center and plasma cell development
Renee Gloury,Dimitra Zotos,Dimitra Zotos,Malou Zuidscherwoude,Malou Zuidscherwoude,Frederic Masson,Frederic Masson,Yang Liao,Yang Liao,Jhaguaral Hasbold,Jhaguaral Hasbold,Lynn M. Corcoran,Lynn M. Corcoran,Philip D. Hodgkin,Philip D. Hodgkin,Gabrielle T. Belz,Gabrielle T. Belz,Wei Shi,Stephen L. Nutt,Stephen L. Nutt,David M. Tarlinton,David M. Tarlinton,Axel Kallies,Axel Kallies +23 more
TL;DR: It is revealed that an essential role for the Id3–E-protein axis in the transcriptional regulation of humoral immunity is revealed and this role is important for the regulation of immunity to infectious disease.
Journal ArticleDOI
Dominance rank-associated gene expression is widespread, sex-specific, and a precursor to high social status in wild male baboons.
Amanda J. Lea,Mercy Y. Akinyi,Ruth Nyakundi,Peter Mareri,Fred Nyundo,Thomas M. Kariuki,Susan C. Alberts,Elizabeth A. Archie,Jenny Tung,Jenny Tung +9 more
TL;DR: It is demonstrated that high status-associated gene expression patterns are precursors, not consequences, of high social status in males, in support of the idea that physiological condition determines who attains high rank.
Journal ArticleDOI
Copper and cerium-regulated gene expression in Methylosinus trichosporium OB3b
Wenyu Gu,Jeremy D. Semrau +1 more
TL;DR: Comparisons of the transcriptome of Methylosinus trichosporium OB3b grown in the presence of varying amounts of copper and cerium suggest that copper plays a larger role in regulating gene expression in methanotrophs, but that significant changes occur when both copper and Cerium are present.
Journal ArticleDOI
Novel significant stage-specific differentially expressed genes in hepatocellular carcinoma.
Arjun Sarathi,Ashok Palaniappan +1 more
TL;DR: This study identified novel significant stage-specific differentially expressed genes which could enhance the understanding of the molecular determinants of hepatocellular carcinoma progression and could serve as biomarkers that potentially underpin diagnosis as well as pinpoint therapeutic targets.
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.