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
RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking.
Margaret M. Parker,Margaret M. Parker,Robert P. Chase,Andrew Lamb,Alejandro Reyes,Aabida Saferali,Aabida Saferali,Jeong H. Yun,Blanca E. Himes,Edwin K. Silverman,Edwin K. Silverman,Craig P. Hersh,Craig P. Hersh,Peter J. Castaldi,Peter J. Castaldi +14 more
TL;DR: Transcriptomic changes at the gene and exon levels from whole blood can refine the understanding of the molecular mechanisms underlying the response to smoking.
Journal ArticleDOI
Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
A. Callegari,Christian Sieben,Alexander Benke,David M. Suter,Beat Fierz,Davide Mazza,Suliana Manley +6 more
TL;DR: In this article, the authors used live-cell single molecule imaging of TF-DNA binding kinetics and genome-wide quantification of p65-mediated transcription to investigate how the duration of TF binding to DNA relates to downstream transcriptional output.
Journal ArticleDOI
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Joseph N. Paulson,Joseph N. Paulson,Cho Yi Chen,Camila M. Lopes-Ramos,Marieke L. Kuijjer,John Platig,Abhijeet R. Sonawane,Maud Fagny,Kimberly Glass,Kimberly Glass,John Quackenbush +10 more
TL;DR: Yet Another RNA Normalization software pipeline (YARN), that includes quality control and preprocessing, gene filtering, and normalization steps designed to facilitate downstream analysis of large, heterogeneous RNA-Seq data sets, is developed and used with data from the Genotype-Tissue Expression (GTEx) project.
Posted ContentDOI
Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors
Kristine M. Abo,Kristine M. Abo,Liang Ma,Liang Ma,Taylor Matte,Taylor Matte,Jessie Huang,Jessie Huang,Konstantinos D. Alysandratos,Konstantinos D. Alysandratos,Rhiannon B. Werder,Rhiannon B. Werder,Aditya Mithal,Mary Lou Beermann,Mary Lou Beermann,Jonathan Lindstrom-Vautrin,Gustavo Mostoslavsky,Laertis Ikonomou,Laertis Ikonomou,Darrell N. Kotton,Darrell N. Kotton,Finn Hawkins,Finn Hawkins,Andrew A. Wilson,Andrew A. Wilson,Carlos Villacorta-Martin +25 more
TL;DR: In order to prepare human culture systems that are amenable to modeling viral infection of both the proximal and distal lung epithelium, iPSC-derived alveolar and airway epithelial cells are adapted to two-dimensional air-liquid interface cultures.
Journal ArticleDOI
Comprehensive analysis of differential expression profiles of mRNAs and lncRNAs and identification of a 14-lncRNA prognostic signature for patients with colon adenocarcinoma.
TL;DR: A 14-lncRNA signature is identified that could predict the survival for COAD patients and is found to be mainly involved in vascular smooth muscle contraction and the cGMP-PKG signaling pathway.
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.