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
Identification and Mode of Action of a Plant Natural Product Targeting Human Fungal Pathogens.
Stéphane Dorsaz,Tiia Snäkä,Quentin Favre-Godal,Pierre Marc Xavier Maudens,Nathalie Boulens,Pascal Furrer,Samad Nejad Ebrahimi,Matthias Hamburger,Eric Allémann,Katia Gindro,Emerson Ferreira Queiroz,Howard Riezman,Jean-Luc Wolfender,Dominique Sanglard +13 more
TL;DR: The results unambiguously identified Erg6, a C-24 sterol methyltransferase absent in mammals, to be the main direct target of tomatidine, a novel antifungal agent targeting Candida albicans systemic infection.
Journal ArticleDOI
CGPS: A machine learning-based approach integrating multiple gene set analysis tools for better prioritization of biologically relevant pathways.
TL;DR: This work develops an ensemble method using a machine learning approach called Combined Gene set analysis incorporating Prioritization and Sensitivity (CGPS) that integrates the results provided by nine prominent GSE tools into a single ensemble score (R score) to sort pathways as integrated results and is the first GSE ensemble method built based on a priori knowledge of pathways and phenotypes.
Journal ArticleDOI
Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions
Lian Narunsky-Haziza,Gregory D. Sepich-Poore,Ilana Livyatan,Omer Asraf,Cameron Martino,Deborah Nejman,Nancy Gavert,Jason E. Stajich,Guy Amit,Antonio Gonzalez,Stephen Wandro,Gili Perry,Ruthie Ariel,Arnon Meltser,Justin P. Shaffer,Qiyun Zhu,Nora Balint-Lahat,Iris Barshack,Maya Dadiani,Einav Nili Gal-Yam,Sandip Pravin Patel,Amir Bashan,Austin D. Swafford,Yitzhak Pilpel,Rob Knight,Ravid Straussman +25 more
TL;DR: In this article , the cancer mycobiome within 17,401 patient tissue, blood, and plasma samples across 35 cancer types in four independent cohorts was comprehensively characterized, with fungal DNA and cells at low abundances across many major human cancers.
Journal ArticleDOI
An EDS1 heterodimer signalling surface enforces timely reprogramming of immunity genes in Arabidopsis.
Deepak D. Bhandari,Dmitry Lapin,Barbara Kracher,Patrick von Born,Jaqueline Bautor,Karsten Niefind,Jane E. Parker +6 more
TL;DR: It is shown that the EP-domain surface of EDS1 heterodimers signals downstream of both receptor types and ensures a rapid transcriptional response in TIR-NLR immunity to bacteria.
Journal ArticleDOI
The proteomic skin profile of moderate-to-severe atopic dermatitis patients shows an inflammatory signature.
Ana B. Pavel,Lisa Zhou,Aisleen Diaz,Benjamin Ungar,Joshua Dan,Helen He,Yeriel Estrada,Hui Xu,Marie Fernandes,Yael Renert-Yuval,James G. Krueger,Emma Guttman-Yassky +11 more
TL;DR: The AD skin proteome shows an inflammatory and cardiovascular signature even in non-lesional skin, emphasizing the need for proactive treatment.
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.