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
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A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.
Xiaohong Li,Guy Brock,Guy Brock,Eric C. Rouchka,Nigel G. F. Cooper,Dongfeng Wu,Timothy E. O'Toole,Ryan Gill,Abdallah M. Eteleeb,Liz O'Brien,Shesh N. Rai +10 more
TL;DR: The proposed Med-pgQ2 and UQ-PGQ2 methods perform slightly better for differential gene analysis of RNA-seq data skewed towards lowly expressed read counts with high variation by improving specificity while maintaining a good detection power with a control of the nominal FDR level.
Posted ContentDOI
WRN Helicase is a Synthetic Lethal Target in Microsatellite Unstable Cancers
Edmond M. Chan,Edmond M. Chan,Tsukasa Shibue,James M. McFarland,Benjamin Gaeta,Justine S. McPartlan,Mahmoud Ghandi,Jie Bin Liu,Jean-Bernard Lazaro,Nancy Dumont,Alfredo Gonzalez,Annie Apffel,Syed O. Ali,Syed O. Ali,Lisa Leung,Emma A. Roberts,Elizaveta Reznichenko,Mirazul Islam,Mirazul Islam,Maria Alimova,Monica Schenone,Yosef E. Maruvka,Yang Liu,Yang Liu,Alan D. D'Andrea,David E. Root,Jesse S. Boehm,Gad Getz,Todd R. Golub,Aviad Tsherniak,Francisca Vazquez,Adam J. Bass,Adam J. Bass +32 more
TL;DR: Analysis of data from large-scale CRISPR/Cas9 knockout and RNA interference silencing screens found that the RecQ DNA helicase WRN was selectively essential in MSI cell lines, yet dispensable in microsatellite stable (MSS) cell lines.
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RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans
Sara Amorim-Vaz,Van Du T. Tran,Sylvain Pradervand,Sylvain Pradervand,Marco Pagni,Alix T. Coste,Dominique Sanglard +6 more
TL;DR: The transcriptome profiles of Candida albicans, the most prevalent fungal pathogen in systemically infected immunocompromised patients, during systemic infection in different hosts are addressed and a strategy for high-resolution quantitative analysis of the C.Albicans transcriptome is developed.
Journal ArticleDOI
Epigenetic dysregulation of naive CD4+ T-cell activation genes in childhood food allergy
David Martino,David Martino,Melanie R Neeland,Thanh D. Dang,Joanna E. Cobb,Justine A. Ellis,Alice Barnett,Mimi L.K. Tang,Peter Vuillermin,Peter Vuillermin,Peter Vuillermin,Katrina J. Allen,Richard Saffery +12 more
TL;DR: The epigenetic regulation of the naive CD4+ T cell activation response among children with IgE-mediated food allergy is studied, finding epigenetic dysregulation in the early stages of signal transduction through the T cell receptor complex.
Journal ArticleDOI
mTORC1 coordinates an immediate unfolded protein response-related transcriptome in activated B cells preceding antibody secretion.
TL;DR: It is shown that mTORC1 signalling but not Xbp1-mediated transcription regulation in activated B cells is important for the induction of a UPR-related transcriptome that precedes full plasma cell functions.
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