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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Necroptosis activation in Alzheimer's disease
Antonella Caccamo,Caterina Branca,Ignazio S. Piras,Eric Ferreira,Matthew J. Huentelman,Winnie S. Liang,Benjamin Readhead,Joel T. Dudley,Elizabeth E. Spangenberg,Kim N. Green,Ramona Belfiore,Wendy Winslow,Salvatore Oddo +12 more
TL;DR: It is found that necroptosis was activated in postmortem human AD brains, positively correlated with Braak stage, and inversely correlated with brain weight and cognitive scores, and the set of genes regulated by RIPK1 overlapped significantly with multiple independent AD transcriptomic signatures, indicating that RIPK 1 activity could explain a substantial portion of transcriptomic changes in AD.
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Linear models enable powerful differential activity analysis in massively parallel reporter assays.
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Adaptive plasticity of IL-10 + and IL-35 + T reg cells cooperatively promotes tumor T cell exhaustion
Deepali V. Sawant,Deepali V. Sawant,Hiroshi Yano,Maria Chikina,Qianxia Zhang,Qianxia Zhang,Mengting Liao,Mengting Liao,Chang Liu,Derrick J Callahan,Zhe Sun,Tao Sun,Tracy Tabib,Arjun Pennathur,David B. Corry,James D. Luketich,Robert Lafyatis,Wei Chen,Amanda C. Poholek,Tullia C. Bruno,Creg J. Workman,Dario A. A. Vignali +21 more
TL;DR: The results reveal previously unappreciated cooperative roles for Treg cell-derived IL-10 and IL-35 in promoting BLIMP1-dependent exhaustion of CD8+ TILs that limits effective anti-tumor immunity.
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Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species
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Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation
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