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
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PRMT5 methylome profiling uncovers a direct link to splicing regulation in acute myeloid leukemia.
Aliaksandra Radzisheuskaya,Aliaksandra Radzisheuskaya,Pavel V. Shliaha,Pavel V. Shliaha,Vasily V. Grinev,Eugenia Lorenzini,Sergey Kovalchuk,Daria Shlyueva,Vladimir Gorshkov,Ronald C. Hendrickson,Ole N. Jensen,Kristian Helin,Kristian Helin +12 more
TL;DR: The arginine methyltransferase PRMT5 modifies the splicing regulator SRSF1 and affects acute myeloid leukemia cell survival by modulating S RSF1 function.
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The START App: a web-based RNAseq analysis and visualization resource
TL;DR: The START (Shiny Transcriptome Analysis Resource Tool) App has the power and flexibility to be resident on a local computer or serve as a web‐based environment, enabling easy sharing of data between researchers and collaborators.
Journal ArticleDOI
Comparison of methods to detect differentially expressed genes between single-cell populations
TL;DR: This work compared five statistical methods to detect differentially expressed genes between two distinct single-cell populations and found the previously introduced reproducibility-optimization method showed good performance in all comparison settings without any single- cell-specific modifications.
Journal ArticleDOI
Genetic dissection of the miR-200–Zeb1 axis reveals its importance in tumor differentiation and invasion
Alexandra C. Title,Sue Jean Hong,Nuno D. Pires,Lynn Hasenöhrl,Svenja Godbersen,Nadine Stokar-Regenscheit,David P. Bartel,Markus Stoffel,Markus Stoffel +8 more
TL;DR: It is shown that miR-200 ablation in the Rip-Tag2 insulinoma mouse model induces beta-cell dedifferentiation, EMT and tumor invasion, and that disruption of Zeb1 regulation by miR -200c is sufficient to drive EMT.
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Analytical tools and current challenges in the modern era of neuroepigenomics
Ian Maze,Li Shen,Bin Zhang,Benjamin A. Garcia,Ning-Yi Shao,Amanda C. Mitchell,HaoSheng Sun,Schahram Akbarian,C. David Allis,Eric J. Nestler +9 more
TL;DR: A comprehensive overview of available tools for analyzing neuroepigenomics data is provided, as well as a discussion of pending challenges specific to the field of neuroscience.
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