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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The ETS transcription factor ELF1 regulates a broadly antiviral program distinct from the type I interferon response
Leon Louis Seifert,Clara Si,Debjani Saha,Mohammad Sadic,Maren de Vries,Sarah Ballentine,Aaron Briley,Guojun Wang,Ana M. Valero-Jimenez,Adil Mohamed,Uwe Schaefer,Hong M. Moulton,Adolfo García-Sastre,Shashank Tripathi,Shashank Tripathi,Brad R. Rosenberg,Meike Dittmann +16 more
TL;DR: Using microscopy to quantify viral infection over time, it is found that ELF1 inhibits eight diverse RNA and DNA viruses after multi-cycle replication and provides an additional layer of the innate host response, independent from the action of type I interferons.
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A phase 2 study of panobinostat with lenalidomide and weekly dexamethasone in myeloma.
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Minimizing Clonal Variation during Mammalian Cell Line Engineering for Improved Systems Biology Data Generation
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TL;DR: The platform enables robust comparative studies of genome engineered CHO cell lines and can be applied to other mammalian cells for diverse biological, biomedical and biotechnological applications.
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Activation of PTHrP-cAMP-CREB1 signaling following p53 loss is essential for osteosarcoma initiation and maintenance
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