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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The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element
Oskar Marín-Béjar,Oskar Marín-Béjar,Aina Maria Mas,Jovanna González,Dannys Martinez,Alejandro Athie,Xabier Morales,Mikel Galduroz,Ivan Raimondi,Elena Grossi,Shuling Guo,Ana Rouzaut,Igor Ulitsky,Maite Huarte +13 more
TL;DR: This work finds that LINC-PINT is downregulated in multiple types of cancer and acts as a tumor suppressor lncRNA by reducing the invasive phenotype of cancer cells, and proposes a new mechanism where the lnc RNA regulates the availability of free PRC2 at the proximity of co-regulated genomic loci.
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Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions
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Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma.
J.A. Ducie,J.A. Ducie,Fanny Dao,Fanny Dao,Michael Considine,Narciso Olvera,Narciso Olvera,Patricia Shaw,Robert J. Kurman,Ie Ming Shih,Robert A. Soslow,Leslie Cope,Douglas A. Levine,Douglas A. Levine +13 more
TL;DR: The data suggest that the molecular features of HGSCs with and without associated STIC lesions are mostly shared, indicating a common biologic origin, likely to be the distal fallopian tube among all cases.
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Circulating tumour cells from patients with colorectal cancer have cancer stem cell hallmarks in ex vivo culture
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Synergistic action of the MCL-1 inhibitor S63845 with current therapies in preclinical models of triple-negative and HER2-amplified breast cancer.
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TL;DR: The MCL-1 inhibitor S63845 is effective in combination with conventional therapy for targeting triple-negative and HER2-amplified breast cancer and a protein that can promote treatment resistance is identified, which may help predict which patients are more likely to benefit from the new treatment.
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