limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie,Belinda Phipson,Di Wu,Yifang Hu,Charity W. Law,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
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TLDR
The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.Abstract:
limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.read more
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Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes.
Laura K. Mackay,Laura K. Mackay,Martina Minnich,Natasja A. M. Kragten,Yang Liao,Yang Liao,Benjamin Nota,Cyril Seillet,Cyril Seillet,Ali Zaid,Kevin Man,Kevin Man,Simon Preston,Simon Preston,David Freestone,Asolina Braun,Erica Wynne-Jones,Felix M. Behr,Regina Stark,Daniel G. Pellicci,Daniel G. Pellicci,Dale I. Godfrey,Dale I. Godfrey,Gabrielle T. Belz,Gabrielle T. Belz,Marc Pellegrini,Marc Pellegrini,Thomas Gebhardt,Meinrad Busslinger,Wei Shi,Wei Shi,Francis R. Carbone,René A. W. van Lier,Axel Kallies,Axel Kallies,Klaas P. J. M. van Gisbergen +35 more
TL;DR: In this paper, the authors identify Hobit and Blimp1 as central regulators of a universal program that instructs tissue retention in diverse tissue-resident lymphocyte populations, including NKT cells and liver-resident NK cells.
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SARS-CoV-2 infection of human ACE2-transgenic mice causes severe lung inflammation and impaired function.
Emma S. Winkler,Adam L. Bailey,Natasha M. Kafai,Sharmila Nair,Broc T. McCune,Jinsheng Yu,Julie M. Fox,Rita E. Chen,James T. Earnest,Shamus P. Keeler,Jon H. Ritter,Liang I. Kang,Sarah Dort,Annette Robichaud,Richard D. Head,Michael J. Holtzman,Michael S. Diamond +16 more
TL;DR: The transgenic mice expressing the human angiotensin I-converting enzyme 2 (ACE2) receptor driven by the cytokeratin-18 (K18) gene promoter are evaluated as a model of SARS-CoV-2 infection to define the basis of lung disease and test immune and antiviral-based countermeasures.
Journal ArticleDOI
Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations
Raphael Bueno,Eric Stawiski,Leonard D. Goldstein,Steffen Durinck,Assunta De Rienzo,Zora Modrusan,Florian Gnad,Thong T. Nguyen,Bijay S. Jaiswal,Lucian R. Chirieac,Daniele Sciaranghella,Nhien Dao,Corinne E. Gustafson,Kiara J. Munir,Jason A. Hackney,Amitabha Chaudhuri,Ravi Gupta,Joseph Guillory,Karen Toy,Connie Ha,Ying-Jiun Chen,Jeremy Stinson,Subhra Chaudhuri,Na Zhang,Thomas D. Wu,David J. Sugarbaker,Frederic J. de Sauvage,William G. Richards,Somasekar Seshagiri +28 more
TL;DR: Recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2 are found and alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs are identified.
Journal ArticleDOI
Landscape of X chromosome inactivation across human tissues
Taru Tukiainen,Taru Tukiainen,Alexandra-Chloé Villani,Alexandra-Chloé Villani,Angela Yen,Angela Yen,Manuel A. Rivas,Manuel A. Rivas,Manuel A. Rivas,Jamie L. Marshall,Jamie L. Marshall,Rahul Satija,Rahul Satija,Matthew Aguirre,Matthew Aguirre,Laura D. Gauthier,Laura D. Gauthier,Mark Fleharty,Andrew Kirby,Andrew Kirby,Beryl B. Cummings,Beryl B. Cummings,Stephane E. Castel,Konrad J. Karczewski,Konrad J. Karczewski,François Aguet,Andrea Byrnes,Andrea Byrnes,Tuuli Lappalainen,Aviv Regev,Aviv Regev,Kristin G. Ardlie,Nir Hacohen,Nir Hacohen,Daniel G. MacArthur,Daniel G. MacArthur +35 more
TL;DR: It is shown that incomplete XCI affects at least 23% of X-chromosomal genes, identified seven genes that escape XCI with support from multiple lines of evidence and demonstrated that escape from XCI results in sex biases in gene expression, establishing incomplete X CI as a mechanism that is likely to introduce phenotypic diversity.
Journal ArticleDOI
T Cell Factor 1-Expressing Memory-like CD8+ T Cells Sustain the Immune Response to Chronic Viral Infections
Daniel T. Utzschneider,Mélanie Charmoy,Vijaykumar Chennupati,Laurène Pousse,Daniela Pais Ferreira,Sandra Calderon-Copete,Maxime Danilo,Francesca Alfei,Maike Hofmann,Dominik Wieland,Sylvain Pradervand,Robert Thimme,Dietmar Zehn,Werner Held +13 more
TL;DR: A small subpopulation of virus-specific CD8(+) T cells that sustained the T cell response during chronic infections was discovered, defined by, and depended on, the expression of the transcription factor Tcf1.
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