Computational deconvolution: extracting cell type-specific information from heterogeneous samples.
Shai S. Shen-Orr,Renaud Gaujoux +1 more
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TLDR
The present state of available deconvolution techniques, their advantages and limitations, are reviewed, with a focus on blood expression data and immunological studies in general.About:
This article is published in Current Opinion in Immunology.The article was published on 2013-10-01 and is currently open access. It has received 244 citations till now. The article focuses on the topics: Deconvolution.read more
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Peripheral blood cellular dynamics of rheumatoid arthritis treatment informs about efficacy of response to disease modifying drugs
Åsa K. Hedman,Eitan Winter,Niyaz Yoosuf,Yair Benita,Louise Berg,Boel Brynedal,Lasse Folkersen,Lars Klareskog,Mateusz Maciejewski,Alexandra Sirota-Madi,Daniel Ziemek,Leonid Padyukov,Shai S. Shen-Orr,Scott A. Jelinsky +13 more
TL;DR: In this paper , the relevance of changes in cell proportions in peripheral blood mononuclear cells (PBMCs) during the development of rheumatoid arthritis and following treatment was determined.
Transcriptomic profiling of whole blood in 22q11.2 reciprocal copy number variants reveals that cell proportion highly impacts gene expression.
Amy Lin,Amy Lin,Jennifer K Forsyth,Jennifer K Forsyth,Gil D Hoftman,Leila Kushan-Wells,Maria Jalbrzikowski,Deepika Dokuru,Giovanni Coppola,Ania Fiksinski,Ania Fiksinski,Janneke Zinkstok,Jacob A. S. Vorstman,Daniel Nachun,Daniel Nachun,Carrie E. Bearden,Carrie E. Bearden +16 more
TL;DR: In this paper, the authors characterized transcriptomic dysregulation in peripheral blood from reciprocal 22q11.2 CNV carriers using differential expression analysis and weighted gene co-expression network analysis to identify modules of co-expressed genes.
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Genetic Loss of Nicotinamide Nucleotide Transhydrogenase Prevents from Cardiometabolic Heart Failure with Preserved Ejection Fraction
TL;DR: In this article , the loss of Nicotinamide Nucleotide Transhydrogenase (NNT) protects against both cardiac and metabolic consequences of HFD+L-NAME, thus highlighting a novel etiology-specific avenue for HFpEF therapeutics.
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Identification of the key immune cells and genes for the diagnostics and therapeutics of meningioma.
Jiawei Chen,Lingyang Hua,Xiupeng Xu,Zeyidan Jiapaer,Jiaojiao Deng,Daijun Wang,Guoping Li,Ye Gong +7 more
TL;DR: In this article , the authors used CIBERSORT algorithm to analyze the immune cell infiltration in samples and found that ADCY1, BMX, KCNA5, SLCO4A1, and TTR are potential therapeutic targets and their associations with macrophages, neutrophils, NK cells, and plasma cells might impact the tumorigenesis of meningiomas.
References
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Journal ArticleDOI
Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
TL;DR: The hierarchical model of Lonnstedt and Speed (2002) is developed into a practical approach for general microarray experiments with arbitrary numbers of treatments and RNA samples and the moderated t-statistic is shown to follow a t-distribution with augmented degrees of freedom.
Journal ArticleDOI
Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1
Roel G.W. Verhaak,Katherine A. Hoadley,Elizabeth Purdom,Victoria Wang,Yuan-yuan Qi,Matthew D. Wilkerson,C. Ryan Miller,Li Ding,Todd R. Golub,Jill P. Mesirov,Gabriele Alexe,Michael S. Lawrence,Michael O'Kelly,Pablo Tamayo,Barbara A. Weir,Stacey Gabriel,Wendy Winckler,Supriya Gupta,Lakshmi Jakkula,Heidi S. Feiler,J. Graeme Hodgson,C. David James,Jann N. Sarkaria,Cameron Brennan,Ari B. Kahn,Paul T. Spellman,Richard K. Wilson,Terence P. Speed,Terence P. Speed,Joe W. Gray,Matthew Meyerson,Gad Getz,Charles M. Perou,Charles M. Perou,D. Neil Hayes +34 more
TL;DR: A robust gene expression-based molecular classification of GBM into Proneural, Neural, Classical, and Mesenchymal subtypes is described and multidimensional genomic data is integrated to establish patterns of somatic mutations and DNA copy number.
Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1
Roel G.W. Verhaak,Katherine A. Hoadley,Elizabeth Purdom,Victoria Wang,Yuan-yuan Qi,Matthew D. Wilkerson,C. Ryan Miller,Li Ding,Todd R. Golub,Jill P. Mesirov,Gabriele Alexe,Michael S. Lawrence,Michael O'Kelly,Pablo Tamayo,Barbara A. Weir,Stacey Gabriel,Wendy Winckler,Supriya Gupta,Lakshmi Jakkula,Heidi S. Feiler,J. Graeme Hodgson,C. David James,Jann N. Sarkaria,Cameron Brennan,Ari B. Kahn,Paul T. Spellman,Richard K. Wilson,Terence P. Speed,Terence P. Speed,Joe W. Gray,Matthew Meyerson,Gad Getz,Charles M. Perou,Charles M. Perou,D. Neil Hayes +34 more
TL;DR: The Cancer Genome Atlas Network recently cataloged recurrent genomic abnormalities in glioblastoma multiforme (GBM) and proposed a robust gene expression-based molecular classification of GBM into Proneural, Neural, Classical, and Mesenchymal subtypes as discussed by the authors.
Journal ArticleDOI
Molecular signatures database (MSigDB) 3.0
Arthur Liberzon,Aravind Subramanian,Reid M. Pinchback,Helga Thorvaldsdottir,Pablo Tamayo,Jill P. Mesirov +5 more
TL;DR: A new version of the database, MSigDB 3.0, is reported, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.
Journal ArticleDOI
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1
David A. Barbie,Pablo Tamayo,Jesse S. Boehm,So Young Kim,Susan Moody,Ian F. Dunn,Anna C. Schinzel,Peter Sandy,Etienne Meylan,Claudia Scholl,Stefan Fröhling,Edmond M. Chan,Martin L. Sos,Kathrin Michel,Craig H. Mermel,Serena J. Silver,Barbara A. Weir,Jan H. Reiling,Qing Sheng,Piyush Gupta,Raymond C. Wadlow,Raymond C. Wadlow,Hanh Le,Sebastian Hoersch,Ben S. Wittner,Ben S. Wittner,Sridhar Ramaswamy,Sridhar Ramaswamy,David M. Livingston,David M. Sabatini,Matthew Meyerson,Matthew Meyerson,Roman K. Thomas,Eric S. Lander,Jill P. Mesirov,David E. Root,D. Gary Gilliland,Tyler Jacks,William C. Hahn +38 more
TL;DR: Observations indicate that TBK1 and NF-κB signalling are essential in KRAS mutant tumours, and establish a general approach for the rational identification of co-dependent pathways in cancer.