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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Gene co-expression modules integrated with immunoscore predicts survival of non-small cell lung cancer.
Xue-Tao Li,Jia-Tao Zhang,Hong-Hong Yan,Jian Su,Mei-Ling Cheng,Qi-Hui Sun,Wen-Zhao Zhong,Yi-Long Wu,Xu-Chao Zhang,Jun Hou +9 more
TL;DR: In this paper, the authors aimed to deconvolve the levels of infiltrating immune cells in non-small cell lung cancer (NSCLC) and identify specific gene co-expression modules associated with prognosis of NSCLC.
Dissertation
Deconvolution of the immune landscape of cancer transcriptomics data, its relationship to patient survival and tumour subtypes
TL;DR: ImSig and the associated analysis framework described in this work, support the retrospective analysis of tissue derived transcriptomics data enabling better characterisation of immune infiltrate associated with disease, and in so doing, provide a resource useful for prognosis and potentially in guiding treatment.
Journal ArticleDOI
Classification of Patients With Sepsis According to Immune Cell Characteristics: A Bioinformatic Analysis of Two Cohort Studies.
TL;DR: A comprehensive tool to identify the immunoparalysis endotype and immunocompetent status in hospitalized patients with sepsis is developed and provides novel clues for further targeting of therapeutic approaches.
Journal ArticleDOI
A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq.
Surya Pandey,Michihiro Takahama,Adam Gruenbaum,Makda Zewde,Katerina Cheronis,Nicolas Chevrier +5 more
TL;DR: This protocol describes collection, storage and lysis of different types of mouse organs for monitoring gene expression on a whole-organism scale, and details protocols to perform high-throughput and low-cost RNA extraction and sequencing, as well as downstream data analysis.
Dissertation
Statistical Modeling and Learning of the Environmental and Genetic Drivers of Variation in Human Immunity
TL;DR: This thesis combines standardised flow cytometry of 173 parameters of innate and adaptive immune cells, genome-wide DNA genotyping, detailed information on life-style and environmental factors and MethylationEPIC array data of the Milieu Interieur cohort, to identify the genetic and environmental drivers of variation in the human immune system.
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.
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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.