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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Methods and systems for determining proportions of distinct cell subsets
TL;DR: In this paper, a regression between a feature profile of a first plurality of distinct components and a reference matrix of feature signatures for a second plurality of different components is used to deconvolution.
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Polled Digital Cell Sorter (p-DCS): Automatic identification of hematological cell types from single cell RNA-sequencing clusters
Sergii Domanskyi,Anthony Szedlak,Nathaniel T Hawkins,Jiayin Wang,Giovanni Paternostro,Carlo Piermarocchi +5 more
TL;DR: A computational tool for processing single cell RNA-seq data that uses a voting algorithm to identify cells based on approval votes received by known molecular markers and automatically assigns a cell type to clusters without an expert curator is presented.
Journal ArticleDOI
Unraveling patterns of disrupted gene expression across a complex tissue
Tina Heger,Matthew Fraleigh +1 more
TL;DR: In this paper , the effects of different cellular composition on whole tissue expression profiles were investigated, and it was shown that differences in cellular composition between tissues can modify expression profiles, potentially altering inferred gene ontological processes and insights into gene network evolution.
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Epigenetic changes with age primes mammary luminal epithelia for cancer initiation
Rosalyn W. Sayaman,Masaru Miyano,Parijat Senapati,Shalabi S,Zirbes A,Michael E. Todhunter,Seewaldt,Susan L. Neuhausen,Martha R. Stampfer,Dustin E. Schones,Mark A. LaBarge +10 more
TL;DR: In this paper, the authors found that the epigenomic and DNA methylation changes were robust indicators of aging luminal cells, and were either directly correlated with expression changes or served as priming events for subsequent dysregulation, such as demethylation of ESR1-binding regions in DNAm-regulatory CXXC5.
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Whole-Tissue Deconvolution and scRNAseq Analysis Identify Altered Endometrial Cellular Compositions and Functionality Associated With Endometriosis
John W. Snedden,r8hfbtq322 +1 more
TL;DR: In this paper , the authors comprehensively characterized immune and non-immune cell types in the endometrium of women with or without disease and their dynamic changes across the menstrual cycle through integrating whole-tissue deconvolution and single-cell RNAseq.
References
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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.