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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Whole-tissue deconvolution and scRNAseq analysis identify altered endometrial cellular compositions and functionality associated with endometriosis
Daniel Bunis,Wanxin Wang,Júlia Vallvé-Juanico,Sahar Houshdaran,Sushmita Sen,Isam Ben Soltane,Idit Kosti,Kim Chi Vo,Juan Irwin,Linda C. Giudice,Marina Sirota +10 more
TL;DR: Cell type deconvolution and single cell RNAseq analysis identify altered endometrial cellular compositions in women with endometriosis, underscoring roles for nonimmune as well as immune cells to the dysfunctionality of this tissue.
Journal ArticleDOI
Basic Gene Expression Characteristics of Glioma Stem Cells and Human Glioblastoma
Daisuke Sakamoto,Toshinori Takagi,Mitsugu Fujita,Seiichi Omura,Yasunori Yoshida,Tomoko Iida,Shinichi Yoshimura +6 more
TL;DR: The factor loadings of the principal component analysis (PCA) suggested that v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN), dipeptidyl- peptidase 4 (DPP4), and macrophage migration-inhibitory factor (MIF) contribute to the stemness of GSCs.
Journal ArticleDOI
Racial and socioeconomic disparity associates with differences in cardiac DNA methylation among men with end-stage heart failure.
Mark E Pepin,Mark E Pepin,Chae-Myeong Ha,Luke A Potter,Sayan Bakshi,Joseph Barchue,Ayman Haj Asaad,Steven M. Pogwizd,Salpy V. Pamboukian,Bertha Hidalgo,Selwyn M. Vickers,Adam R. Wende +11 more
TL;DR: A bimodal signature of cardiac DNA methylation in heart failure corresponds with racial differences in all-cause mortality following mechanical circulatory support as discussed by the authors, showing that race differences in promoter m...
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Further evidence for depletion of peripheral blood natural killer cells in patients with schizophrenia: A computational deconvolution study.
TL;DR: The results indicate that patients with schizophrenia present innate immunity dysregulation in terms of NK cells depletion and increased levels of granulocytes.
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Sequential compression across latent space dimensions enhances gene expression signatures
TL;DR: Ensembles of features from different unsupervised algorithms discover biological signatures in large transcriptomic datasets to enhance biological signature discovery by compressing input data into a single pre-selected dimensionality.
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.