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
Citations
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Robust enumeration of cell subsets from tissue expression profiles
Aaron M. Newman,Chih Long Liu,Michael R. Green,Andrew J. Gentles,Weiguo Feng,Yue Xu,Chuong D. Hoang,Maximilian Diehn,Arash Ash Alizadeh +8 more
TL;DR: CIBERSORT outperformed other methods with respect to noise, unknown mixture content and closely related cell types when applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors.
Journal ArticleDOI
xCell: digitally portraying the tissue cellular heterogeneity landscape
TL;DR: This work presents xCell, a novel gene signature-based method, and uses it to infer 64 immune and stromal cell types and shows that xCell outperforms other methods.
Journal ArticleDOI
Determining cell type abundance and expression from bulk tissues with digital cytometry.
Aaron M. Newman,Chloé B. Steen,Chloé B. Steen,Chih Long Liu,Andrew J. Gentles,Aadel A. Chaudhuri,Florian Scherer,Michael S. Khodadoust,Mohammad Shahrokh Esfahani,Bogdan A. Luca,David F. Steiner,Maximilian Diehn,Ash A. Alizadeh +12 more
TL;DR: The utility of CIBERSORTx is evaluated in multiple tumor types, including melanoma, where single-cell reference profiles were used to dissect bulk clinical specimens, revealing cell-type-specific phenotypic states linked to distinct driver mutations and response to immune checkpoint blockade.
Journal ArticleDOI
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
Etienne Becht,Nicolas A. Giraldo,Nicolas A. Giraldo,Nicolas A. Giraldo,Laetitia Lacroix,Laetitia Lacroix,Laetitia Lacroix,Bénédicte Buttard,Bénédicte Buttard,Bénédicte Buttard,Nabila Elarouci,Florent Petitprez,Janick Selves,Pierre Laurent-Puig,Catherine Sautès-Fridman,Catherine Sautès-Fridman,Catherine Sautès-Fridman,Wolf H. Fridman,Wolf H. Fridman,Wolf H. Fridman,Aurélien de Reyniès +20 more
TL;DR: The Microenvironment Cell Populations-counter method is introduced, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data and demonstrates that MCP-counter overcomes several limitations or weaknesses of previously proposed computational approaches.
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A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
Maayan Baron,Adrian Veres,Samuel L. Wolock,Aubrey L. Faust,Renaud Gaujoux,Amedeo Vetere,Jennifer Hyoje Ryu,Bridget K. Wagner,Shai S. Shen-Orr,Allon M. Klein,Douglas A. Melton,Itai Yanai +11 more
TL;DR: A droplet-based, single-cell RNA-seq method is implemented to determine the transcriptomes of over 12,000 individual pancreatic cells from four human donors and two mouse strains and provides a resource for the discovery of novel cell type-specific transcription factors, signaling receptors, and medically relevant genes.
References
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DNA methylation arrays as surrogate measures of cell mixture distribution
Eugene Andres Houseman,William P. Accomando,Devin C. Koestler,Brock C. Christensen,Carmen J. Marsit,Heather H. Nelson,John K. Wiencke,Karl T. Kelsey +7 more
TL;DR: This work presents a method, similar to regression calibration, for inferring changes in the distribution of white blood cells between different subpopulations using DNA methylation signatures, in combination with a previously obtained external validation set consisting of signatures from purified leukocyte samples.
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TL;DR: A computational method that infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations is described, revealing that genome-doubling events are common in human cancer, likely occur in cells that are already aneuploid, and influence pathways of tumor progression.
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Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
Daniel Ramsköld,Shujun Luo,Yu-Chieh Wang,Robin Li,Qiaolin Deng,Omid R. Faridani,Gregory A. Daniels,Irina Khrebtukova,Jeanne F. Loring,Louise C. Laurent,Gary P. Schroth,Rickard Sandberg,Rickard Sandberg +12 more
TL;DR: Applying Smart-Seq to circulating tumor cells from melanomas, it is found that although gene expression estimates from single cells have increased noise, hundreds of differentially expressed genes could be identified using few cells per cell type.
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Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
Noa Novershtern,Noa Novershtern,Noa Novershtern,Aravind Subramanian,Lee N. Lawton,Raymond H. Mak,W. Nicholas Haining,Marie McConkey,Naomi Habib,Nir Yosef,Cindy Y. Chang,Cindy Y. Chang,Tal Shay,Garrett M. Frampton,Adam Drake,Ilya B. Leskov,Björn Nilsson,Björn Nilsson,Fred Preffer,David Dombkowski,John W. Evans,Ted Liefeld,John S. Smutko,Jianzhu Chen,Nir Friedman,Richard A. Young,Todd R. Golub,Todd R. Golub,Todd R. Golub,Aviv Regev,Aviv Regev,Aviv Regev,Benjamin L. Ebert,Benjamin L. Ebert,Benjamin L. Ebert +34 more
TL;DR: In this paper, the authors profiled gene expression in 38 distinct purified populations of human hematopoietic cells and used probabilistic models of gene expression and analysis of cis-elements in gene promoters to decipher the general organization of their regulatory circuitry.
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Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses.
Hazel M. Davey,Douglas B. Kell +1 more
TL;DR: Flow cytometry is a technique, which allows one to analyze cells rapidly and individually and permits the quantitative analysis of microbial heterogeneity, and offers many advantages over conventional measurements for both routine and more exploratory analyses of microbial properties.