viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia
TL;DR: In this article, the authors present viSNE, a tool that allows one to map high-dimensional cytometry data onto two dimensions, yet conserve the highdimensional structure of the data by using all pairwise distances in high dimension to determine each cell's location in the plot.
Abstract: New high-dimensional, single-cell technologies offer unprecedented resolution in the analysis of heterogeneous tissues. However, because these technologies can measure dozens of parameters simultaneously in individual cells, data interpretation can be challenging. Here we present viSNE, a tool that allows one to map high-dimensional cytometry data onto two dimensions, yet conserve the high-dimensional structure of the data. viSNE plots individual cells in a visual similar to a scatter plot, while using all pairwise distances in high dimension to determine each cell's location in the plot. We integrated mass cytometry with viSNE to map healthy and cancerous bone marrow samples. Healthy bone marrow automatically maps into a consistent shape, whereas leukemia samples map into malformed shapes that are distinct from healthy bone marrow and from each other. We also use viSNE and mass cytometry to compare leukemia diagnosis and relapse samples, and to identify a rare leukemia population reminiscent of minimal residual disease. viSNE can be applied to any multi-dimensional single-cell technology.
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TL;DR: Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together.
5,506 citations
TL;DR: Monocle is described, an unsupervised algorithm that increases the temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points that revealed switch-like changes in expression of key regulatory factors, sequential waves of gene regulation, and expression of regulators that were not known to act in differentiation.
Abstract: Defining the transcriptional dynamics of a temporal process such as cell differentiation is challenging owing to the high variability in gene expression between individual cells. Time-series gene expression analyses of bulk cells have difficulty distinguishing early and late phases of a transcriptional cascade or identifying rare subpopulations of cells, and single-cell proteomic methods rely on a priori knowledge of key distinguishing markers. Here we describe Monocle, an unsupervised algorithm that increases the temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. Applied to the differentiation of primary human myoblasts, Monocle revealed switch-like changes in expression of key regulatory factors, sequential waves of gene regulation, and expression of regulators that were not known to act in differentiation. We validated some of these predicted regulators in a loss-of function screen. Monocle can in principle be used to recover single-cell gene expression kinetics from a wide array of cellular processes, including differentiation, proliferation and oncogenic transformation.
4,119 citations
01 May 2015
TL;DR: Drop-seq as discussed by the authors analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin, and identifies 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes.
Abstract: Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT.
3,365 citations
TL;DR: This work presents Scanpy, a scalable toolkit for analyzing single-cell gene expression data that includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks, and AnnData, a generic class for handling annotated data matrices.
Abstract: Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks. Its Python-based implementation efficiently deals with data sets of more than one million cells (
https://github.com/theislab/Scanpy
). Along with Scanpy, we present AnnData, a generic class for handling annotated data matrices (
https://github.com/theislab/anndata
).
3,343 citations
Cites methods from "viSNE enables visualization of high..."
...Specifically, SCANPY provides preprocessing comparable to SEURAT [10] and CELL RANGER [6], visualization through TSNE [11, 12], graph-drawing [13– 15] and diffusion maps [11, 16, 17], clustering similar *Correspondence: alex.wolf@helmholtz-muenchen.de; fabian.theis@helmholtz-muenchen.de 1Helmholtz Zentrum München – German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany 2Department of Mathematics, Technische Universität München, Munich, Germany to PHENOGRAPH [18–20], identification of marker genes for clusters via differential expression tests and pseudotemporal ordering via diffusion pseudotime [21], which compares favorably [22] with MONOCLE 2 [22], and WISHBONE [23] (Fig....
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...Parts of the toolkit rely on SCIKIT-LEARN [27], STATSMODELS [38], SEABORN [39], NETWORKX [28], IGRAPH [14], the TSNE package of [40], and the Louvain clustering package of [41]....
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...Specifically, SCANPY provides preprocessing comparable to SEURAT [10] and CELL RANGER [6], visualization through TSNE [11, 12], graph-drawing [13– 15] and diffusion maps [11, 16, 17], clustering similar...
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...We use pseudotemporal ordering from a root cell in the CD34+ cluster and detect a branching trajectory, visualized with TSNE and diffusion maps. b Speedup over CELL RANGER R kit....
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...TSNE and graph-drawing (Fruchterman–Reingold) visualizations show cell-type annotations obtained by comparisons with bulk expression....
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TL;DR: Comparing the performance of UMAP with five other tools, it is found that UMAP provides the fastest run times, highest reproducibility and the most meaningful organization of cell clusters.
Abstract: Advances in single-cell technologies have enabled high-resolution dissection of tissue composition. Several tools for dimensionality reduction are available to analyze the large number of parameters generated in single-cell studies. Recently, a nonlinear dimensionality-reduction technique, uniform manifold approximation and projection (UMAP), was developed for the analysis of any type of high-dimensional data. Here we apply it to biological data, using three well-characterized mass cytometry and single-cell RNA sequencing datasets. Comparing the performance of UMAP with five other tools, we find that UMAP provides the fastest run times, highest reproducibility and the most meaningful organization of cell clusters. The work highlights the use of UMAP for improved visualization and interpretation of single-cell data.
3,016 citations
References
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Journal Article•
TL;DR: A new technique called t-SNE that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map, a variation of Stochastic Neighbor Embedding that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map.
Abstract: We present a new technique called “t-SNE” that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map. The technique is a variation of Stochastic Neighbor Embedding (Hinton and Roweis, 2002) that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map. t-SNE is better than existing techniques at creating a single map that reveals structure at many different scales. This is particularly important for high-dimensional data that lie on several different, but related, low-dimensional manifolds, such as images of objects from multiple classes seen from multiple viewpoints. For visualizing the structure of very large datasets, we show how t-SNE can use random walks on neighborhood graphs to allow the implicit structure of all of the data to influence the way in which a subset of the data is displayed. We illustrate the performance of t-SNE on a wide variety of datasets and compare it with many other non-parametric visualization techniques, including Sammon mapping, Isomap, and Locally Linear Embedding. The visualizations produced by t-SNE are significantly better than those produced by the other techniques on almost all of the datasets.
30,124 citations
TL;DR: This work proposes a heuristic method that is shown to outperform all other known community detection methods in terms of computation time and the quality of the communities detected is very good, as measured by the so-called modularity.
Abstract: We propose a simple method to extract the community structure of large networks. Our method is a heuristic method that is based on modularity optimization. It is shown to outperform all other known community detection method in terms of computation time. Moreover, the quality of the communities detected is very good, as measured by the so-called modularity. This is shown first by identifying language communities in a Belgian mobile phone network of 2.6 million customers and by analyzing a web graph of 118 million nodes and more than one billion links. The accuracy of our algorithm is also verified on ad-hoc modular networks. .
13,519 citations
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
Abstract: RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.
11,528 citations
TL;DR: In this paper, the authors proposed a simple method to extract the community structure of large networks based on modularity optimization, which is shown to outperform all other known community detection methods in terms of computation time.
Abstract: We propose a simple method to extract the community structure of large networks. Our method is a heuristic method that is based on modularity optimization. It is shown to outperform all other known community detection methods in terms of computation time. Moreover, the quality of the communities detected is very good, as measured by the so-called modularity. This is shown first by identifying language communities in a Belgian mobile phone network of 2 million customers and by analysing a web graph of 118 million nodes and more than one billion links. The accuracy of our algorithm is also verified on ad hoc modular networks.
11,078 citations
TL;DR: Single-cell “mass cytometry” analyses provide system-wide views of immune signaling in healthy human hematopoiesis, against which drug action and disease can be compared for mechanistic studies and pharmacologic intervention.
Abstract: Flow cytometry is an essential tool for dissecting the functional complexity of hematopoiesis. We used single-cell "mass cytometry" to examine healthy human bone marrow, measuring 34 parameters simultaneously in single cells (binding of 31 antibodies, viability, DNA content, and relative cell size). The signaling behavior of cell subsets spanning a defined hematopoietic hierarchy was monitored with 18 simultaneous markers of functional signaling states perturbed by a set of ex vivo stimuli and inhibitors. The data set allowed for an algorithmically driven assembly of related cell types defined by surface antigen expression, providing a superimposable map of cell signaling responses in combination with drug inhibition. Visualized in this manner, the analysis revealed previously unappreciated instances of both precise signaling responses that were bounded within conventionally defined cell subsets and more continuous phosphorylation responses that crossed cell population boundaries in unexpected manners yet tracked closely with cellular phenotype. Collectively, such single-cell analyses provide system-wide views of immune signaling in healthy human hematopoiesis, against which drug action and disease can be compared for mechanistic studies and pharmacologic intervention.
2,147 citations