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gwaybio / cell_state_papers

Cataloging papers on cell state - Data, experiments, methods, and theory
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Topslam: Waddington Landscape Recovery for Single Cell Experiments #4

Open gwaybio opened 7 years ago

gwaybio commented 7 years ago

https://doi.org/10.1101/057778

Authors

Zwiessele, M. and Lawrence, N.D.

Year

2016

Abstract

We present an approach to estimate the nature of the Waddington (or epigenetic) landscape that underlies a population of individual cells. Through exploiting high resolution single cell transcription experiments we show that cells can be located on a landscape that reflects their differentiated nature. Our approach makes use of probabilistic non-linear dimensionality reduction that respects the topology of our estimated epigenetic landscape. In simulation studies and analyses of real data we show that the approach, known as topslam, outperforms previous attempts to understand the differentiation landscape. Hereby, the novelty of our approach lies in the correction of distances before extracting ordering information. This gives the advantage over other attempts, which have to correct for extracted time lines by post processing or additional data.

gwaybio commented 7 years ago

Experimental Methods

Simulation of differentation patterns and apply four different landscape creation approaches: PCA, ICA, t-SNE, and their method (Bayesian GPLVM)

Also apply these methods to qPCR data of 437 cells across mouse developmental stages (one to 64 cell state)

Computational Methods

Their method extracts the latent representation dimensionality (can be thought of as cell states?) and determines a non-linear model of single cell data. This underlying model is used to build a graph (or some sort of clustering or ordering of cells) to uncover trajectories.

Code is made available here