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Topslam: Waddington Landscape Recovery for Single Cell Experiments

View ORCID ProfileMax Zwiessele, View ORCID ProfileNeil D Lawrence
doi: https://doi.org/10.1101/057778
Max Zwiessele
1University of Sheffield, Department of Computerscience
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  • For correspondence: m.zwiessele@sheffield.ac.uk
Neil D Lawrence
1University of Sheffield, Department of Computerscience
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Abstract

We present an approach to estimating 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 13, 2017.
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Topslam: Waddington Landscape Recovery for Single Cell Experiments
Max Zwiessele, Neil D Lawrence
bioRxiv 057778; doi: https://doi.org/10.1101/057778
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Topslam: Waddington Landscape Recovery for Single Cell Experiments
Max Zwiessele, Neil D Lawrence
bioRxiv 057778; doi: https://doi.org/10.1101/057778

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