Jun 8, 2016

Topslam: Waddington Landscape Recovery for Single Cell Experiments

BioRxiv : the Preprint Server for Biology
Max Zwiessele, Neil D Lawrence

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.

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Mentioned in this Paper

Transcription, Genetic
Cell Differentiation Process
Study of Epigenetics
Simulation
Analysis
Population Group
Anatomy, Regional
Landscapes
Epigenetic Process
Research Study

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