Modeling and visualizing cell type switching

DOI10.1155/2014/293980MaRDI QIDQ2262444zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Ahmadreza Ghaffarizadeh, Gregory J. Podgorski, Nicholas S. Flann

Publication date 16 March 2015

Published in Computational \& Mathematical Methods in Medicine (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1155/2014/293980

Mathematics Subject Classification ID

Cell biology (92C37)

Review text

Summary: Understanding cellular differentiation is critical in explaining development and for taming diseases such as cancer. Differentiation is conventionally represented using bifurcating lineage trees. However, these lineage trees cannot readily capture or quantify all the types of transitions now known to occur between cell types, including transdifferentiation or differentiation off standard paths. This work introduces a new analysis and visualization technique that is capable of representing all possible transitions between cell states compactly, quantitatively, and intuitively. This method considers the regulatory network of transcription factors that control cell type determination and then performs an analysis of network dynamics to identify stable expression profiles and the potential cell types that they represent. A visualization tool called \textit{CellDiff3D} creates an intuitive three-dimensional graph that shows the overall direction and probability of transitions between all pairs of cell types within a lineage. In this study, the influence of gene expression noise and mutational changes during myeloid cell differentiation are presented as a demonstration of the \textit{CellDiff3D} technique, a new approach to quantify and envision all possible cell state transitions in any lineage network.

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Cites work

• Bioinformatics

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• Single-cell multi-omic velocity infers dynamic and decoupled gene regulation
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