Molecular Interaction Networks to Select Factors for Cell Conversion

Ouyang, John F, Kamaraj, Uma S, Polo, Jose M, Gough, Julian and Rackham, Owen J L (2019) Molecular Interaction Networks to Select Factors for Cell Conversion. Methods in Molecular Biology, 1975, 333-361. (doi:10.1007/978-1-4939-9224-9_16).

Abstract

The process of identifying sets of transcription factors that can induce a cell conversion can be time-consuming and expensive. To help alleviate this, a number of computational tools have been developed which integrate gene expression data with molecular interaction networks in order to predict these factors. One such approach is Mogrify, an algorithm which ranks transcriptions factors based on their regulatory influence in different cell types and tissues. These ranks are then used to identify a nonredundant set of transcription factors to promote cell conversion between any two cell types/tissues. Here we summarize the important concepts and data sources that were used in the implementation of this approach. Furthermore, we describe how the associated web resource ( www.mogrify.net ) can be used to tailor predictions to specific experimental scenarios, for instance, limiting the set of possible transcription factors and including domain knowledge. Finally, we describe important considerations for the effective selection of reprogramming factors. We envision that such data-driven approaches will become commonplace in the field, rapidly accelerating the progress in stem cell biology.

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Contributors

Author: Owen J L Rackham

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