Gene pair signatures in cell type transcriptomes reveal lineage control View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-04-21

AUTHORS

Merja Heinäniemi, Matti Nykter, Roger Kramer, Anke Wienecke-Baldacchino, Lasse Sinkkonen, Joseph Xu Zhou, Richard Kreisberg, Stuart A. Kauffman, Sui Huang, Ilya Shmulevich

ABSTRACT

The distinct cell types of multicellular organisms arise owing to constraints imposed by gene regulatory networks on the collective change of gene expression across the genome, creating self-stabilizing expression states, or attractors. We curated human expression data comprising 166 cell types and 2,602 transcription-regulating genes and developed a data-driven method for identifying putative determinants of cell fate built around the concept of expression reversal of gene pairs, such as those participating in toggle-switch circuits. This approach allows us to organize the cell types into their ontogenic lineage relationships. Our method identifies genes in regulatory circuits that control neuronal fate, pluripotency and blood cell differentiation, and it may be useful for prioritizing candidate factors for direct conversion of cell fate. More... »

PAGES

577-583

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmeth.2445

DOI

http://dx.doi.org/10.1038/nmeth.2445

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1022144263

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/23603899


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