Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks

BMC Systems Biology
Isaac CrespoAntonio del Sol

Abstract

Cellular differentiation and reprogramming are processes that are carefully orchestrated by the activation and repression of specific sets of genes. An increasing amount of experimental results show that despite the large number of genes participating in transcriptional programs of cellular phenotypes, only few key genes, which are coined here as reprogramming determinants, are required to be directly perturbed in order to induce cellular reprogramming. However, identification of reprogramming determinants still remains a combinatorial problem, and the state-of-art methods addressing this issue rests on exhaustive experimentation or prior knowledge to narrow down the list of candidates. Here we present a computational method, without any preliminary selection of candidate genes, to identify reduced subsets of genes, which when perturbed can induce transitions between cellular phenotypes. The method relies on the expression profiles of two stable cellular phenotypes along with a topological analysis stability elements in the gene regulatory network that are necessary to cause this multi-stability. Since stable cellular phenotypes can be considered as attractors of gene regulatory networks, cell fate and cellular reprogramming in...Continue Reading

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Citations

Aug 27, 2015·Scientific Reports·Lamia'a BahnassawyJens Christian Schwamborn
Oct 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jeong-Rae KimKwang-Hyun Cho
Jun 21, 2016·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Vladimir Espinosa Angarica, Antonio Del Sol
Mar 1, 2016·Mathematical Biosciences·Hojjatullah Moradi, Vahid Johari Majd
Sep 1, 2016·Journal of Cellular Physiology·Shima Rastegar-PouyaniAbdulshakour Mohammadnia
Mar 9, 2018·Royal Society Open Science·Arnaud Poret, Carito Guziolowski
Mar 24, 2017·Bioinformatics·Sascha JungAntonio Del Sol
Mar 28, 2021·Neurobiology of Aging·Caterina GiovagnoniDaniel L A van den Hove
Mar 18, 2021·Physical Biology·Souvadra HatiMohit Kumar Jolly
Sep 3, 2021·Nature Communications·Enrico Borriello, Bryan C Daniels
Nov 9, 2021·Frontiers in Big Data·Domenico SgarigliaFabricio Alves Barbosa da Silva

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Software Mentioned

GeneNetWeaver
Patway
MedScan
Perl

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