title: Genes related to differentiation are correlated with the gene regulatory network structure.
abstract: BACKGROUND
  Many secondary messengers, receptors and transcription factors are related to cell differentiation. Their role in cell differentiation can be affected by their position in the gene regulatory network. Here, we test whether the properties of the gene regulatory network can highlight which genes and proteins are associated with cell differentiation. We use a previously developed purely theoretical algorithm built to detect nodes that can induce a state change in Boolean gene regulatory networks, and show that most genes predicted to participate in differentiation in the theoretical framework are also experimentally known to be associated with such differentiation. These results show that genes related to differentiation are associated with specific features of the genetic regulatory network. The proposed algorithm produces a better classification than simple network measures such as the nodes degree or centrality. Boolean networks were used in many previous theoretical models. Here, we show a direct application of such networks to the detection of genes and subnetworks related to differentiation. The subnetwork emerging from the genes and edges that are predicted to be associated with differentiation are the most active molecular pathways experimentally described to be involved in cell differentiation.
  
  
  METHODS
  http://peptibase.cs.biu.ac.il/homepage/Boolean_network_conversion_code.zip.
authors: Department of Cell and Developmental Biology and Department of Genetics, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel and Department of Mathematics and Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel.
authors: Matan
authors: M
authors: Bodaker
authors: Eran
authors: E
authors: Meshorer
authors: Eduardo
authors: E
authors: Mitrani
authors: Yoram
authors: Y
authors: Louzoun
mesh_terms: D000465:Algorithms; D002454:Cell Differentiation / Q000235:genetics*; D053263:Gene Regulatory Networks; D025941:Protein Interaction Mapping