TY - CHAP
T1 - Learning robust dynamic networks in prokaryotes by gene expression networks iterative explorer (GENIE)
AU - Harari, Oscar
AU - Rubio-Escudero, Cristina
AU - Traverso, Patricio
AU - Santos, Marcelo
AU - Zwir, Igor
PY - 2008
Y1 - 2008
N2 - Genetic and genomic approaches have been used successfully to assign genes to distinct regulatory networks, but the uncertainty concerning the connections between genes, the ambiguity inherent to the biological processes, and the impossibility of experimentally determining the underlying biological properties only allow a rough prediction of the dynamics of genes. Here we describe the GENIE methodology that formulates alternative models of genetic regulatory networks based on the available literature and transcription factor binding site evidence. It also provides a framework for the analysis of these models optimized by genetic algorithms, inferring their optimal parameters, simulating their behavior, evaluating them by integrating robustness, realness and flexibility criteria, and contrasting the predictions to experimentally results obtained by Gene Fluorescence Protein analysis. The application of this method to the regulatory network of the bacterium Salmonella enterica uncovered new mechanisms that enable the inter-connection of the PhoP/PhoQ and the PmrA/PmrB two component systems. The predictions were experimentally verified to establish that both transcriptional and post-transcriptional mechanisms are employed to connect these two systems.
AB - Genetic and genomic approaches have been used successfully to assign genes to distinct regulatory networks, but the uncertainty concerning the connections between genes, the ambiguity inherent to the biological processes, and the impossibility of experimentally determining the underlying biological properties only allow a rough prediction of the dynamics of genes. Here we describe the GENIE methodology that formulates alternative models of genetic regulatory networks based on the available literature and transcription factor binding site evidence. It also provides a framework for the analysis of these models optimized by genetic algorithms, inferring their optimal parameters, simulating their behavior, evaluating them by integrating robustness, realness and flexibility criteria, and contrasting the predictions to experimentally results obtained by Gene Fluorescence Protein analysis. The application of this method to the regulatory network of the bacterium Salmonella enterica uncovered new mechanisms that enable the inter-connection of the PhoP/PhoQ and the PmrA/PmrB two component systems. The predictions were experimentally verified to establish that both transcriptional and post-transcriptional mechanisms are employed to connect these two systems.
UR - http://www.scopus.com/inward/record.url?scp=44949134074&partnerID=8YFLogxK
U2 - 10.1007/978-3-540-78987-1_27
DO - 10.1007/978-3-540-78987-1_27
M3 - Chapter
AN - SCOPUS:44949134074
SN - 9783540789864
T3 - Studies in Computational Intelligence
SP - 299
EP - 311
BT - Nature Inspired Cooperative Strategies for Optimization (NICSO 2007)
A2 - Krasnogor, Natalio
A2 - Nicosia, Giuseppe
A2 - Pavone, Mario
A2 - Pelta, David
ER -