TY - JOUR
T1 - A qualitative analysis of ubiquitous regulatory motifs in Saccharomyces cerevisiae genetic networks
AU - Camacho, Erika
AU - Radulescu, Anca
AU - Wirkus, Stephen
AU - Marshall, Pamela
PY - 2019/4/1
Y1 - 2019/4/1
N2 - This work examines bistability and multistability within a Recurrent Neural Network model (RNN) for a 2-node and 3-node system under many different regulation scenarios. We determine parameter regions where there is bistability, multistability, or other stable modes in the expression states of the systems described by this network model. Our results show that although bistability can be generated with autoregulation it is also the case that both autorepression or no autoregulation can yield bistability as long as a sigmoidal behavior is present. Additionally, our results show the importance of considering more than a single connection when inferring a network as the observed biological result is averaged over many outcomes, which has implications for many algorithms that infer gene regulatory networks using the RNN models.
AB - This work examines bistability and multistability within a Recurrent Neural Network model (RNN) for a 2-node and 3-node system under many different regulation scenarios. We determine parameter regions where there is bistability, multistability, or other stable modes in the expression states of the systems described by this network model. Our results show that although bistability can be generated with autoregulation it is also the case that both autorepression or no autoregulation can yield bistability as long as a sigmoidal behavior is present. Additionally, our results show the importance of considering more than a single connection when inferring a network as the observed biological result is averaged over many outcomes, which has implications for many algorithms that infer gene regulatory networks using the RNN models.
KW - Bifurcation
KW - Gene network
KW - Recurrent neural network
UR - http://www.scopus.com/inward/record.url?scp=85054017531&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85054017531&partnerID=8YFLogxK
U2 - 10.1016/j.cnsns.2018.09.001
DO - 10.1016/j.cnsns.2018.09.001
M3 - Article
AN - SCOPUS:85054017531
SN - 1007-5704
VL - 69
SP - 148
EP - 167
JO - Communications in Nonlinear Science and Numerical Simulation
JF - Communications in Nonlinear Science and Numerical Simulation
ER -