Dynamic modeling of the cellular senescence gene regulatory network.

ABSTRACT: Cellular senescence is a cell fate that prominently impacts physiological and pathophysiological processes. Diverse cellular stresses induce it, and dramatic gene expression changes accompany it. However, determining the interactions comprising the gene regulatory network (GRN) governing senescence remains challenging. Recent advances in signal processing techniques provide opportunities to reconstruct GRNs. Here, we describe a GRN for senescence integrating time-series transcriptome and transcription factor depletion datasets. Specifically, we infer a set of differential equations using the "Sparse Identification of Nonlinear Dynamics" (SINDy) algorithm, discriminate genes with potential hidden regulators, validate the inferred GRN for time-points not included in the training data, and co

SUBMITTER: Nabuco Leva Ferreira de Freitas JA 

PROVIDER: S-EPMC10015196 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature