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Identifying the dynamic gene regulatory network during latent HIV-1 reactivation using high-dimensional ordinary differential equations.

ABSTRACT: Reactivation of latently infected cells has emerged as an important strategy for eradication of HIV. However, genetic mechanisms of regulation after reactivation remain unclear. We describe a five-step pipeline to study the dynamics of the gene regulatory network following a viral reactivation using high-dimensional ordinary differential equations. Our pipeline implements a combination of five different methods, by detecting temporally differentially expressed genes (step 1), clustering genes with similar temporal expression patterns into a small number of response modules (step2), performing a functional enrichment analysis within each gene response module (step 3), identifying a network structure based on the gene response modules using ordinary differential equations (ODE) and a high-dimensional variable selection technique (step 4), and obtaining a gene regulatory model based on refined parameter estimates using nonlinear least squares (step 5). We applied our pipeline to a time course gene expression data of latently infected T-cells following a latency-reversion.

SUBMITTER: Song J

PROVIDER: S-EPMC8442249 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Network Reconstruction From High-Dimensional Ordinary Differential Equations.

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