Leveraging transcription factor physical proximity for enhancing gene regulation inference.

ABSTRACT:

Motivation

Gene regulation inference, a key challenge in systems biology, is crucial for understanding cell function, as it governs processes such as differentiation, cell state maintenance, signal transduction, and stress response. Leading methods utilize gene expression, chromatin accessibility, transcription factor (TF) DNA binding motifs, and prior knowledge. However, they overlook the fact that TFs must be in physical proximity to facilitate transcriptional gene regulation.

Results

To fill the gap, we develop GRIP-Gene Regulation Inference by considering TF Proximity-a gene regulation inference method that directly considers the physical proximity between regulating TFs. Specifically, we use the distance in a protein-protein interaction (PPI) network to estimate the phy

SUBMITTER: Huang X 

PROVIDER: S-EPMC12261443 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature