NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.

ABSTRACT:

Motivation

Transcription factor (TF) coordination plays a key role in gene regulation via direct and/or indirect protein-protein interactions (PPIs) and co-binding to regulatory elements on DNA. Single-cell technologies facilitate gene expression measurement for individual cells and cell-type identification, yet the connection between TF-TF coordination and target gene (TG) regulation of various cell types remains unclear.

Results

To address this, we introduce our innovative computational approach, Network Regression Embeddings (NetREm), to reveal cell-type TF-TF coordination activities for TG regulation. NetREm leverages network-constrained regularization, using prior knowledge of PPIs among TFs, to analyze single-cell gene expression data, uncovering cell-type coordinating

SUBMITTER: Khullar S 

PROVIDER: S-EPMC12011367 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature