GRNdb

GRNdb catalogs transcription factor-centered gene regulatory networks (regulons) across human and mouse conditions to support analysis of gene expression regulation and heterogeneity.

Key Features:

• Extensive Data Integration: Integrates large-scale single-cell RNA-seq and bulk RNA-seq data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project, encompassing over 633,000 cells, more than 27,700 bulk samples, and 184 physiological and pathological conditions across human and mouse.
• Predictive Modeling: Utilizes known transcription factor–target relationships to predict gene regulatory networks at both single-cell and bulk resolutions, yielding 77,746 predicted GRNs and 19,687,841 TF–target pairs with associated binding motifs.
• Dynamic Network Analysis: Captures condition-specific changes in GRNs to enable comparison of regulatory network dynamics across diverse physiological and pathological states.
• Cancer-related Analyses: Enables analysis of gene expression profiles, expression correlations, and associations between expression levels and patient survival across diverse cancers.

Scientific Applications:

• Developmental biology: Elucidates transcription factor–target interactions and regulatory programs underlying development in human and mouse.
• Disease pathogenesis: Identifies condition-specific regulatory changes and dysregulated regulators implicated in disease processes, including cancer.
• Therapeutic target discovery: Supports identification of candidate regulatory factors and target genes for follow-up experimental validation.
• Comparative single-cell and bulk analysis: Facilitates comparison of cell-type-resolved and tissue-level regulatory networks derived from single-cell RNA-seq and bulk RNA-seq.

Methodology:

Integrates single-cell RNA-seq and bulk RNA-seq from TCGA and GTEx and predicts GRNs using known TF–target relationships, producing 77,746 predicted GRNs, 19,687,841 TF–target pairs, and associated binding motifs at single-cell and bulk resolutions.