FXR

FXR integrates publicly available Farnesoid X receptor (FXR) ChIP-seq datasets across mouse, rat, and human to produce a consolidated binding atlas for meta-analysis of FXR genomic interactions and regulatory pathways.

Key Features:

• Standardized biocuration: A harmonized biocuration pipeline standardizes processing of disparate FXR ChIP-seq datasets to enable consistent downstream analysis from raw sequencing reads to functional pathways.
• Dataset integration: Aggregates public FXR ChIP-seq data across species (mouse, rat, human) and experimental conditions to address heterogeneity and incomplete datasets.
• FXR binding atlas: Virtually merges individual murine datasets to construct a consolidated "FXR binding atlas" that increases effective sequencing depth.
• Enhanced detection: Increased sequencing depth and consolidation reveal novel FXR binding sites and signaling pathways not detected in isolated studies.
• Cross-species comparison: Enables quantitative comparison of FXR binding patterns across species and conditions.

Scientific Applications:

• Meta-analysis of ChIP-seq data: Consolidates multiple FXR ChIP-seq experiments to produce a more comprehensive map of FXR genomic interactions.
• Comparative genomics: Quantifies overlap of FXR binding sites across species, reporting ~48% similarity between mouse and human datasets and ~55% similarity between mouse and rat datasets.
• In vivo versus in vitro assessment: Indicates greater similarity among in vivo data across species compared to human in vitro data.
• Regulatory and translational insight: Supports identification of FXR-regulated genes and signaling pathways relevant to therapeutic targeting in liver disease.

Methodology:

Integration of publicly available FXR ChIP-seq datasets using a standardized biocuration pipeline, virtual merging of murine datasets to build a consolidated binding atlas, and end-to-end analysis from raw sequencing reads to affected functional pathways for meta-analysis.