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Related Experiment Video

Updated: Jan 24, 2026

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies
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A Comprehensive FXR Signaling Atlas Derived from Pooled ChIP-seq Data.

Emilian Jungwirth1, Katrin Panzitt2, Hanns-Ulrich Marschall3

  • 1Institute of Computational Biotechnology, Graz University of Technology, Austria.

Studies in Health Technology and Informatics
|May 24, 2019
PubMed
Summary

Combining publicly available ChIP-seq data for the liver receptor FXR (farnesoid X receptor) reveals a more comprehensive understanding of its signaling pathways. This FXR super-signaling atlas overcomes limitations of individual datasets.

Keywords:
ChIP-seqENCODEFXR

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Area of Science:

  • Genomics
  • Molecular Biology
  • Systems Biology

Background:

  • Chromatin immunoprecipitation sequencing (ChIP-seq) identifies genome-wide transcription factor (TF) binding sites.
  • The farnesoid X receptor (FXR) is a nuclear receptor crucial for regulating metabolic pathways in the liver.

Purpose of the Study:

  • To create a comprehensive FXR signaling atlas by re-analyzing, standardizing, and integrating all accessible public FXR ChIP-seq datasets.
  • To enhance the understanding of FXR's regulatory roles in liver metabolism.

Main Methods:

  • Standardized re-analysis of all available FXR ChIP-seq datasets across different species (mouse, rat, human) and conditions.
  • Comparative analysis of datasets from raw reads to functional pathway outcomes.
  • Integration of data to create a unified FXR super-signaling atlas.

Main Results:

  • Public FXR ChIP-seq datasets exhibit significant heterogeneity in baseline quality.
  • Combining datasets improved analytical depth, enabling the identification of more TF binding sites (peaks) and associated functional pathways.
  • The integrated atlas provides a broader view of FXR signaling than individual studies.

Conclusions:

  • Individual FXR ChIP-seq studies are insufficient to capture the full scope of FXR signaling.
  • An integrated "FXR super-signaling atlas" significantly enhances the understanding of FXR's regulatory capacities and its role in liver metabolism.