A Comprehensive FXR Signaling Atlas Derived from Pooled ChIP-seq Data

Emilian Jungwirth, Katrin Panzitt, Hanns-Ulrich Marschall, Martin Wagner, Gerhard G Thallinger

Research output: Contribution to journalArticleResearchpeer-review

Abstract

BACKGROUND: ChIP-seq is a method to identify genome-wide transcription factor (TF) binding sites. The TF FXR is a nuclear receptor that controls gene regulation of different metabolic pathways in the liver.

OBJECTIVES: To re-analyze, standardize and combine all publicly available FXR ChIP-seq data sets to create a global FXR signaling atlas.

METHODS: All data sets were (re-)analyzed in a standardized manner and compared on every relevant level from raw reads to affected functional pathways.

RESULTS: Public FXR data sets were available for mouse, rat and primary human hepatocytes in different treatment conditions. Standardized re-analysis shows that the data sets are surprisingly heterogeneous concerning baseline quality criteria. Combining different data sets increased the depth of analysis and allowed to recover more peaks and functional pathways.

CONCLUSION: Published single FXR ChIP-seq data sets do not cover the full spectrum of FXR signaling. Combining different data sets and creating a "FXR super-signaling atlas" enhances understanding of FXR signaling capacities.

Original languageEnglish
Pages (from-to)105-112
Number of pages8
JournalStudies in health technology and informatics
Volume260
DOIs
Publication statusPublished - 2019
Event13th Health Informatics Meets Digital Health Conference - Wien, Austria
Duration: 28 May 2019 → …

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Atlases
Transcription factors
Binding sites
Gene expression
Liver
Transcription Factors
Rats
Genes
Cytoplasmic and Nuclear Receptors
Metabolic Networks and Pathways
Datasets
Hepatocytes
Binding Sites
Genome

Keywords

  • Animals
  • Binding Sites
  • Chromatin Immunoprecipitation
  • Data Analysis
  • Databases, Factual
  • Gene Expression Regulation
  • Genome
  • Humans
  • Mice
  • Rats
  • Receptors, Cytoplasmic and Nuclear

Cooperations

  • BioTechMed-Graz

Cite this

A Comprehensive FXR Signaling Atlas Derived from Pooled ChIP-seq Data. / Jungwirth, Emilian; Panzitt, Katrin; Marschall, Hanns-Ulrich; Wagner, Martin; Thallinger, Gerhard G.

In: Studies in health technology and informatics, Vol. 260, 2019, p. 105-112.

Research output: Contribution to journalArticleResearchpeer-review

Jungwirth, Emilian ; Panzitt, Katrin ; Marschall, Hanns-Ulrich ; Wagner, Martin ; Thallinger, Gerhard G. / A Comprehensive FXR Signaling Atlas Derived from Pooled ChIP-seq Data. In: Studies in health technology and informatics. 2019 ; Vol. 260. pp. 105-112.
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AB - BACKGROUND: ChIP-seq is a method to identify genome-wide transcription factor (TF) binding sites. The TF FXR is a nuclear receptor that controls gene regulation of different metabolic pathways in the liver.OBJECTIVES: To re-analyze, standardize and combine all publicly available FXR ChIP-seq data sets to create a global FXR signaling atlas.METHODS: All data sets were (re-)analyzed in a standardized manner and compared on every relevant level from raw reads to affected functional pathways.RESULTS: Public FXR data sets were available for mouse, rat and primary human hepatocytes in different treatment conditions. Standardized re-analysis shows that the data sets are surprisingly heterogeneous concerning baseline quality criteria. Combining different data sets increased the depth of analysis and allowed to recover more peaks and functional pathways.CONCLUSION: Published single FXR ChIP-seq data sets do not cover the full spectrum of FXR signaling. Combining different data sets and creating a "FXR super-signaling atlas" enhances understanding of FXR signaling capacities.

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