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

Journal article
Authors Emilian Jungwirth
Katrin Panzitt
Hanns-Ulrich Marschall
Martin Wagner
Gerhard G Thallinger
Published in Studies in health technology and informatics
Volume 260
Pages 105-112
ISSN 1879-8365
Publication year 2019
Published at Institute of Medicine, Department of Molecular and Clinical Medicine
Pages 105-112
Language en
Links www.ncbi.nlm.nih.gov/entrez/query.f...
Subject categories Gastroenterology and Hepatology

Abstract

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.To re-analyze, standardize and combine all publicly available FXR ChIP-seq data sets to create a global FXR signaling atlas.All data sets were (re-)analyzed in a standardized manner and compared on every relevant level from raw reads to affected functional pathways.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.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.

Page Manager: Webmaster|Last update: 9/11/2012
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