Please use this identifier to cite or link to this item: doi:10.22028/D291-37452
Title: CRUP : a comprehensive framework to predict condition-specific regulatory units
Author(s): Ramisch, Anna
Heinrich, Verena
Glaser, Laura V.
Fuchs, Alisa
Yang, Xinyi
Benner, Philipp
Schöpflin, Robert
Li, Na
Kinkley, Sarah
Römer-Hillmann, Anja
Longinotto, John
Heyne, Steffen
Czepukojc, Beate
Kessler, Sonja M.
Kiemer, Alexandra K.
Cadenas, Cristina
Arrigoni, Laura
Gasparoni, Nina
Manke, Thomas
Pap, Thomas
Pospisilik, John A.
Hengstler, Jan
Walter, Jörn
Meijsing, Sebastiaan H.
Chung, Ho-Ryun
Vingron, Martin
Language: English
Title: Genome Biology
Volume: 20
Issue: 1
Publisher/Platform: BMC
Year of Publication: 2019
Free key words: Enhancer prediction
Enhancer dynamics
Gene regulation
Random forest
Differential analysis
Histone modification
3D interaction
DDC notations: 500 Science
Publikation type: Journal Article
Abstract: We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units. We thoroughly test and then apply CRUP to a rheumatoid arthritis model, identifying enhancer-gene pairs comprising known disease genes as well as new candidate genes.
DOI of the first publication: 10.1186/s13059-019-1860-7
URL of the first publication:
Link to this record: urn:nbn:de:bsz:291--ds-374521
ISSN: 1474-760X
Date of registration: 29-Sep-2022
Description of the related object: Supplementary information
Related object:
Faculty: NT - Naturwissenschaftlich- Technische Fakultät
Department: NT - Biowissenschaften
NT - Pharmazie
Professorship: NT - Prof. Dr. Alexandra K. Kiemer
NT - Prof. Dr. Jörn Walter
Collections:SciDok - Der Wissenschaftsserver der Universität des Saarlandes

Files for this record:
File Description SizeFormat 
s13059-019-1860-7.pdf2,62 MBAdobe PDFView/Open

This item is licensed under a Creative Commons License Creative Commons