CRUP: a comprehensive framework to predict condition-specific regulatory units.
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ABSTRACT:
SUBMITTER: Ramisch A
PROVIDER: S-EPMC6839171 | biostudies-literature | 2019 Nov
REPOSITORIES: biostudies-literature
Publications
CRUP: a comprehensive framework to predict condition-specific regulatory units.
Ramisch Anna A Heinrich Verena V Glaser Laura V LV Fuchs Alisa A Yang Xinyi X Benner Philipp P Schöpflin Robert R Li Na N Kinkley Sarah S Römer-Hillmann Anja A Longinotto John J Heyne Steffen S Czepukojc Beate B Kessler Sonja M SM Kiemer Alexandra K AK Cadenas Cristina C Arrigoni Laura L Gasparoni Nina N Manke Thomas T Pap Thomas T Pospisilik John A JA Hengstler Jan J Walter Jörn J Meijsing Sebastiaan H SH Chung Ho-Ryun HR Vingron Martin M
Genome biology 20191108 1
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 u ...[more]
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