CRUP: a comprehensive framework to predict condition-specific regulatory units.
Anna Ramisch,Verena Heinrich,Laura V. Glaser,Alisa Fuchs,Xinyi Yang,Philipp Benner,Robert Schoepflin,Na Li,Sarah Kinkley,Anja Römer-Hillmann,John Longinotto,Steffen Heyne,Beate Czepukojc,Sonja M. Kessler,Sonja M. Kessler,Alexandra K. Kiemer,Cristina Cadenas,Laura Arrigoni,Nina Gasparoni,Thomas Manke,Thomas Pap,Andrew Pospisilik,Jan G. Hengstler,Jörn Walter,Sebastiaan H. Meijsing,Ho-Ryun Chung,Martin Vingron +26 more
TL;DR: The software Condition-specific Regulatory Units Prediction (CRUP) is presented to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes, solely based on histone modification ChIP-seq data.
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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.
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CRUP: a comprehensive framework to predict condition-specific regulatory units.
Anna Ramisch,Verena Heinrich,Laura V. Glaser,Alisa Fuchs,Xinyi Yang,Philipp Benner,Robert Schoepflin,Na Li,Sarah Kinkley,Anja Römer-Hillmann,John Longinotto,Steffen Heyne,Beate Czepukojc,Sonja M. Kessler,Sonja M. Kessler,Alexandra K. Kiemer,Cristina Cadenas,Laura Arrigoni,Nina Gasparoni,Thomas Manke,Thomas Pap,Andrew Pospisilik,Jan G. Hengstler,Jörn Walter,Sebastiaan H. Meijsing,Ho-Ryun Chung,Martin Vingron +26 more
TL;DR: The software Condition-specific Regulatory Units Prediction (CRUP) is presented to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes, solely based on histone modification ChIP-seq data.
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