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  CRUP: a comprehensive framework to predict condition-specific regulatory units

Ramisch, A., Heinrich, V., Glaser, L. V., Fuchs, A., Yang, X., Benner, P., et al. (2019). CRUP: a comprehensive framework to predict condition-specific regulatory units. Genome Biology: Biology for the Post-Genomic Era, 20: 20:227. doi:10.1186/s13059-019-1860-7.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0005-61C5-F Version Permalink: http://hdl.handle.net/21.11116/0000-0005-61C6-E
Genre: Journal Article

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 Creators:
Ramisch, Anna1, Author              
Heinrich, Verena2, Author              
Glaser, Laura V.3, Author              
Fuchs, Alisa4, Author
Yang, Xinyi4, Author              
Benner, Philipp2, Author              
Schöpflin, Robert5, Author              
Li, Na4, Author
Kinkley, Sarah6, Author              
Römer-Hillmann, Anja4, Author
Longinotto, John4, Author
Heyne, Steffen4, Author
Czepukojc, Beate4, Author
Kessler, Sonja M.4, Author
Kiemer, Alexandra K.4, Author
Cadenas, Cristina4, Author
Arrigoni, Laura4, Author
Gasparoni, Nina4, Author
Manke, Thomas4, Author
Pap, Thomas4, Author
Pospisilik, Andrew4, AuthorHengstler, Jan4, AuthorWalter, Jörn4, AuthorMeijsing, Sebastiaan3, Author              Chung, Ho-Ryun4, AuthorVingron, Martin2, Author               more..
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              
3Mechanisms of Transcriptional Regulation (Sebastiaan H. Meijsing), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479641              
4External Organizations, ou_persistent22              
5Research Group Development & Disease (Head: Stefan Mundlos), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433557              
6Chromatin Structure and Function (Sarah Kinkley), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_3149476              

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Free keywords: Enhancer predition, Enhancer dynamics, Gene regulation, Epigenetics, Random forest, Differential analysis, Histone modification, 3D interaction
 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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Language(s): eng - English
 Dates: 2019-10-142019-11-08
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1186/s13059-019-1860-7
 Degree: -

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Title: Genome Biology : Biology for the Post-Genomic Era
Source Genre: Journal
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Publ. Info: London : BioMed Central Ltd.
Pages: - Volume / Issue: 20 Sequence Number: 20:227 Start / End Page: - Identifier: ISSN: 1465-6906
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000224390