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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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© The Author(s). 2019

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 Urheber:
Ramisch, Anna1, Autor           
Heinrich, Verena2, Autor           
Glaser, Laura V.3, Autor           
Fuchs, Alisa4, Autor
Yang, Xinyi4, Autor           
Benner, Philipp2, Autor           
Schöpflin, Robert5, Autor           
Li, Na4, Autor
Kinkley, Sarah6, Autor           
Römer-Hillmann, Anja4, Autor
Longinotto, John4, Autor
Heyne, Steffen4, Autor
Czepukojc, Beate4, Autor
Kessler, Sonja M.4, Autor
Kiemer, Alexandra K.4, Autor
Cadenas, Cristina4, Autor
Arrigoni, Laura4, Autor
Gasparoni, Nina4, Autor
Manke, Thomas4, Autor
Pap, Thomas4, Autor
Pospisilik, Andrew4, AutorHengstler, Jan4, AutorWalter, Jörn4, AutorMeijsing, Sebastiaan3, Autor           Chung, Ho-Ryun4, AutorVingron, Martin2, Autor            mehr..
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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Schlagwörter: Enhancer predition, Enhancer dynamics, Gene regulation, Epigenetics, Random forest, Differential analysis, Histone modification, 3D interaction
 Zusammenfassung: 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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Sprache(n): eng - English
 Datum: 2019-10-142019-11-08
 Publikationsstatus: Online veröffentlicht
 Seiten: -
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: DOI: 10.1186/s13059-019-1860-7
 Art des Abschluß: -

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Titel: Genome Biology : Biology for the Post-Genomic Era
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: London : BioMed Central Ltd.
Seiten: - Band / Heft: 20 Artikelnummer: 20:227 Start- / Endseite: - Identifikator: ISSN: 1465-6906
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000224390