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

Ramisch, A.; Heinrich, V.; Glaser, L. V.; Fuchs, A.; Yang, X.; Benner, P.; Schoepflin, R.; Li, N.; Kinkley, S.; Hillmann, A.; Longinotto, J.; Heyne, S.; Czepukojc, B.; Kessler, S. M.; Kiemer, A. K.; Cadenas, C.; Arrigoni, L.; Gasparoni, N.; Manke, T.; Pap, T.; Pospisilik, A.; Hengstler, J.; Walter, J.; Meijsing, S. H.; Chung, H.-R.; Vingron, M.

doi:10.1101/501601

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bioRxiv · 10.1101/501601

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

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Abstract

We present the software CRUP (Condition-specific Regulatory Units Prediction) 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 lines 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.\n\nAvailabilityhttps://github.com/VerenaHeinrich/CRUP

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Ramisch, A., Heinrich, V., Glaser, L. V., Fuchs, A., Yang, X., Benner, P., Schoepflin, R., Li, N., Kinkley, S., Hillmann, A., Longinotto, J., Heyne, S., Czepukojc, B., Kessler, S. M., Kiemer, A. K., Cadenas, C., Arrigoni, L., Gasparoni, N., Manke, T., Pap, T., Pospisilik, A., Hengstler, J., Walter, J., Meijsing, S. H., Chung, H.-R., Vingron, M.. 2018-12-19. CRUP: A comprehensive framework to predict condition-specific regulatory units. https://doi.org/10.1101/501601

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