Print Email Facebook Twitter Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex Title Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex Author Babaei, S. Mahfouz, A.M.E.T.A. Hulsman, M. Lelieveldt, B.P.F. De Ridder, J. Reinders, M.J.T. Faculty Electrical Engineering, Mathematics and Computer Science Department Intelligent Systems Date 2015-05-12 Abstract The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains challenging. We address this by characterizing the topology of the cortical chromatin interaction network using scale-aware topological measures. We demonstrate that based on these characterizations it is possible to accurately predict spatial co-expression between genes in the mouse cortex. Consistent with previous findings, we find that the chromatin interaction profile of a gene-pair is a good predictor of their spatial co-expression. However, the accuracy of the prediction can be substantially improved when chromatin interactions are described using scale-aware topological measures of the multi-resolution chromatin interaction network. We conclude that, for co-expression prediction, it is necessary to take into account different levels of chromatin interactions ranging from direct interaction between genes (i.e. small-scale) to chromatin compartment interactions (i.e. large-scale). Subject chromatintopologyanimal performancemammalian genomicschromosomescentralitychromosome 16chromosome mappingOA-Fund TU Delft To reference this document use: http://resolver.tudelft.nl/uuid:6bb81f94-c110-4fa4-89d7-8b0690fbc664 Publisher Public Library of Science ISSN 1553-734X Source https://doi.org/10.1371/journal.pcbi.1004221 Source PLoS Computational Biology, 10 (4), 2015 Part of collection Institutional Repository Document type journal article Rights © 2015 The Author(s)This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Files PDF Reinders_2015.pdf 2.57 MB Close viewer /islandora/object/uuid:6bb81f94-c110-4fa4-89d7-8b0690fbc664/datastream/OBJ/view