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Please use this identifier to cite or link to this item: http://hdl.handle.net/10119/10712

Title: Reconstruction of Histone Modification Network from Next-generation Sequencing Data
Authors: Le, Ngoc Tu
Ho, Tu Bao
Keywords: histone modification network
next-generation sequencing data
Issue Date: 2011-10
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Magazine name: 2011 IEEE 11th International Conference on Bioinformatics and Bioengineering (BIBE2011)
Start page: 181
End page: 188
DOI: 10.1109/BIBE.2011.35
Abstract: Post-translational modifications (PTMs) of histoneproteins play critical roles in establishing functionallyseparated domains on chromatin and regulating importantbiological processes, such as transcription. These modifications often act in cooperative manner, forming complicated “histone codes”. Elucidation of functional relationships among them will, therefore, significantly increase our understanding of cell differentiation, development, and cancer pathogenesis. Biological evidence has shown that nucleosome positioning can provide invaluable information about interactive effects of PTMs. However, to our knowledge, none of previous works has exploited this information in the reconstruction of histonemodification networks.We propose a computational approach based on Bayesiannetwork to reconstruct a network representing functionalrelationships of histone modifications. Our approach employed the search-and-score method to infer the network structure using interactive information of histone modifications, which is measured by the correlation between each modification with nucleosome positioning. When applied on human CD4+ T cell ChIP-Seq dataset, containing 38 different histone modifications and binding information of three other proteins, H2A.Z, PolII and CTCF, our method not only outperformed previous approaches in recovering known relationships but also suggested many new ones, confirming its validity and efficiency. Our unbiased method for inferring the network structure can also be applied to reconstruct interaction networks of other epigenetic factors.
Rights: This is the author's version of the work. Copyright (C) 2011 IEEE. 2011 IEEE 11th International Conference on Bioinformatics and Bioengineering (BIBE2011), 2011, 181-188. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
URI: http://hdl.handle.net/10119/10712
Material Type: author
Appears in Collections:a11-1. 会議発表論文 (Conference Papers)

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