Sohn, Kyung-Ah and Ho, Joshua W K and Djordjevic, Djordje and Jeong, Hyun-Hwan and Park, Peter J and Kim, Ju Han (2015) hiHMM: Bayesian non-parametric joint inference of chromatin state maps. Bioinformatics, 31 (13). pp.2066-74. ISSN 1367-4811 (OA)
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Abstract
MOTIVATION
Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. To perform a principled comparison of evolutionarily distant epigenomes, we must consider species-specific biases such as differences in genome size, strength of signal enrichment and co-occurrence patterns of histone modifications.
RESULTS
Here, we present a new Bayesian non-parametric method called hierarchically linked infinite HMM (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison among them. We demonstrate the utility of this method using synthetic data as well as multiple modENCODE ChIP-seq datasets.
CONCLUSION
The hierarchical and Bayesian non-parametric formulation in our approach is an important extension to the current set of methodologies for comparative chromatin landscape analysis.
(NHGRI grant U01HG004258, a Human Frontier Science Program (HFSP) grant RGY0084/2014, Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT and Future Planning (MSIP) (2010-0028631 & 2014R1A1A3051169)).
| Item Type: | Article |
|---|---|
| Additional Information: | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| Subjects: | R Medicine > R Medicine (General) |
| Depositing User: | Repository Administrator |
| Date Deposited: | 19 Jan 2016 04:54 |
| Last Modified: | 09 May 2016 06:24 |
| URI: | https://eprints.victorchang.edu.au/id/eprint/193 |
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