Please use this identifier to cite or link to this item:
http://bura.brunel.ac.uk/handle/2438/9657
Full metadata record
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Bao, Y | - |
dc.contributor.author | Vinciotti, V | - |
dc.contributor.author | Wit, E | - |
dc.contributor.author | Hoen, P | - |
dc.date.accessioned | 2015-01-06T09:45:25Z | - |
dc.date.available | 2014-04 | - |
dc.date.available | 2015-01-06T09:45:25Z | - |
dc.date.issued | 2014 | - |
dc.identifier.citation | Biostatistics, 15 (2): 296 - 310, (2014) | en_US |
dc.identifier.issn | 1465-4644 | - |
dc.identifier.issn | 1468-4357 | - |
dc.identifier.uri | http://biostatistics.oxfordjournals.org/content/15/2/296 | - |
dc.identifier.uri | http://bura.brunel.ac.uk/handle/2438/9657 | - |
dc.description.abstract | Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) experiments have now become routine in biology for the detection of protein-binding sites. In this paper, we present a Markov random field model for the joint analysis of multiple ChIP-seq experiments. The proposed model naturally accounts for spatial dependencies in the data, by assuming first-order Markov dependence and, for the large proportion of zero counts, by using zero-inflated mixture distributions. In contrast to all other available implementations, the model allows for the joint modeling of multiple experiments, by incorporating key aspects of the experimental design. In particular, the model uses the information about replicates and about the different antibodies used in the experiments. An extensive simulation study shows a lower false non-discovery rate for the proposed method, compared with existing methods, at the same false discovery rate. Finally, we present an analysis on real data for the detection of histone modifications of two chromatin modifiers from eight ChIP-seq experiments, including technical replicates with different IP efficiencies. | en_US |
dc.format.extent | 296 - 310 | - |
dc.format.extent | 296 - 310 | - |
dc.format.extent | 296 - 310 | - |
dc.format.extent | 296 - 310 | - |
dc.language | eng | - |
dc.language.iso | en | en_US |
dc.publisher | Oxford University Press | en_US |
dc.subject | ChIP-sequencing | en_US |
dc.subject | Markov random field model | en_US |
dc.subject | Mixture distributions | en_US |
dc.title | Joint modeling of ChIP-seq data via a Markov random field model | en_US |
dc.type | Article | en_US |
dc.identifier.doi | http://dx.doi.org/10.1093/biostatistics/kxt047 | - |
dc.relation.isPartOf | Biostatistics | - |
dc.relation.isPartOf | Biostatistics | - |
dc.relation.isPartOf | Biostatistics | - |
dc.relation.isPartOf | Biostatistics | - |
pubs.issue | 2 | - |
pubs.issue | 2 | - |
pubs.issue | 2 | - |
pubs.issue | 2 | - |
pubs.volume | 15 | - |
pubs.volume | 15 | - |
pubs.volume | 15 | - |
pubs.volume | 15 | - |
pubs.organisational-data | /Brunel | - |
pubs.organisational-data | /Brunel/Brunel Staff by College/Department/Division | - |
pubs.organisational-data | /Brunel/Brunel Staff by College/Department/Division/College of Engineering, Design and Physical Sciences | - |
pubs.organisational-data | /Brunel/Brunel Staff by College/Department/Division/College of Engineering, Design and Physical Sciences/Dept of Mathematics | - |
pubs.organisational-data | /Brunel/Brunel Staff by College/Department/Division/College of Engineering, Design and Physical Sciences/Dept of Mathematics/Mathematical Sciences | - |
pubs.organisational-data | /Brunel/Brunel Staff by Institute/Theme | - |
pubs.organisational-data | /Brunel/Brunel Staff by Institute/Theme/Institute of Environmental, Health and Societies | - |
pubs.organisational-data | /Brunel/Brunel Staff by Institute/Theme/Institute of Environmental, Health and Societies/Synthetic Biology | - |
pubs.organisational-data | /Brunel/University Research Centres and Groups | - |
pubs.organisational-data | /Brunel/University Research Centres and Groups/Brunel Business School - URCs and Groups | - |
pubs.organisational-data | /Brunel/University Research Centres and Groups/Brunel Business School - URCs and Groups/Centre for Research into Entrepreneurship, International Business and Innovation in Emerging Markets | - |
pubs.organisational-data | /Brunel/University Research Centres and Groups/School of Health Sciences and Social Care - URCs and Groups | - |
pubs.organisational-data | /Brunel/University Research Centres and Groups/School of Health Sciences and Social Care - URCs and Groups/Brunel Institute for Ageing Studies | - |
pubs.organisational-data | /Brunel/University Research Centres and Groups/School of Health Sciences and Social Care - URCs and Groups/Brunel Institute of Cancer Genetics and Pharmacogenomics | - |
pubs.organisational-data | /Brunel/University Research Centres and Groups/School of Health Sciences and Social Care - URCs and Groups/Centre for Systems and Synthetic Biology | - |
Appears in Collections: | Dept of Mathematics Research Papers |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
Fulltext.pdf | 196.74 kB | Adobe PDF | View/Open |
Items in BURA are protected by copyright, with all rights reserved, unless otherwise indicated.