Show simple item record

dc.contributor.authorZheng Hen
dc.contributor.authorWang Hen
dc.contributor.authorDewhurst RJen
dc.contributor.authorRoehe Ren
dc.date.accessioned2019-02-05T08:36:18Z
dc.date.available2019-02-05T08:36:18Z
dc.date.issued2018
dc.identifier.urihttps://doi.org/10.1109/TCBB.2018.2879342
dc.identifier.urihttp://hdl.handle.net/11262/11584
dc.description.abstractThe importance of the composition and signature of rumen microbial communities has gained increasing attention. One of the key techniques was to infer co-abundance networks through correlation analysis based on relative abundances. While substantial insights and progress have been made, it has been found that due to the compositional nature of data, correlation analysis derived from relative abundance could produce misleading results and spurious associations. In this study, we proposed the use of a framework including a compendium of two correlation measures and three dissimilarity metrics in an attempt to mitigate the compositional effect in the inference of significant associations in the bovine rumen microbiome. We tested the framework on rumen microbiome data including both 16S rRNA and KEGG genes associated with methane production in cattle. Based on the identification of significant positive and negative associations supported by multiple metrics, two co-occurrence networks, e.g. co-presence and mutual-exclusion networks, were constructed. Significant modules associated with methane emissions were identified. In comparison to previous studies, our analysis demonstrates that deriving microbial associations based on the correlations between relative abundances may not only lead to missing information but also produce spurious associations. To bridge together different co-presence and mutual-exclusion relations, a multiplex network model has been proposed for integrative analysis of co-occurrence networks which has great potential to support the prediction of animal phytotypes and to provide additional insights into biological mechanisms of the microbiome associated with the traits.en
dc.description.sponsorshipScottish Government RESAS Strategic Research Programme (RD2.3.1)en
dc.language.isoenen
dc.relation.isformatof14983en
dc.relation.ispartofIEEE/ACM Transactions on Computational Biology and Bioinformaticsen
dc.subjectCompositional dataen
dc.subjectCo-occurrence networksen
dc.subjectRumen microbiomeen
dc.subjectMethane emissionen
dc.titleImproving the inference of co-occurence networks in the bovine rumen microbiomeen
dc.typeArticleen
rioxxterms.publicationdate2018-11-02
rioxxterms.typeJournal Article/Reviewen
dcterms.dateAccepted2018-10-25
refterms.accessExceptionNAen
refterms.dateDeposit2019-02-05
refterms.dateEmbargoEnd2019-11-21
refterms.dateFreeToDownload2019-11-21
refterms.dateFreeToRead2019-11-21
refterms.dateToSearch2019-11-21
refterms.depositExceptionNAen
refterms.panelUnspecifieden
refterms.technicalExceptionNAen
refterms.versionAMen


Files in this item

FilesSizeFormatView

There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record