CpGmotifs : a tool to discover DNA motifs associated to CpG methylation events

Show simple item record

dc.contributor.author Scala, Giovanni
dc.contributor.author Federico, Antonio
dc.contributor.author Greco, Dario
dc.date.accessioned 2021-07-21T12:02:01Z
dc.date.available 2021-07-21T12:02:01Z
dc.date.issued 2021-05-26
dc.identifier.citation Scala , G , Federico , A & Greco , D 2021 , ' CpGmotifs : a tool to discover DNA motifs associated to CpG methylation events ' , BMC Bioinformatics , vol. 22 , no. 1 , 278 . https://doi.org/10.1186/s12859-021-04191-8
dc.identifier.other PURE: 166787141
dc.identifier.other PURE UUID: 8fdc7117-ccff-4fb0-b08b-ce5c0c2be33c
dc.identifier.other WOS: 000658428600004
dc.identifier.other ORCID: /0000-0001-9195-9003/work/97321459
dc.identifier.uri http://hdl.handle.net/10138/332508
dc.description.abstract BackgroundThe investigation of molecular alterations associated with the conservation and variation of DNA methylation in eukaryotes is gaining interest in the biomedical research community. Among the different determinants of methylation stability, the DNA composition of the CpG surrounding regions has been shown to have a crucial role in the maintenance and establishment of methylation statuses. This aspect has been previously characterized in a quantitative manner by inspecting the nucleotidic composition in the region. Research in this field still lacks a qualitative perspective, linked to the identification of certain sequences (or DNA motifs) related to particular DNA methylation phenomena.ResultsHere we present a novel computational strategy based on short DNA motif discovery in order to characterize sequence patterns related to aberrant CpG methylation events. We provide our framework as a user-friendly, shiny-based application, CpGmotifs, to easily retrieve and characterize DNA patterns related to CpG methylation in the human genome. Our tool supports the functional interpretation of deregulated methylation events by predicting transcription factors binding sites (TFBS) encompassing the identified motifs.ConclusionsCpGmotifs is an open source software. Its source code is available on GitHub https://github.com/Greco-Lab/CpGmotifs and a ready-to-use docker image is provided on DockerHub at https://hub.docker.com/r/grecolab/cpgmotifs. en
dc.format.extent 10
dc.language.iso eng
dc.relation.ispartof BMC Bioinformatics
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject DNA methylation
dc.subject DNA motifs
dc.subject DNA methylation signature
dc.subject Transcription factors
dc.subject R-Shiny
dc.subject 1182 Biochemistry, cell and molecular biology
dc.title CpGmotifs : a tool to discover DNA motifs associated to CpG methylation events en
dc.type Article
dc.contributor.organization Institute of Biotechnology
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.1186/s12859-021-04191-8
dc.relation.issn 1471-2105
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

Files in this item

Total number of downloads: Loading...

Files Size Format View
s12859_021_04191_8.pdf 1.151Mb PDF View/Open

This item appears in the following Collection(s)

Show simple item record