DaVIE: Database for the Visualization and Integration of Epigenetic data.
One of the challenges in the analysis of large data sets, particularly in a population-based setting, is the ability to perform comparisons across projects. This has to be done in such a way that the integrity of each individual project is maintained, while ensuring that the data are comparable acr...
Main Authors: | , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2014-09-01
|
Series: | Frontiers in Genetics |
Subjects: | |
Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00325/full |
id |
doaj-8c52240e53374a32b31676dbea700a84 |
---|---|
record_format |
Article |
spelling |
doaj-8c52240e53374a32b31676dbea700a842020-11-25T00:52:31ZengFrontiers Media S.A.Frontiers in Genetics1664-80212014-09-01510.3389/fgene.2014.00325109205DaVIE: Database for the Visualization and Integration of Epigenetic data.Anthony Peter Fejes0Meaghan J Jones1Michael S Kobor2Centre for Molecular Medicine and Therapeutics/University of British ColumbiaCentre for Molecular Medicine and Therapeutics/University of British ColumbiaCentre for Molecular Medicine and Therapeutics/University of British ColumbiaOne of the challenges in the analysis of large data sets, particularly in a population-based setting, is the ability to perform comparisons across projects. This has to be done in such a way that the integrity of each individual project is maintained, while ensuring that the data are comparable across projects. These issues are beginning to be observed in human DNA methylation studies, as the Illumina 450k platform and next generation sequencing-based assays grow in popularity and decrease in price. This increase in productivity is enabling new insights into epigenetics, but also requires the development of pipelines and software capable of handling the large volumes of data. The specific problems inherent in creating a platform for the storage, comparison, integration and visualization of DNA methylation data include data storage, algorithm efficiency and ability to interpret the results to derive biological meaning from them. Databases provide a ready-made solution to these issues, but as yet no tools exist that that leverage these advantages while providing an intuitive user interface for interpreting results in a genomic context.We have addressed this void by integrating a database to store DNA methylation data with a web interface to query and visualize the database and a set of libraries for more complex analysis. The resulting platform is called DaVIE: Database for the Visualization and I of Epigenetics data. DaVIE can use data culled from a variety of sources, and the web interface includes the ability to group samples by sub-type, compare multiple projects and visualize genomic features in relation to sites of interest. We have used DaVIE to identify patterns of DNA methylation in specific project and across different projects, identify outlier samples, and cross-check differentially methylated CpG sites identified in specific projects across large numbers of samples.http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00325/fullbioinformaticsdatabaseepigeneticsvisualization450k methylation array |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Anthony Peter Fejes Meaghan J Jones Michael S Kobor |
spellingShingle |
Anthony Peter Fejes Meaghan J Jones Michael S Kobor DaVIE: Database for the Visualization and Integration of Epigenetic data. Frontiers in Genetics bioinformatics database epigenetics visualization 450k methylation array |
author_facet |
Anthony Peter Fejes Meaghan J Jones Michael S Kobor |
author_sort |
Anthony Peter Fejes |
title |
DaVIE: Database for the Visualization and Integration of Epigenetic data. |
title_short |
DaVIE: Database for the Visualization and Integration of Epigenetic data. |
title_full |
DaVIE: Database for the Visualization and Integration of Epigenetic data. |
title_fullStr |
DaVIE: Database for the Visualization and Integration of Epigenetic data. |
title_full_unstemmed |
DaVIE: Database for the Visualization and Integration of Epigenetic data. |
title_sort |
davie: database for the visualization and integration of epigenetic data. |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2014-09-01 |
description |
One of the challenges in the analysis of large data sets, particularly in a population-based setting, is the ability to perform comparisons across projects. This has to be done in such a way that the integrity of each individual project is maintained, while ensuring that the data are comparable across projects. These issues are beginning to be observed in human DNA methylation studies, as the Illumina 450k platform and next generation sequencing-based assays grow in popularity and decrease in price. This increase in productivity is enabling new insights into epigenetics, but also requires the development of pipelines and software capable of handling the large volumes of data. The specific problems inherent in creating a platform for the storage, comparison, integration and visualization of DNA methylation data include data storage, algorithm efficiency and ability to interpret the results to derive biological meaning from them. Databases provide a ready-made solution to these issues, but as yet no tools exist that that leverage these advantages while providing an intuitive user interface for interpreting results in a genomic context.We have addressed this void by integrating a database to store DNA methylation data with a web interface to query and visualize the database and a set of libraries for more complex analysis. The resulting platform is called DaVIE: Database for the Visualization and I of Epigenetics data. DaVIE can use data culled from a variety of sources, and the web interface includes the ability to group samples by sub-type, compare multiple projects and visualize genomic features in relation to sites of interest. We have used DaVIE to identify patterns of DNA methylation in specific project and across different projects, identify outlier samples, and cross-check differentially methylated CpG sites identified in specific projects across large numbers of samples. |
topic |
bioinformatics database epigenetics visualization 450k methylation array |
url |
http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00325/full |
work_keys_str_mv |
AT anthonypeterfejes daviedatabaseforthevisualizationandintegrationofepigeneticdata AT meaghanjjones daviedatabaseforthevisualizationandintegrationofepigeneticdata AT michaelskobor daviedatabaseforthevisualizationandintegrationofepigeneticdata |
_version_ |
1725241990561398784 |