Abstract:
: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 Integration 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 projects and across different projects, identify outlier samples, and cross-check differentially methylated CpG sites identified in specific projects across large numbers of samples. A demonstration server has been setup using GEO data at http://echelon.cmmt.ubc.ca/dbaccess/, with login "guest" and password "guest." Groups may download and install their own version of the server following the instructions on the project's wiki.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Fejes AP,Jones MJ,Kobor MSdoi
10.3389/fgene.2014.00325subject
Has Abstractpub_date
2014-09-18 00:00:00pages
325issn
1664-8021journal_volume
5pub_type
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pub_type: 杂志文章
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pub_type: 杂志文章
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journal_title:Frontiers in genetics
pub_type: 杂志文章
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00623
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.00661
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abstract::Colitis-associated cancer (CAC) has been linked to microRNA (miRNA) aberrant expression elicited by inflammation. In this study, we used the AOM/DSS-induced CAC mice model to explore the ectopic expression of miRNAs in the precancerous stage of CAC. As a result, we found that miR-31-5p, miR-223-3p, and let-7f-5p were ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00585
更新日期:2019-06-19 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00492
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2011.00054
更新日期:2011-08-31 00:00:00
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pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.603552
更新日期:2020-10-29 00:00:00
abstract::Advances in the field of sequencing techniques have resulted in the greatly accelerated production of huge sequence datasets. This presents immediate challenges in database maintenance at datacenters. It provides additional computational challenges in data mining and sequence analysis. Together these represent a signi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00280
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doi:10.3389/fgene.2020.563166
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pub_type: 杂志文章
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journal_title:Frontiers in genetics
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doi:10.3389/fgene.2014.00233
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abstract::In recent years, the prevalence of obesity and cancer have been rising. Since this poses a serious threat to human health, the relationship between the two has attracted much attention. This study examined whether fat mass and obesity-associated (FTO) genes are linked, taking into account a Genome-wide Association Stu...
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doi:10.3389/fgene.2013.00135
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pub_type: 杂志文章
doi:10.3389/fgene.2020.00537
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abstract::MicroRNAs (miRNAs) are known to be important post-transcriptional regulators that are involved in the etiology of complex psychiatric traits. The present study aimed to incorporate miRNAs information into pathway analysis using a genome-wide association dataset to identify relevant biological pathways for bipolar diso...
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pub_type: 杂志文章
doi:10.3389/fgene.2012.00293
更新日期:2012-12-18 00:00:00
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doi:10.3389/fgene.2018.00148
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更新日期:2020-10-15 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00225
更新日期:2014-07-21 00:00:00