Details zur Publikation

Kategorie Textpublikation
Referenztyp Zeitschriften
DOI 10.1186/s12859-022-04836-2
Lizenz creative commons licence
Titel (primär) EpiVisR: exploratory data analysis and visualization in epigenome-wide association analyses
Autor Röder, S. ORCID logo ; Herberth, G. ORCID logo ; Zenclussen, A.C.; Bauer, M.
Quelle BMC Bioinformatics
Erscheinungsjahr 2022
Department IMMU
Band/Volume 23
Seite von art. 292
Sprache englisch
Topic T9 Healthy Planet
Keywords Visualization; EWAS; DNAm; Profile plot; Shiny application
Abstract Background

With the widespread availability of microarray technology for epigenetic research, methods for calling differentially methylated probes or differentially methylated regions have become effective tools to analyze this type of data. Furthermore, visualization is usually employed for quality check of results and for further insights. Expert knowledge is required to leverage capabilities of these methods. To overcome this limitation and make visualization in epigenetic research available to the public, we designed EpiVisR.

The EpiVisR tool allows to select and visualize combinations of traits (i.e., concentrations of chemical compounds) and differentially methylated probes/regions. It supports various modes of enriched presentation to get the most knowledge out of existing data: (1) enriched Manhattan plot and enriched volcano plot for selection of probes, (2) trait-methylation plot for visualization of selected trait values against methylation values, (3) methylation profile plot for visualization of a selected range of probes against selected trait values as well as, (4) correlation profile plot for selection and visualization of further probes that are correlated to the selected probe. EpiVisR additionally allows exporting selected data to external tools for tasks such as network analysis.

The key advantage of EpiVisR is the annotation of data in the enriched plots (and tied tables) as well as linking to external data sources for further integrated data analysis. Using the EpiVisR approach will allow users to integrate data from traits with epigenetic analyses that are connected by belonging to the same individuals. Merging data from various data sources among the same cohort and visualizing them will enable users to gain more insights from existing data.
dauerhafte UFZ-Verlinkung
Röder, S., Herberth, G., Zenclussen, A.C., Bauer, M. (2022):
EpiVisR: exploratory data analysis and visualization in epigenome-wide association analyses
BMC Bioinformatics 23 , art. 292 10.1186/s12859-022-04836-2