Contact our Customer Care Team:
Freecall 1300 247 301
Phone +61 3 9321 3700
CustomerCare@agrf.org.au
www.agrf.org.au
Contact our Customer Care Team:
Freecall 1300 247 301
Phone +61 3 9321 3700
CustomerCare@agrf.org.au
www.agrf.org.au
Contact our Customer Care Team:
Freecall 1300 247 301
Phone +61 3 9321 3700
CustomerCare@agrf.org.au
www.agrf.org.au
UpSetR diagram
The EPIC array number on the UsetR diagram and the heatmap correspond to nearby SNPs, not the actual methylation probes on the EPIC array.
Table with all matched SNPs detected in all selected genes.
MethylationEPIC v2 and selected genotyping content search application
This R-Shiny application provides a user-friendly interface for searching, comparing, and analysing the content of Illumina's mainstream genotyping and methylation chips. This application searches for Gene and SNP IDs. It consists of three main tabs: 'Genes', 'SNPs', and 'Info'.
Genes Tab: Users can input RefSeq gene IDs to generate bar plots showing the number of associated markers: SNPs for genotyping arrays and CpG sites for the EPIC methylation v2.0 chip. The search looks for letter patterns; case-sensitive multiple matches may occur, especially for genes with numerical suffixes. Detailed information about markers with matched gene symbols is displayed in a table. The UpSet plot shows the total number of matched SNPs for the EPIC array. The methylation array does not use probes for SNPs, they are not physically present on the EPIC chip. The SNPs shown are RS-IDs collected within a 1Kb distance for all CpG probes on the array, matched for gene symbols. As such, you may observe more hits in your UpSet plot than shown on the bar chart on the left side for the EPIC array. This approach for loose SNPs search was undertaken in an effort to determine the number of SNPs located near EPIC's methylation probes that intersect with the genotyping chip for the gene of interest. If such shared SNPs exist, the intersect number will be shown on the vertical bars with rows at the bottom of the figure connected by vertical lines.
SNPs Tab: Users can input SNP IDs manually or upload a file at this tab. The application searches for exact matches for these SNPs across genotyping chip content and SNPs associated with EPIC's CpG probes. Matched annotation is displayed in a table. A heatmap visualisation shows marker counts across genes (rows) and chips (columns). The UpSet plot on this tab shows only exact matches for the SNPs list entered or uploaded by the user. The search is performed across over 13M RS-IDs associated with the EPIC chip and can be slow.
Info Tab: Presents a summary table with information about two microarray content, including gene coverage and additional details.
Overall, the application simplifies comparisons of microarray contents by providing visualisations and detailed statistics for particular selections of genes and SNPs of interest.
Note: The chip annotation used for chromosomes and coordinates is hg19. Array annotation files were downloaded from Illumina website and were modified to make uniform dataset.
The array files were harmonized across seven genotyping chips by using rs-ids as a key. This means that gene names and transcripts from seven illumina genotyping chip's were collected, combined, and re-incorporated back to the chip records for each rs-id.
The Illumina sourced EPIC array annotation was only modified for the Chr and MapInfo fields. The original chromosome coordinate numbers were converted from hg38 to hg19 using R libraries: rtracklayer and GenomicRanges, with a downloaded chain file from UCSC .
Shiny application code and additional files and documentation available on GitHUB
Disclaimer:
This Shiny application is in the development stage and is provided for generalized informational and demonstration purposes. The Australian Genome Research Facility (AGRF) and the developer of this application accept no responsibility or liability for any decisions made based on the results or information provided by this application. Users should independently verify the accuracy and reliability of the data presented and exercise their own judgment when interpreting the results. The use of this application is at the user's own risk.