inst/shiny/myapp/instructions.md

In methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation

Step by step instructions for methylGSA shiny app

Xu Ren and Pei Fen Kuan

2020-02-20

This app is a web interface for gene set testing using the outcome of differential methylation.

Step 1

Click on "Browse" to upload differential methylation result.

Users are expected to upload a txt file with 1st column CpG IDs, and 2nd column p-values correspond to the CpGs. For example:

cg13869341    0.307766 cg14008030    0.257672 cg12045430    0.552322 cg20826792    0.056383 cg00381604    0.468549 cg20253340    0.483770 cg21870274    0.812402 ... ... ... cg21106100    0.079276 cg08265308    0.748265 cg14273923    0.553923

Files should be no more than 100MB. Please check cpg_file_example.txt for a toy dataset on Illumina 450 K Beadchip.

Step 2

Choose array type and group.

Array type: 450K: Illumina 450 K Beadchip EPIC: Illumina EPIC Beadchip

Group: Group is the type of CpG to be considered in methylRRA or methylglm. By default, group is all, which means all CpGs are considered regardless of their gene group. If group is body, only CpGs on gene body will be considered. If group is promoter1 or promoter2, only CpGs on promoters will be considered. Based on the annotation in IlluminaHumanMethylation450kanno.ilmn12.hg19 and IlluminaHumanMethylationEPICanno.ilm10b4.hg19, body, promoter1 and promoter2 are defined as: body: CpGs whose gene group correspond to “Body” or “1stExon” promoter1: CpGs whose gene group correspond to “TSS1500” or “TSS200” promoter2: CpGs whose gene group correspond to “TSS1500”, “TSS200”, “1stExon”, or “5’UTR”

Step 3

Select gene sets to test.

Gene Ontology: http://www.geneontology.org KEGG (Kyoto Encyclopedia of Genes and Genomes): https://www.genome.jp/kegg/ Reactome: https://reactome.org

Step 4

Select gene set sizes.

Gene sets outsize this range will not be tested.

Step 5

Select gene set testing method.

Check this page for a description of methods.

Step 6

Hit "GO!".

Gene set testing is running in the background. Depending on the number of gene sets tested, it may take several seconds to several minutes. Once it is done, the result is going to show up on the right hand panel.

Interpreting the results

The result of gene set testing is presented in two formats, namely table and box plot.

Hit "Download as csv" or "Download as txt" to save the results table to a csv or txt file:

Various options are provided for users to customize the box plot:

Number of gene sets to display: The number of genes sets to display on the plot. x-axis: Either the number of significant genes in each gene set or the total number of genes. The number of significant genes is not available for methylglm and methylRRA(GSEA) because they are FCS methods. Color by: Color the barplot by either raw p-value or adjusted p-value.

Hit "Download as pdf" or "Download as png" to save the boxplot to a pdf or png file:

methylGSA documentation built on Nov. 8, 2020, 8:29 p.m.