Annotate Enhancers - GianlucaMattei/methyl.O GitHub Wiki

Annotate Methylated Enhancers:

In order to assess the effect of methylation on gene expression, enhancers cannot be excluded from the analysis. Enhancer elements are regions along the DNA able to mediate the recruitment of TFs enhancing the expression of distal genes; for this reason we implemented the possibility to annotate this type of regions. The annotation is based on Hacer database which in turn is based on FANTOM5 and 4DGenome for enhancer-gene association. The resulting table is similar to the one in figure 2 and also in this case the returned results are ranked by a score that can be weighted by the option score modifier. The score modifier ranges from 0 to 1, where 0 returns a score based only on the database and 1 on the overlapped enhancers shifting the results on the effect of DMRs on gene expression. Other information returned are the presence (1 or 0) of the enhancer associated genes, with the corresponding gene symbols, in the NCG and COSMIC databases.

R:

The DMRs can be annotated by the function annotateEnhancers which accepts as input the data.frame object with the genomic coordinates (chr, start and end) on the first three columns and a beta difference value on the fourth column. Other options permit to specify the genome assembly version (hg), the beta difference value threshold for filtering DMRs (thr.beta), the type of metric to filter the DMRs, the threshold value for the selected metric, the score modifier (score.modifier) which works as previously explained. The metrics to filter the DMRs can be 1) the percentage of the enhancer overlapped with the DMR, 2) the length, in bp, of the overlap between the enhancers and 3) the DMR and the length, in bp of the DMR. Finally, the column where to find the beta difference values can be set in col.betadiff option.

annotatedEnhancers <- annotateEnhancers(DMRsSubset, hg='hg19', thr.beta = 0.3, overlap.param.thr = 40, 
param.type = "overlap.percentage", score.modifier = 0.5, col.betadiff = 4)

GUI:

The tab Annotated Methylated Enhancers returns a table similar to that in Annotate Methylated Regions. In the left panel the customizable options are in order

Command	Description
Type of Parameter to filter Overlapping Methylation	The metrics to filter the DMRs can be 1) the percentage of the enhancer overlapped with the DMR, 2) the length, in bp, of the overlap between the enhancer and 3) the DMR and the length, in bp of the DMR.
Overlapping Methylation Value Threshold for Filtering	Threshold value for the selected parameter.
Beta Diff. Threshold	The beta threshold for each DMRs to be considered in the annotation
Score Modifier	Ranging from 0 to 1, where 0 returns a score based only on the databases and 1 on the characteristics of overlaps.
Column Position of Beta Diff.	Select the column number where to find the beta difference

Table 5: Parameters of Annotate Methylated Enhancers tab

Additional plots in the GUI are returned: one for the selected parameter distribution and one for the beta difference values distribution. Both are customizable by the red gear button above the plots.