Integration of Expression Data with Annotated Enhancers - GianlucaMattei/methyl.O GitHub Wiki
Integration of Expression Data with Annotated Enhancers:
We implemented in methyl.O the possibility to investigate by data integration the effects on gene expression of methylation levels of enhancer elements. The results of this analysis can be plotted or retrieved in a data frame. The data frame contains informations about the genomic coordinates of DMRs (seqnames, start, end), about the coordinates of enhancer (annot.seqnames, annot.start, annot.end), the target genes (target.gene), the beta difference occurring on DMRs (beta), the expression log. fold change (logFC) and the score (score). The score is computed as described in Expression Data Integration. As introduced in Annotate Methylated Enhancers, also in this case we introduced the possibility to correlate the hyper and hypo-methylated enhancers separately. In fact. hyper-methylation of these regions prevents the binding with TFs and consequently the expression enhancement of distal genes but expression of distal genes can still be mediated by TFs binding to their promoters.
R:
The function associateEnh2Expr is used to correlate the annotated enhancers resulting from the function annotateEnhancers to expression data. The genome assembly needs to be specified in the option (hg) as well as the enhancer database to be used (enhancer.db). As for the associateFeat2Exprs function, it is possible to specify the column in the expression file under which to find the gene IDs (col.genes), the log. fold change (col.logFC), the column where to find the statistics (col.stat), choose whether gene IDs need to be converted (convert.genes), define the ID type of genes to convert (convert.from) and set the threshold for statistical significance and for the log. fold change. Other parameters permit to customize the methylation characteristics to filter the DMRs: the beta difference threshold (beta.thr), the method to compute the overlap between the DMRs and the enhancers (param.type) and the value threshold for overlaps (overlap.param.thr). The remaining options, that allow to define the methods to compute the correlation, to set the graphical parameters and if return a table or a plot, work as in the associateFeat2Exprs function where they have been described in detail.
GUI:
The tab Methylated Enhancers vs Expression permits to correlate the methylation levels of enhancers to expression profile of target genes. In the main part of the page are shown the plot and the table of results. In the left panel is possible to load the expression profile file and are shown the following options:
| 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. |
| Statistic Threshold | Threshold value for the selected statistics. |
| LogFC Threshold | Threshold value for expression log. fold change. |
| Enhancer Methylation Beta Threshold | The beta threshold for each DMRs to be considered in the annotation |
| Select enhancer DB | Select the DB to use |
| Select Correlation Type | Set the method to compute the correlation |
| Column Position of Gene ID | Set the column position in the expression file where to find gene IDs |
| Column Position of Used Statistics | Set the column position in the expression file where to find the statistics (p.value or adj p.value) |
| Column position of logFC | Set the column position in the expression file where to get the log. fold changes values. |
| Select TRUE if Gene IDs are not Symbols | If selected, gene IDs are not official symbols |
| Select Gene IDs Annotation Type to Translate | If the above option is TRUE, then select the type of IDs provided. |