4.4 - Regulatory TF plots

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

library(ELMER.data)
library(ELMER)
library(DT)
library(dplyr)
library(BiocStyle)

TF ranking plot

For a given enriched motif, all human TF are ranked by the statistical $-log_{10}(P-value)$ assessing the anti-correlation level of candidate Master Regulator TF expression with average DNA methylation level for sites with the given motif. As a result, the most anti-correlated TFs will be ranked in the first positions. By default, the top 3 most anti-correlated TFs and all TF classified by TFClass database in the same (sub)family are highlighted with colors blue, red and orange, respectively.

TF ranking plot: family classification

Shown are TF ranking plots based on the score ($-log_{10}(P value))$ of association between TF expression and DNA methylation of an enriched motif in the LUSC cancer type. The dashed line indicates the boundary of the top 5% association score. The top 3 associated TFs and the TF family members=(dots in red) that are associated with that specific motif are labeled in the plot

r(P-value)$ assessing the anti-correlation level of candidate Master Regulator TF expression with average DNA methylation level for sites with the given motif. As a result, the most anti-correlated TFs will be ranked in the first positions. By default, the top 3 most anti-correlated TFs, and all TF classified by TFClass database in the same family and subfamily are highlighted with colors blue, red and orange, respectively."} load("result/getTF.hypo.TFs.with.motif.pvalue.rda") motif <- colnames(TF.meth.cor)[1] TF.rank.plot(motif.pvalue = TF.meth.cor, motif = motif, save = FALSE)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.