# 4.4 - Regulatory TF plots

# TF ranking plot

For a given enriched motif, all human TF are ranked by the statistical −l o g10(P−v a l u e) 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 (−l o g10(P v a l u e)) 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

    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)

    ## Retrieving TFClass family classification from ELMER.data.

    ## Retrieving TFClass subfamily classification from ELMER.data.

    ##
    |                                                    |  0%
    |====================================================|100% ~0 s remaining
    |====================================================|100%                      Completed after 0 s

    ## $HXA9_HUMAN.H11MO.0.B

TF ranking plot: For a given enriched motif, all human TF are ranked by the statistical −l o g10(P−v a l u e) 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.

    ##
    ## attr(,"split_type")
    ## [1] "array"
    ## attr(,"split_labels")
    ##   X1
    ## 1  1