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Fig. 4 | Genome Biology

Fig. 4

From: Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

Fig. 4

LungNet predicts preferential inactivation of lung-specific TFs in LSCC. a Color bars compare the estimated average TF-activity levels of the 38 TFs in LSCC compared to their NADJ tissue. In bold, we indicate those TFs which exhibit statistically significant lower TF-activity levels in LSCC. b Example boxplots of estimated TF-activity levels for six selected lung-specific TFs. P values are from a one-tailed Wilcoxon rank sum test. c Boxplot comparing t-statistics of differential TF activity between LSCC and NADJ for the 38 TFs against the corresponding t-statistics obtained after randomizing the gene targets for each of the 38 TFs. P value is from a paired Wilcoxon rank sum test. d Scatterplot of the t-statistics of differential TF activity (y-axis) against the t-statistics of differential expression between LSCC and NADJ tissue. Green dashed lines indicate line of statistical significance, with red line indicating the regression of y-values against x-values. Above the plot, we show the PCC and P value. e Scatterplot of the Pcc between the TF-activity level estimated using mRNA expression and the corresponding one estimated using DNAm (x-axis), against the corresponding P value in a –log10 basis (y-axis), for each of the 38 TFs. Green dashed horizontal and vertical lines indicate significance threshold P = 0.05 and PCC = 0, respectively. P value is from a one-tailed Wilcoxon rank sum test, testing the null hypothesis that the PCC values are drawn from a distribution centered at PCC = 0. f Color bars comparing the mean relative TF-activity levels between LSCC and NADJ, as estimated from promoter DNAm levels. In bold, we indicate those TFs which passed a statistical significance P value threshold of 0.05

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