Figure 3

REACTIN algorithm identifies significant activity difference of ER alpha (Haib_T47d_Eralphaa_Gen1h) in the Hess dataset. (a) Genes with higher t-scores (ER+ vs ER-) are more likely to be regulated by ER alpha. Genes are sorted in a decreasing order according to their t-scores (ER+ vs ER-). The –log10(P-value) is calculated by TIP, indicating the probability of a gene is bound by ER alpha in Haib_T47d_Eraphaa_Gen1h ChIP-seq data. The green lines indicates ER alpha target genes identified by peak-based method; (b) The correlation between the t-scores of genes and TF binding scores calculated by TIP; (c) The foreground and background functions for Haib_T47d_Eraphaa_Gen1h binding profile. The foreground and background functions are defined in Formula (xx) and (xx). Note the maximum deviation is obtained at the 18.9% percentile of all genes. (d) GSEA results for the ER alpha target gene sets defined by peak-based method (the green lines in (a)). Note that it cannot detect the activity difference of ER alpha between ER+ and ER- samples.