Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site
Figure 6
Testing our method on ATM-induced expression data.
A. Analysis of G = 138 ATM-dependent genes [37] for M = NF-kB.01 over representation. The dependence of –log[ p (M,G,W)] on the score threshold T is shown for 23 overlapping windows. Three upstream windows, (TSS- 100), (50–150) and (100–200) passed the hypergeometric test at an FDR of 10%. B. putative NF-kB.01 BSs of the 138 ATM-dependent genes; score (vertical axis) versus location (horizontal axis). Our algorithm identifies the location and scores that are indicative of functionality of the BS (rectangle enclosed by the red dashed line). Solid colored symbols mark genes whose expression was validated by PCR. The other genes in the box are marked with blank colored symbols, those that are likely targets of NF-kB outside the box–by X. We list next to the gene names the fold change as measured by the microarray and by PCR (in parentheses). The black dots are belong to the rest of the 138 genes,with putative BS outside the area indicative of functionality.