Results

Click on the link ``Centered data'' under static heatmap column of the result table. Figure shows heatmap of 15 Tfs and figure displays corresponding legends for each of the TFs.

Figure: Legend for 15 TFs

Figure: Heatmap of 15 TFs

We can see that in addition to most of the genes having a ChIP-seq peak for E2F1 within the regulatory region examined (-4kb to +1kb around TSS marked by 0), there were several other transcription factors such as N-myc,Tcfp2l1,c-Myc etc. that seem to have unusually many peaks for these gene. We can then focus on each of the TFs separately to take a closer look. We will illustrate the case using n-Myc TF.

We can select n-Myc TF out of 15 Tfs using ``select sample'' option in step 1 as shown in figure . Expand ``Transcription Factor'' and select n-Myc TF and click radio button ``include'' to select this sample. Then select ``TranscriptionFactor'' in step 2. select Cluster on ``Genes'' and ``compute LR'' options and click ``Analyze''.

Figure: Select n-Myc TF

Then click on the link ``Centered data'' under static heatmap column of the result table. Figure shows increased binding around TSS of the promoter region (-4kb to +1kb in this case) for some of these genes.

Figure: n-Myc TF heatmap

Here, we used the comparison to ``random'' sample by LRpath. Instead of the p-values, in this situation Genomics Portals by default uses the maximum ``peak intensity'' calculated for each gene across its whole regulatory region. Such statistical analysis confirmed that in addition to E2F1 (p-value < 10-14), n-Myc (p-value < 10-7), Tcfp2l1 (p-value < .001), c-Myc (p-value < .01), and Klf4 (p-value < 0.01) all show signs of increased binding to regulatory regions of these genes.