Demo workflow 3 explanations
When you follow the link to the workflow, you will encounter the inquiry
which you should just close (press Close button), unless you wish to get the User Guide.
Now (but please, give the interface a bit time to establish), you should see a page like this.
When it looks more like this go to the grey bar on top (indicated by the red arrow) and shift it downwards with the left mouse button being pushed.
Next, please press the button “Run workflow” in the start page shown above, and confirm that you are going to overwrite previous results in the following mask
(default is “Cancel”, which would interrupt your demo run.)
You will now see how the workflow proceeds when the progress bar is increasing and the building blocks in the workflow schema (section at the lower right of the screen) are successively greyed out.
As soon as the workflow is completed, the page will look like this.
The following pages will open automatically one by one. The table shown under the tab Profile (red oval), which you can also find in your results folder (blue oval), you see the TRANSFAC® matrices for which enriched matches were found in the analyzed promoter set, their chosen cut-offs for the MATCH program and the corresponding logo plots. Note that the matrix links require a valid TRANSFAC® license to become active (login required).
The Site search table shows the enrichment of the mentioned matrices in the test promoter set vs a control set (here: untreated tissue).
In the table Transcription factors ENSEMBL, the genes for the mentioned TFs are tabulated as far as they could be identified in the Ensembl database.
The table Master regulators upstream 10 shows the potential master regulators, located in the signaling network where several signaling cascades converge at a distance of up to 10 steps. Note that the ranking of identified master regulators can differ a bit from run to run based on a random background set calculation within the algorithm. Please note also that the molecule ID links in the first column require a valid TRANSPATH® license to become active (login required).
The visualization of the top 3 identified master regulators can be found as diagrams in your result folder (blue circle).