Frequently Asked Questions

Q. What is the difference between "Target CAGE peak region hits" and "Target TFBS hits"?

A. The Fisher statistic reflects the proportion of CAGE peak regions that contain at least one binding site for the given TF compared to the same proportion for the background. We therefore report the total number of CAGE peak regions in the target set containing the TFBS under "Target CAGE peak region hits".

The Z-score statistic reflects the frequency of TFBSs in the target CAGE peak regions compared to the frequency in the background. Therefore, we report the total number of TFBSs for the target set under "Target TFBS hits".

For example, if you perform human analysis using the sample CAGE peaks for both target and background provided on the website and leave all other filters and parameters as default, you'll see that NFYB is the top-scoring TFBS for the Z-score analysis and ranked 29th for the Fisher analysis. If you click on the number under "Target CAGE peak region hits" in the table (it should be 41), you'll see that there are 41 regions containing one or more predicted NFYB binding sites. The total count of NFYB binding sites is 83, which is the number reported under "Target TFBS hits".

Q. I submitted an analysis to CAGEd-oPOSSUM and never received any results. What happened?

A. Depending on the size of the target and background sets entered and the parameters selected as well as the load on the system (how many other analyses are running at the same time), your analysis may take several hours to complete. Please be patient. If it has been more than a few hours and you still haven't received your results, it may be that your analysis failed for some reason. The CAGEd-oPOSSUM system makes every attempt to catch errors and notify you of problems, however there are cases where the job gets killed off at the system level due to excessive memory or processing demands (especially if multiple CAGEd-oPOSSUM jobs are running at the same time). If this is the case you can try re-submitting the job at another time when there is less likely to be high server demand or try splitting the analysis into smaller subsets. If the problem persists of if this is not a viable option please contact the CAGEd-oPOSSUM team and inform us of the problem. Please include the Job ID of the job that failed in your communications to help us diagnose the problem.

Q. How often will CAGEd-oPOSSUM be updated?

A. There is no fixed schedule for CAGEd-oPOSSUM updates. CAGEd-oPOSSUM may be updated periodically as new data becomes available and / or as new analysis methods are introduced.

Q. If I use CAGEd-oPOSSUM in my work how do I cite it?

A. Please see the Citing CAGEd-oPOSSUM section in the main Help page.