Sunday, July 28, 2013

v22 (1 of 3): call super enhancer using ROSE

We release version 22 of our Browser with the first integrated app: ROSE-the super enhancer calling tool. You can find applications of ROSE in these two papers from the Cell journal:  Loven, J. et. al. and Warren A. et. al. You can get the source code of ROSE from bitbucket.

This work is done in collaboration with Dr. Charles Lin from James E. Bradner's lab at Harvard Medical School.


Call super enhancer with ROSE

At the time of writing, ROSE can be used for following genomes: hg18, hg19, mm9, rn4, dm3, danRer7.

Follow these steps to submit a "call super enhancer" job.

1. Open the browser and display one of the supported genomes.

2. Upload a set of transcription regulator binding regions that you would like to check for existence of super enhancers. The binding regions must be submitted as a gene set. Most easy way is to upload them from a tabular text file.

3. Submit a custom BAM track containing read alignment data from the transcription regulator ChIP-Seq experiment. Optionally you can submit a ChIP-Seq Input track, from which the "background" will be subtracted.

4. Click "Apps" then "Call super enhancer". The ROSE interface will be shown as in the following screenshot:



5. Assign binding sites, BAM track, and enter your email address in the form. Click "Submit" button to run the job. Once the job is submitted, you can close this panel and continue using the browser. After a short while our server will finish processing your job and will send you an email with the key to retrieve results.

The amount of time is heavily determined by number of binding sites you submit. Typically less than 10min for 5000 binding sites in human genome. Also the server load level will also impact the speed of job processing.

6. Retrieve job with your key. When the job is successfully processed, you can either download the results as a compressed file archive, or visualize it:


Following screenshot shows the "Call super enhancer" results visualized as an interactive scatterplot, where top ranked dots are super enhancer candidates. You can also display super enhancers as bed track by click the button on top of the graph: