BARTweb help page

BARTweb is an interactive web server to predict functional transcription factors that regulate a given gene list or associate with a genomic profile. It is a web interface to BART Python package.

If you use BARTweb in your data analysis or publish the results of BARTweb, please cite the following publication(s) in the main text of your paper:

If your analysis is from a gene list, please also cite the following paper:

Manual

bartweb_guidelines

Submit a job

The first three options (species, data type and input data) are required.

Species: Currently, only human (hg38) and mouse (mm10) genomes are supported.

Input data type: A gene list has to be official gene symbols in text format. ChIP-seq data can be mapped reads in both BAM and BED format. Please make sure your ChIP-seq data are mapped to the correct genome version (hg38 or mm10).

If you leave an e-mail address, BARTweb will send you e-mail notifications about the job key, job status, and result URL.

Once you press the Submit button, BARTweb will redirect you to the key demonstration page.


After submitting a job,
Copy your key or redirect to the result page

bartweb_key_page_2

In Key page, you can either click the Copy Key button to copy your job key to the clipboard and paste it somewhere for your record or click the Get your result link to redirect you to the result page and wait until the job completes.

Usually, a job will take 1-2 hours to run. You can always click the Result button on the navigation bar and use your key to get your result or the job status.


Job processing page

If your job is not finished running, the title will indicate still running status with a processing log presented in a text area; if the job is failed running, the title will indicate ends with error with the processing log indicating the error. If you are not sure why your job ends with error, please contact us with your job key for more information.

If you want to share your result with others, you can send them the result link URL. Anyone can open and view an analysis result with the link URL or a job key.

If your job is done successfully, the analysis result can be retrieved with the job key anytime within 180 days after the job submission.


How to interpret BART result

bartweb_result_2


Output 1: Transcription factor prediction table

We take this sub-table of our pre-run result as an example to illustrate.

You can hover your mouse on the header of the table.


Output 2: Data files and plots for download

Besides the transcription factor table, we also have other output data files available for download including the predicted genomic regulatory (enhancer) profile and analysis plots for each transcription factor. The plots are in high resolution, which can be directly used for publication.