BARTweb help page

BARTweb is an interactive web server to predict functional transcriptional regulators 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 paper in the main text of your manuscript:

Tutorial Video

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:

If an email address is provided, BARTweb will send email notifications with the job key, job status, and the result URL.

After clicking the “Submit” button, BARTweb will redirect to the result page.


Result page

It usually takes a few minutes to run a job. You can click the “Result” button on the navigation bar or use the job key to get the result or the job status anytime. If the job has not finished, you will see the “still-running” status in the title and a processing log presented. You can click the “Copy Key” button to copy the job key to the clipboard and keep it for your record. If the job fails, the detailed error message will be shown in the processing log. If you cannot figure out possible causes of the error, you are welcome to contact us with the job key for help.

You can share your BART analysis result with others by providing them with the result link URL or the job key. Anyone with a result URL or a job key can open and view the BART analysis result at the user’s own risk.

For successfully finished jobs, the analysis result will be stored on the web server and can be retrieved with the job key for 180 days after the job submission.


How to interpret the BART result

bartweb_result


Output 1: Transcriptional regulator (TR) prediction table

We take this sub-table of a pre-run result from a gene set that were downregulated upon OCT4 (POU5F1) knocked down in a human embryonic stem cell as an example to illustrate. Another pre-run result from a ChIP-seq profile upon AR being enhanced in a human prostatic carcinoma cell line LNCaP is also provided as a reference for ChIP-seq data input.


Output 2: Data files and figure images

Besides the transcriptional regulator table, other output data files are also available for download, including the predicted genomic regulatory (cis-regulatory element) profile and analysis plots for each regulator. The image files are in high resolution with publication quality.