johannesmp/nw_celltoxicitydb

Reference website for a paper created in collaboration with the Peter lab of Northwestern University.

6mer Seed Toxicity

A tool to look up the toxicity of any siRNA, shRNA or miRNA with known 6mer seed sequence.

About

This site was created in collaboration with the Peter Lab at the Feinberg School of Medicine of Northwestern University.

It allows to determine the activity of any siRNA, shRNA, or miRNA to be toxic through induction of DISE (death induced by survival gene elimination) in human (HeyA8 - ovarian, H460 - lung and H4 - brain) and mouse (M565 - liver, 3LL - lung and GL261 - brain) cancer cell lines.

The app is entirely static, hosted with Github Pages and all data filtering and download file generation occurs locally without any server requests made apart from the initial browser request.

How to use

Please refer to the sections at the bottom of the live website.

References

Gao, Q.Q., Putzbach, W.E., Murmann, A.E., Chen, S., Sarshad, A.A., Peter, J.M., Bartom, E.T., Hafner, M. and Peter, M.E. (2018) 6mer seed toxicity in tumor suppressive microRNAs. Nature Comm, in press. Preprint at BioRxiv: https://doi.org/10.1101/284406

Libraries Used

• JQuery 3.3.1: Dom manipulation
• JQuery Highlight: Dom highlighting
• D3 4.13.0: CSV loading and data visualization
• Async 2.6.0: Asynchronous javascript
• Bootstrap 4.0.0: UI Framework
• Bootstrap Toggle 2.2.2: easy smartphone-style toggles
• DataTables 1.10.16: table UI and data manipulation
• FileSaverJS 1.3.5 and BlobJS: Fallback for local file saving
• FontAwesome 5.0.8 (Free): Icons
• Google Analytics

License

This project is available under the MIT license.

nw_celltoxicitydb's Issues

include miRNA count in "Download CVS"

Describe: Currently the webpage shows columns called "miRNA" that lists the number of human microRNAs that share the same seed of the same row. When I down load the file "Download CVS" there is currently no column that lists this number.
Please, add a column to the downloadable file that lists the number of microRNAs named.

Change headers in down loadabel file

Description: There are a few columns with the wrong headers.
When the "Download CVS" file is down loaded, a wrong header is displayed for the listed microRNAs.

The wrong name is "avg_brain". When you change the name, the corrected name could be "human miRNAs" or use a name that Marcus prefers (later we may want to add mouse miRNAs, that is why I would use the term human as well, and not just "miRNAs").
There are also two redundant headers that do not list any data. These column headers are called "avg_lung" and "miRNAs". Those two you can just delete, as the columns are empty of data.

Thank you :-)

human miRNA list with links to other web page

What information do you need compiled so that you can upload new miRNAs with links to our web page?

Currently, we have listed all human miRNAs in our 6merdb.org web page, and each button for each miRNA has a link to the web page https://www.mirbase.org/ so that the users can look up additional information for all the individual miRNAs.
For a planned future version, we want to include all mouse miRNA names and the links to the external miRbase-org web page.

In order for me to prepare and compile the necessary information for the mouse miRNAs could you please send me the list you have used for the human miRNAs and the links as an example?

Test bug

Describe the issue:
What do I expect: