6mer Seed Toxicity
A tool to look up the toxicity of any siRNA, shRNA or miRNA with known 6mer seed sequence.
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 and H460 - lung) and mouse (M565 - liver and 3LL - lung) 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
See the 'Info' section at the bottom of the page.
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
- JQuery 3.3.1: Dom manipulation
- JQuery Highlight: Dom highlighting
- D3 4.13.0: CSV loading and data visualization
- 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
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This project is available under the MIT license.