User-Defined Subtypes

Usage:

  1. Specify mutated gene of interest to define a specific subtype
  2. In the next page, select the mutation(s) of interest and hit "Execute"
  3. Identify vulnerabilities for cancer cell lines with mutation(s) of interest
  4. Click on genes highlighted in red to find out the chemicals that target them

Method:

  1. Identifies all the unique cell lines with the selected mutations
  2. Runs a hypergeometric enrichment test to identify genes whose knockdown specifically kills these cell lines
  3. Corrects for multiple hypothesis testing
  4. Links gene products to chemicals interacting with them, if they exist

Tips:

  • Make sure the gene is in the autocomplete list.
  • Try synonyms if necessary. Ex: ERBB2 instead of HER2.
  • Do not input more than ~100 unique cell lines.

Acknowledgements:

Author: Murat Can Cobanoglu. Contact: murat.cobanoglu@utsouthwestern.edu

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