Hi, how can I do to see if a protein/gene is mutated in all pancreatic cell lines for exemple? thank you for your help, I’m new here
There are two way you could go about doing this:
Searching by Lineage and Individual Cell Line
Search the pancreas lineage on the DepMap portal. This will bring you to two data tables: one showing all cell lines in the pancreas lineage, and another showing dependencies enriched in pancreas lineage (see here: Pancreas DepMap Context Summary). Download the list of all pancreatic cell lines.
Once you have a list of all pancreatic cell lines, you can search for those cell lines directly on the portal. Scroll down to the bottom of the cell line overview page and you should see a “Mutations” database. (PK59 for example: PK59 DepMap Cell Line Summary)
You can filter the “Mutations” database for specific genes and variant types to see which alterations are present in which genes for that cell line.
This method will take longer, but will provide a bit more granularity about the specific kind of mutation seen in each gene in the cell line(s) you look at.
Using Cell Line Selector
You can reach the cell line selector tool under Tools–>Cell Line Selector.
Click on “Create custom list” in the upper left.
Filter by lineage and select pancreas, then click “save”. This will give you a list of all cell lines of the pancreas lineage.
If you click on “Add a data column” on the right, select “Gene”, then choose your gene of interest, then choose the “Mutation” dataset, then click “add column”. This allows you to filter by pancreas lineage and gene/mutation presence. However, you will not be able to see any specifics about the mutation, only that there is indeed a mutation present in that gene.
This method is faster, but you will not be able to see mutation-specific information with the same level of granularity that you would by using the first method.
Hope this helps!