Hi,
I need to select a cell line of specific cancer with specific gene amplification. How do I do that. I tried using cell line selector, I am not understanding which cell line has maximum expression. For example CCNE1 in bowel cancer. Can any one help? Thank you.
If I understand you correctly, it sounds like you want to filter by “bowel” by clicking on the funnel at the top of cellligner.
That narrows the set down to 89 lines. You say you’re interested in gene applification of CCNE1, so I’d add a track by clicking on the button on the right to add the copy number profile of CCNE1:
You also mention that you were interested in which has maximum expression, so perhaps you want to define “amplified” not as copy-number-amplified but expression-amplified. I can also add a track for expression of CCNE1:
Now clicking at the triangle at the top, I can sort by the expression to see which bowl line has the highest expression:
It’s hard to see in this view the overall distribution of CCNE1 and CCNE1 expression, and I don’t know which would be better to use as the definition for “amplified”, so I could alternatively bring the bowl group into data explorer and see about picking things there:
I’ve used the lasso tool in the top right to pick the few lines which are concordant with CCNE CN amplified and CN high expression, and one can use the “save selected cell lines” button on the left to save those into a context.
Thank you for giving clear stepwise explanations.
Very helpful.
Regards
