2
$\begingroup$

I am doing a pathway enrichment analysis of a sets of proteins. Specific cell types (cardiospheres) were used to perform the experiment and for the quantification of proteins was used mass spectrometry. I am using gProfiler to perform pathway analysis, should I use custom background of all of those proteins identified from the experiment? or should I used without custom background?

Thank you!

UPDATE: Also, I am doing an enrichment analysis of the interactome of the set of proteins of interest. In that case should I used a custom background for the enrichment analysis or not?

Thanks!!

$\endgroup$

1 Answer 1

1
$\begingroup$

I would defninitely go with a custom background which should be all the proteins that were actually measured in your experiment since you should only take into account what was measured.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.