Pathway enrichment analysis with or without custom background 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!!
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.