Dear all, 

I have some questions regarding the functioning of the enrichPathway function. 

I know that the default input requires that all genes should be 'translated' to ENTREZID coding. I have my data in UNIPROT code, and when I make the translation, almost 20% of the proteins fail to map.  

I used  http://www.uniprot.org/uploadlists/ and the bitr() function in R for mapping ID, and comparably they output a similar quantity of ´translations´, ending with a similar amount of identity loss. That is why I would like to make my enrichment analysis using Uniprot identities directly. 

I would like to make the enrichPathway function to accept UNIPROT identities so I won't have that loss, but it came to my knowledge through Dr. Guangchuang Yu that this is not possible because the ReactomePA package relies on reactome.db and this last one is merely annotated in ENTREZID. 

I tried to input my Uniprot identities directly in the Reactome.org Website and the number of enriched pathways is very similar, even ReactomePA enrich slightly more pathways. Nevertheless, some pathways are enriched by Reactome.org that are not enriched by ReactomePA and vice-versa, and the number of identities per enriched pathway is lower by ReactomePA (I assume, because of the loss by translation). 

I am researching for options to evaluate how important (´significant´?) is this loss of information when I am doing pathway analyses because I know that no database is completely annotated and one should expect this kind of things to happen.

I would appreciate any advice that I could receive about how to approach this issue for my enrichment analysis, even recommendations of other software or enrichment databases.  

As the creator of reactome.db, I could support a uniprot to reactome pathway mapping in my package.
However, we are past feature freeze in this release cycle. This would mean that this addition would only be available in half a year. Obviously, I could make it available somewhere else, but it would technically be outside of bioconductor, which makes it difficult/weird for ReactomePA to be able to use this functionality.

I am fine with making this change, I think I could even do it today. However, I am not sure how it would help you right now.
Although if ReactomePA is willing to make a special version available to you at the moment as well, that might work.