I want to map a large list of genes (basically all of UCSC's known genes) to Reactome pathways. I tried using the UCSC Table Browser and it mapped a lot of the genes to pathways, but there's still a lot missing.
For example, I know the gene SETD2 plays a role in R-HSA-3214841, but according to the Table Browser it doesn't
On the Reactome download page there's a list of mapping files but oddly they don't include all the pathways that are in the 'complete list of pathways.txt' file.
Again, the example being that R-HSA-3214841 is only in the complete pathways file, NOT in any of the mapping files.
Anyone know how can map the remaining genes to pathways? Am I completely missing something?