Reactome Pathway Analysis Identifiers not found

Question

[bachs]

Hi,

I am trying to use Reactome for enrichment analysis for a several datasets. For one dataset, I input 435 genes as gene symbols into the analysis tools, projecting to human equivalents and leaving the interactors box unchecked.

The results returned showed that 219 identifiers were not found which seems to be a very high proportion of the total input genes. Having repeated this with Entrez and Ensembl ID’s the identifiers not found remain around 200; by including interactors, it is reduced to 160 genes.

Is there anyway to reduce the amount of identifiers not found? Can I still use the results from the analysis even if there's a high proportion of the identifiers not found?

Thank you!

Answer 1

[levshagam]

I faced similar problem and think this is due to the fact that not all proteins are characterized by Reactome so far. So, you still can use the results but also consider that unmatched identifiers should be considered as part of the interpretation of analysis results (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4407007/)