REACTOME and Ingenuity Pathway Analysis have inconsistent results

Question

[Kim]

Hello everyone

I have a lists of genes for human and mouse. For the human gene list, I previously used REACTOME (https://reactome.org/) for pathway analysis. However, as this tool is only available for human, I later have a license to use Ingenuity Pathway Analysis (IPA) to do pathway analysis for mouse data. Before working on the mouse gene list, I re-ran the human gene list with IPA to check if the two tools provide consistent result and turns out they do not, even very different.​ Do you know the reason for this result? Which tool is better?

Thank you very much

[russhh]

forgive me, but the reason they give different results is because they are different tools, that use different calculations and that use a different knowledgebase to compute their pathway results.

[Kim]

Hi Thank you for your answer. I don't have a bioinformatic background so it's surprising (and also frustrating) to me to see the result inconsistent. I think the knowledgebase is freely accessible and they would have that in common, just the algorithms are different, so the results shouldn't be too different. Which pathway analysis tool do you prefer?

[Buffo]

If you have expression data I suggest you to use webgestalt, it uses a ranked list. It is very easy to use and very accurate, at least for human and mouse.

Answer 1

[Buffo]

It is supposed that IPA is a deeply curated and larger database than other public ones. If it is true, obtain different results would be normal, but you can compare the number of related genes on each pathway and how do they deal with redundancy.