What is the difference between Enrichr and ShinyGO? Which one is the best?

Question

[mr.onkology]

Hi! i'm newbie here I'm doing my research in ontolgies. But I feel confused, when I enter a group of genes to find the pathway in cancer, the results in Enrichr and ShinyGO are different. Sometimes, it doesn't show any results at all, especially in ShinyGO with "No significant enrichment found!". So, i have to choose one of them, which one is more complete or the best one for discovering pathway in cancer based on our list of genes? I really hope anyone here could help me. Thank you

Enrichr: https://maayanlab.cloud/Enrichr/ ShinyGO: http://bioinformatics.sdstate.edu/go/

[kalavattam]

Hi there: The short answer is that both Enrichr and ShinyGO make use of different methods, so neither is definitively "best." It's important to understand the databases each tool uses, how up-to-date these are, how the tools calculate statistical significance, the specific context of your research, and so on. Doing this leg work will help you interpret the results more effectively. I caution against selecting a method based on the results it returns without at least a basic understanding of how the method works. A good start could be looking over the documentation and papers associated with the tools.

I'm not associated with the creation or maintenance of this site, and I have no vested interest in it; I'm just an occasional user. With that said, the Biostars Handbook, written by the creator of this site along with some contributing authors, has a helpful extended discussion on the basics of gene ontology analyses. However, I don't think the handbook explicitly discusses Enrichr and ShinyGO.

Good luck with your research.

[mr.onkology]

Thank you very much for your explanation, now I understand what to do next. And do you have any recommendations for webtools besides ShinyGO that you might have used to make or find KEGG pathways in cancer based on list of genes? Thank you

[kalavattam]

To perform gene ontology (GO) analyses for a recent project, we made use of YeastMine, which is part of InterMine. To conduct GO analyses with InterMine, you could:

1. Access an InterMine instance like YeastMine for yeast or HumanMine for human data.
2. Use the query builder to select genes of interest.
3. Apply the GO enrichment tool to identify overrepresented GO terms associated with the selected genes.

There are also InterMine instances for other organisms.

[mr.onkology]

Okay, that's clear. Thank you so much for helping me