Recommended reliable enrichment tool

Question

[noamizc]

TL;DR looking for a recommended enrichment tool

Hey guys I have a list of genes that I want to enrich. I've used Enrichr, which was very user-friendly, and let me run the enrichment on different libraries, but it seems the results are different from the data on the website it is taken from (like Gene Ontology, or Human Phenotype Ontology). In the Enrichr data a specific term can have 10 genes, while the term in the website which has 15 genes.

So I'm looking for an alternative reliable, up to date and hopefully user-friendly, enrichment tool

Answer 1

[EagleEye]

Have you tried GeneSCF? This uses current databases.

Answer 2

[geneontologyhelp]

If you're specifically trying to do GO enrichment, we recommend using PANTHER. Users can perform enrichment analyses directly from the home page of the GOC website. Info about the tool, how to use it, and how to interpret the results are available from the GO Enrichment Analysis page. More detailed PANTHER help can be found on the PANTHER website.

PANTHER, which supports the backend of the GO enrichment, provides the list of the species found on the right side of GO website. Besides those 144 genomes, PANTHER supports another 1533 genomes from the Reference Proteome project for users to generate GO annotations. More detailed PANTHER help can be found on the PANTHER website. [Statistics are from PANTHER 19.0]

If your organism is not one of the nearly 1700 genomes supported in PANTHER, there are two options:

• The first option is to contact the Reference Proteome project, and work with them to incorporate the genome in their project. Once that is done, you can use the regular process to generate the GO annotation file.
• The second option is to score your genomes against the PANTHER HMM library. Read our Nature protocol paper, and find the details in Box 2 of the paper.

Also, the GO citation policy asks all tools providing users with GO to also include the version of GO the tool is using. If you encounter a tool not providing this information (a version number looks like 2024-11-03), please refer them to our citation policy or let us know and we'll contact them directly!