I've been using DAVID for gene ontology IDs for years but this -> Tools To Find Gene Ontology Term Enrichment says it hasn't been updated in like 6 years. Is there anything else that's useful and up-to-date? I usually use Uniprot, KEGG, and GO IDs for everything. http://geneontology.org/ wants me to input a species but the species I deal with aren't really model organisms. I have a lot of random microbes.
What can I use instead of DAVID? Preferably accessible through Python or web interface. If there is some REALLY good that's for R I'm open but that's a last resort for me (It takes me a while to do anything in R).
The Gene Ontology consortium has created their own enrichment tool through AmiGO 2 http://amigo.geneontology.org/amigo (and/or with Panther http://pantherdb.org/webservices/go/overrep.jsp). This will be the most up-to-date tool you can use.
Intermine provides up-to-date enrichment tools (web interfaces or accessible by API) for a lot of species here: http://intermine.org/ Choose the closest species mine if you can, it doesn't need to be a perfect match - especially for GO which is species-neutral; though some of the other functions they index can (or should) be species-aware. For microbes, YeastMine/Saccharomyces cerevisiae database might be the best? InterMine/MODs get updated GO annotations as they come out, or very soon after (~ up to 3 month delay depending on production cycles).
Amigo2, with its clean web interface and the integration of many tools, is my personal favourite.
The Gene Ontology is also stored in enter link description here - it has a web API, an R package to connect to it - at actually I wrote some code to access it via python which I hope to feed back into Biopython one day (I saw in that other thread that you'd like to have that). However, the OLS gives you ontology terms for your search, so this might not be what you want (or not enough) in terms of enrichment. But get back at me if your interested.
Cheers.
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How are you getting your gene IDs? If they are from sequencing experiments, then I definitely recommend the GOSeq bioconductor package (R, sorry) for enrichements. However, for organisms it doesn't know about (it knows about quite a lot), you will have to build the gene-term associations yourself, for example from a bioconductor annotationsDB pacakge or just a list of gene-go term associations.
I had this happening w/ my
R:( https://support.bioconductor.org/p/86107/#86126DAVID was very recently updated so for now it should be ok to use it.
Enrichr, very useful and frequently updated.
The new versino wasn't recognizing any of my uniprot IDs :(
A: Inconsistent numbers when using Kegg pathway analysis via DAVID?