DAVID pathway analysis

Question

[yourA]

Hi,

First time posting so apologies if this is posted to the wrong forum.

Does anybody know if there is an issue with the DAVID website. I've tried accessing it from several computers but it won't load. I could get in last week but when using the conversion tool it would stop at 30% complete. I've tried emailing them but have not got a reply.

Thanks,
Alan

[Gjain]

The result of http://downforeveryoneorjustme.com/david.ncifcrf.gov says that it's just down for me and up for everyone, but clearly its not loading for me too.

UPDATE: I checked on another source: http://www.isitdownrightnow.com/david.ncifcrf.gov.html and this one says that it's down for everyone.

[yourA]

Thank you Gjain,

Should have known there would be a site for checking the status of other sites. Useful tool for next time.

Alan

[maayan.avi]

Hi Alan and Gjain,

Please try our tools Enrichr and PAEA. We offer more gene set libraries and better enrichment analysis algorithms.

Cheers,
Avi

Answer 1

[Andrew Su]

I hate to be snarky, but if DAVID is down then that's good for everyone.

DAVID hasn't updated their Gene Ontology annotations in over five years:

Google Scholar says 2121 pubs cited DAVID in 2014, when annotations were 5 yrs old #ugh #bioinformatics #geneontology pic.twitter.com/P2VYMIOv9u

— Andrew Su (@andrewsu) April 28, 2015

Lots of gene annotations have been added (and some deleted) in those years. Despite many pleas from the biocuration community over many years, the maintainers of DAVID are either unwilling or unable to make these updates. So unless you want your analyses to be based on five year old knowledge, find another enrichment tool. (I suggest Panther http://pantherdb.org/ because it is developed by one of the Gene Ontology PIs.)

Take the oath! Thou shalt not use DAVID!

Answer 2

[andrew]

Until it comes back up, you might try iPathwayGuide as an alternative. We offer an easy to use web application that is 100% free to use for doing pathway analysis among other analyses. You can watch a short overview video about the application below.

Answer 3

[mikhail.shugay]

In past 2 months at least for me it was going up and down. However, the problem was that even when it was up, I was never able to see it loading the functional annotation results page. It would be very sad if this great web resource is not maintained anymore..

[pld]

I don't think it has been updated for quite some time, and with some coming changes to the NCI, it wouldn't surprise me to see it be discontinued.

Answer 4

[EagleEye]

How about considering real-time update tool like GeneSCF,

Gene Set Clustering based on Functional annotation (GeneSCF)

[GenoMax]

Does this work for any genome now?

[EagleEye]

Yes it does now with v1.1. It supports all organism from KEGG and GeneOntology.