Question: Limitations of DAVID pathways
0
gravatar for rr14049
20 months ago by
rr140490
United Kingdom
rr140490 wrote:

Hi all,

Sorry for posting what is probably a dumb question but I'm a masters student writing up my thesis and just needed some help.

I understand DAVID is an over-representation analysis (ORA) based tool and understand the limitations associated with that but are there any specific limitations of DAVID itself? One thing I've read is that it hasn't been updated since 2010 but I'm not sure if that is actually true any longer (the beta version of 6.8 was released last May). Some details regarding all this would be massively appreciated. Thanks

rna-seq • 485 views
ADD COMMENTlink modified 20 months ago by Devon Ryan1.9k • written 20 months ago by rr140490
2
gravatar for Devon Ryan
20 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

The "hasn't been updated since 2010" thing is no longer the case, it has a new team taking care of it. The common critique applied to DAVID and similar tools is that they're only as good as their underlying databases. DAVID and most other tools use public databases, which can never compete with private ones (e.g., what you'll get in IPA from Ingenuity). Further, you'll get results biases toward cancer and things like that, simply because some ontologies are more complete. Having said that, it's a nice enough tool, use the results as a complement to what you already know/expect about the system and follow-up experiments.

ADD COMMENTlink written 20 months ago by Devon Ryan1.9k

Thank you so much for your help! I used the KEGG database in DAVID for my project, is this one of the more frequently updated public databases?

ADD REPLYlink written 20 months ago by rr140490

KEGG itself has been subscription only for the past few years and it's unlikely that DAVID has a license that allows external people to use it. You could email them and ask though.

ADD REPLYlink written 20 months ago by Devon Ryan1.9k
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