UCSC_TFBS option in DAVID

Question

[zizigolu]

hi,

I read some posts in biostars refer to UCSC_TFBS option in DAVID but I could not find anything so in DAVID. may someone tell me please where is this option? I searched functional annotation part, protein-interactions but nothing I found

thank you

Answer 1

[GenoMax]

Until someone from NCBI confirms that DAVID is being monitored/looked after by a real person(s) you should try to find an alternate source for those services.
Enrichr appears to be a popular replacement. See if that works for your genome.

[User 59]

For those coming to this question in the future, read this: http://biorxiv.org/content/early/2016/04/19/049288

[User 59]

Well in a cruel twist of fate: DAVID has just been updated, probably within hours of this comment:

https://david.ncifcrf.gov/content.jsp?file=release.html

[ivivek_ngs]

Finally all the rants did add to the positive outcome ... Now will have to again try to re-do some analysis testing DAVID with others to find out its improvement. The ad-hoc list of tasks for my own personal enrichment of tools just goes on increasing. But am glad it really worked out after all those blog posts. Just my random outcry. :P

[zizigolu]

the updated DAVID includes protein_interactions option even for plants what I think was absent previous updating.

[GenoMax]

So it begins ....
Contact email addresses are still old. It may be a while before the owners (if they are new) feel confident about accepting credit :-)

[ivivek_ngs]

+1 for Enrichr and the preprint , it was highlighted , DAVID is really being outdated and one should also read the article highlighted by Daniel Swan, it is quite important to work with updated tools as far as the field is concerned to formulate testable hypothesis.

Answer 2

[Denise CS]

If you are interested in mouse or human, try the Ensembl regulatory build. It contains the annotation of TFBS based on ENCODE, Blueprint and Roadmap data. It can be viewed on the browser, downloaded from the FTP or accessed via BioMart, Perl API or REST API.

[ivivek_ngs]

I think the OP does not work with human or mice if I can correctly recall from her previous posts and she is interested in other species Arabidopsis sp so I would suggest to look at the below links

http://plantpan2.itps.ncku.edu.tw/

TAIR

Hope these helps

[Denise CS]

I see. Have you heard of AthaMap? It may be useful as well.

[ivivek_ngs]

Looks very interesting , so now the OP has a lot of options , just be careful and chose the one with most updated annotations, that is all what I would suggest and also see to what extent all these are cited and have been widely used.

[zizigolu]

thank you

you all right I am working with plants and fortunately in paper proposed by Daniel Swan I found GOEAST that even covers rarely cited plants