Question: UCSC_TFBS option in DAVID
0
gravatar for F
2.7 years ago by
F3.3k
Iran
F3.3k wrote:

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

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by F3.3k
6
gravatar for genomax
2.7 years ago by
genomax62k
United States
genomax62k wrote:

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.

ADD COMMENTlink written 2.7 years ago by genomax62k
3

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

ADD REPLYlink written 2.7 years ago by Daniel Swan13k
3

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

ADD REPLYlink written 2.7 years ago by Daniel Swan13k
1

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

ADD REPLYlink written 2.7 years ago by ivivek_ngs4.6k

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by F3.3k
1

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 :-)

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax62k
1

+1 for Enrichr and the preprint , it was highlighted , DAVID is really being outdated and one should also read the article highlighted by Daniel Swan, it is quite important to work with updated tools as far as the field is concerned to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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by ivivek_ngs4.6k
1
gravatar for Denise - Open Targets
2.7 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.7k wrote:

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.

ADD COMMENTlink written 2.7 years ago by Denise - Open Targets4.7k
1

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by ivivek_ngs4.6k
2

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

ADD REPLYlink written 2.7 years ago by Denise - Open Targets4.7k
1

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.

ADD REPLYlink written 2.7 years ago by ivivek_ngs4.6k
1

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by F3.3k
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