Question: Transcription Factors Annotation
1
gravatar for elb
6.8 years ago by
elb160
Torino
elb160 wrote:

I have a list of genes and I would like to retrieve informations about them, for example if a gene is a transcription factor or not (not if it is a transcriptional target of a transcription factor, but if it is itself a transcription factor). No other informations I need. Is there a tool (for example an R library) to download computationally the informations i need? I have thousand of genes...

Thanks in advance

Eleonora

• 3.7k views
ADD COMMENTlink modified 6.8 years ago by seidel6.8k • written 6.8 years ago by elb160

Similar Question here: http://www.biostars.org/post/show/8042/determine-transcription-factors-for-genes/

ADD REPLYlink written 6.8 years ago by Niallhaslam2.2k
2
gravatar for Pierre Lindenbaum
6.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

Using GeneWikiPlus: http://genewikiplus.org/wiki/Category:Transcription_factors (there must be an API somewherre (Andrew ?))

or GO:

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003700&format=text#term=annotation

ADD COMMENTlink written 6.8 years ago by Pierre Lindenbaum120k

As much as I love Gene Wiki+ (and it is near and dear to my heart), I don't think it's the best resource for this query. The EBI link from Pierre (or the analogous one from the GO consortium http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0003700) would probably be better. There are undoubtedly good R libraries for downloading annotations and reasoning over the ontology as well...

ADD REPLYlink written 6.8 years ago by Andrew Su4.8k
2
gravatar for seidel
6.8 years ago by
seidel6.8k
United States
seidel6.8k wrote:

You didn't mention what organism(s) you are interested in, and the annotation state of a genome can be heavily organism dependent, however, if you want to stick with R and the gene ontology you could use the annotation packages from bioconductor to map between gene ids and GO terms. This assumes they have one for your organism. They have names like org.[species abbreviation].eg.db; for instance fly would be: org.Dm.eg.db. They are basically data structures with all kinds of ID and chromosomal location mappings. With the GO ids in hand you could then use the GO.db package to specifically map to "Transcription Factor".

Another way to map between your genes and GO ids, and various other kinds of annotation in R would be to use the biomaRt library (assumes there's a BioMart, such as ensembl, etc., for your organism).

ADD COMMENTlink written 6.8 years ago by seidel6.8k

I'm referring to human genes. Sorry if I forgot to mention this information. I 'll try to annotate using R as you suggest me. Thanks a lot!

ADD REPLYlink written 6.8 years ago by elb160
0
gravatar for elb
6.8 years ago by
elb160
Torino
elb160 wrote:

Dear Andrew and Pierre, first of all thank you for your help. I think I will consider the GO option. The point is that I searched in TRANSFAC (the principal db for TFs) but the public access allow you only to retrieve 1/3 of all known TFs. Otherwise, you have to buy the license. Since GO is very complex to interrogate I think I will use perhaps the R library ("annotate"). Anyway thanks a lot!!!!!

Eleonora

ADD COMMENTlink written 6.8 years ago by elb160
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