Question: Is there any databases preloaded with GO annotations for each species?
0
gravatar for Amk
3.9 years ago by
Amk120
Amk120 wrote:

Hi all,

We all know different ways to annotate the genes with GO terms. My question is that if I want to compare GO terms of my species of interest (which I already have) with another species, it will be ease of task if there is a database where we can retrieve the GO annotation for other species. So that I can do a comparative study with both organism. As I am new to this field, sorry if this question doesn't make sense. I am happy if I get suggestions and tips from you.

Thank you.
Amk

go annotation • 1.2k views
ADD COMMENTlink modified 3.9 years ago by Giovanni M Dall'Olio26k • written 3.9 years ago by Amk120
2
gravatar for Giovanni M Dall'Olio
3.9 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

In R, you can access all GO terms associated to a species from the annotation packages:

> library(org.Mm.eg.db)     # install with biocLite('org.Mm.eg.db') first
> library(org.Hs.eg.db)
> mouse.GO = as.data.frame(org.Mm.egGO)
> human.GO = as.data.frame(org.Hs.egGO)
> head(human.GO)
  gene_id      go_id Evidence Ontology
1       1 GO:0008150       ND       BP
2       2 GO:0001869      IDA       BP
3       2 GO:0002576      TAS       BP
4       2 GO:0007264      TAS       BP
5       2 GO:0007596      TAS       BP
6       2 GO:0007597      TAS       BP

 

I am not sure what is the best way to compare two datasets from different species. The GOSemSim allows to compare set of GO terms from the same species, but currently the comparison between different species is not implemented. In any case you may read the GoSemSim documentation to learn about the different metrics to compare sets of GO term.

 

 

ADD COMMENTlink written 3.9 years ago by Giovanni M Dall'Olio26k

Dear Giovanni,

Thank you for your suggestion. I will look on to that package.

Amk

ADD REPLYlink written 3.9 years ago by Amk120
1
gravatar for mkulecka
3.9 years ago by
mkulecka310
European Union
mkulecka310 wrote:

What about BioMart? I have never used it personally in this way but I know it offers a wide variety of annotations for many organisms (including GO terms of course). Its available here: http://www.biomart.org/ or here: http://www.ensembl.org/biomart/martview/5a29cfe7faa42e6a75840221e6b15761 and also as R (https://www.bioconductor.org/packages/release/bioc/html/biomaRt.html) or python (https://pypi.python.org/pypi/biomart/0.4.0) package. 

ADD COMMENTlink written 3.9 years ago by mkulecka310

Dear mkulecka,

Thank you for the suggestion. I came to see the feature from Uniprot that if you search with the organism name you will be able to download the GO annotations and Gene lists also. That made my day. 

Regards,
Amk

ADD REPLYlink written 3.9 years ago by Amk120
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