Question: GO tools: no annotation file for my species
0
gravatar for vasilislenis
2.7 years ago by
vasilislenis100
United Kingdom
vasilislenis100 wrote:

Hello,

I would like to use the Generic ontology term finder (online tool) for a list of genes but at the third step, it asks me to choose the annotation. The problem is that my species (Ovis aries) is not on the list. I have noticed that in several tools the annotation list is limmited in a specipic number of species. Is there any tool that it has a wider list of annotation files or a way to tranform my genes into another species? I tried biomart from Ensembl in order to convert my genes into human (orthologs) but it gives me as output only the IDs of the genes that are orthologous and not the coresponted IDs of human genes.

I'm really sorry if my question is a little bit complicated but I'm a little bit new in this kind of analysis. Thank you very much in advance.

go terms ensembl • 895 views
ADD COMMENTlink modified 2.7 years ago by EagleEye6.2k • written 2.7 years ago by vasilislenis100

What filters and attributes did you use in BioMart?

ADD REPLYlink written 2.7 years ago by Emily_Ensembl18k

Hi Emily, I chose the orthologous "human genes only" as a filter and the "Ensembl gene ID" and "associated gene name" as attributes. the problem is that I have only the list of the IDs and the name of genes and not another column with the list of IDs of the human genes. Thank you very much!

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by vasilislenis100

The "orthologous human genes only" just gives you a list of sheep genes which have a human orthologue. To actually get the orthologues in your output, go into "Attributes" -> "Homologues", open "Orthologues" then select "Human Ensembl Gene ID" and "Human associated gene name".

Filters will only affect which genes you're selecting. Attributes are how you specify columns in your table.

ADD REPLYlink written 2.7 years ago by Emily_Ensembl18k

Thank you very much! The only funny thing is that even if I choose to appear gene ID and gene name for sheep genome and gene ID and gene name for human, the output is gene ID (sheep) transcript ID (sheep) gene ID (human) gene name (human), which is not bad, I can extract the column of interest but it is a little bit funny!

ADD REPLYlink written 2.7 years ago by vasilislenis100
0
gravatar for Medhat
2.7 years ago by
Medhat8.2k
Texas
Medhat8.2k wrote:

It exist here

http://biit.cs.ut.ee/gprofiler/index.cgi

ADD COMMENTlink written 2.7 years ago by Medhat8.2k

Thank you very much for your quick answer. Yes, it is there. It is a little bit painful since I have to copy/paste my genes (I cannot find somewhere to upload a file with my genes) but I believe that it does my job :)

ADD REPLYlink written 2.7 years ago by vasilislenis100
0
gravatar for EagleEye
2.7 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

How about this using GeneSCF (KEGG annotation is available for your species),

Gene ontology in sheep

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by EagleEye6.2k
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