Question: Gene ontology in sheep
0
gravatar for Martin B.
2.7 years ago by
Martin B.10
Basque Country
Martin B.10 wrote:

Hello, I would like to know which web tool can I use to analise the gene ontology or pathways of a list of genes from sheep (ovis aries) I have, since I don't see sheep as an option in the webs I have checked. Could I use the cow (bos taurus) if sheep was not available? I've got the list of genes by miRNA target prediction tools.

mirna go gene ontology pathway • 1.5k views
ADD COMMENTlink modified 2.7 years ago by EagleEye6.2k • written 2.7 years ago by Martin B.10

use the link below from Kegg server

https://www.genome.jp/kegg-bin/get_htext?htext=oas00001&filedir=%2fkegg%2fbrite%2foas&length=

U can download the information as htext.

ADD REPLYlink written 7 months ago by mks002150
2
gravatar for EagleEye
2.7 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

GeneSCF supports all organisms from Gene Ontology and KEGG. Use "prepare-database" module from GeneSCF, Gene Set Clustering based on Functional annotation (GeneSCF)

./prepare_database -db=GO_all -org=goa_cow

If you are interested in KEGG pathways use,

./prepare_database -db=KEGG -org=oas (for sheep)

./prepare_database -db=KEGG -org=bta (for cow)

This will extract all Gene Ontology GOterms ID, names and corresponding genes in simple table (text) format in GeneSCF path "geneSCF-master-v1.1/class/lib/db".

For more supported organisms by GeneSCF,

KEGG

http://rest.kegg.jp/list/organism

GO (Use "id" from following link)

http://www.geneontology.org/gene-associations/go_annotation_metadata.all.json

More information , please refer GeneSCF documentation

ADD COMMENTlink modified 2.5 years ago • written 2.7 years ago by EagleEye6.2k
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