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.
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
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version 2.3.6
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.