Question

Gene ontology in sheep

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8.5 years ago

Martin B. ▴ 10

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.

gene ontology go miRNA pathway • 4.0k views

ADD COMMENT • link updated 8.5 years ago by EagleEye 7.6k • written 8.5 years ago by Martin B. ▴ 10

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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 REPLY • link 6.5 years ago by mks002 ▴ 220

score 2 · Answer 1 · 2016-06-17

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