Question

Getting BP, MF and CC from GO IDs

0

Entering edit mode

7.5 years ago

EVR ▴ 610

HI,

I have a list of GO Ids and I want to know their BP, MF and CC. Is it possible to get those BPs, MFs or CC either through online resource or in R. Thanks in advance.

Gene Ontology • 5.5k views

ADD COMMENT • link updated 7.5 years ago by EagleEye 7.5k • written 7.5 years ago by EVR ▴ 610

score 0 · Answer 1 · 2016-10-10

0

Entering edit mode

7.5 years ago

Michael 54k

Check out

library(Go.db) in R/Bioconductor
and amigo

ADD COMMENT • link 7.5 years ago by Michael 54k

score 0 · Answer 2 · 2016-10-10

0

Entering edit mode

7.5 years ago

EagleEye 7.5k

Using GeneSCF, you can download complete GO (BP,CC,MF) as simple text file along with the genes in each process.

Gene Set Clustering based on Functional annotation (GeneSCF)

Example like this.

ADD COMMENT • link 7.5 years ago by EagleEye 7.5k

0

Entering edit mode

Bu the input file requires either Gene Id or Gene Symbol. In my case i have only GO iDs. How can your tool can be modified to extract ontology from GO IDs

ADD REPLY • link 7.5 years ago by EVR ▴ 610

0

Entering edit mode

Use 'prepare_database' module from GeneSCF.

./prepare_database -db=GO_all -org=hsa

The above biostar page for GeneSCF 'Two step process' explains in detail.

ADD REPLY • link 7.5 years ago by EagleEye 7.5k