Getting BP, MF and CC from GO IDs

Question

[EVR]

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.

Answer 1

[Michael]

Check out

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

Answer 2

[EagleEye]

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.

[EVR]

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

[EagleEye]

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.