Tool for Human Gene Functional classes in R

Question

[saamar.rajput]

I am looking for a tool that would help me extract detailed information about a list of genes, whether it is kinases or proteases etc. Is there any package in R that would take a list of genes as input (gene symbol or entrez id ) and output the functionality of each gene.

Answer 1

[Denise CS]

You can use biomaRt in Bioconductor using the MIM gene or GO molecular function term as attributes.

[saamar.rajput]

i have already got the GO ids for my genes but now how do i extract some information from the GO ids for each gene? for example i want to extract JAK-STAT cascade or cellular protein metabolic process, how do i extract that?

Answer 2

[Satyajeet Khare]

I use clusterProfiler for functional analysis along with Bitr.

[Guangchuang Yu]

and here is an example of using bitr to map GO to gene and vice versa by specify the fromType and toType.

Answer 3

[EagleEye]

GeneSCF will be simple and perfect for your task (but NOT in R).

Gene Set Clustering based on Functional annotation (GeneSCF)